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1868 lines
62 KiB
Plaintext
1868 lines
62 KiB
Plaintext
# File: dssp-extension.dic
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# Date: 30-May-2023
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data_dssp-extension.dic
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_datablock.id dssp-extension.dic
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_datablock.description
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;
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This data block holds the dictionary for Secondary Structure information as written by e.g. DSSP
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;
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_dictionary.title dssp-extension.dic
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_dictionary.datablock_id dssp-extension.dic
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_dictionary.version 1.1
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loop_
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_dictionary_history.version
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_dictionary_history.update
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_dictionary_history.revision
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1.0 2023-05-30
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;
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Initial release
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;
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1.1 2025-02-26
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;
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Changes (mlh)
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+ Added dictionary blocks
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;
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########################################
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## Category dssp_struct_bridge_pairs ##
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########################################
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save_dssp_struct_bridge_pairs
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#
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_category.description 'dssp_struct_bridge_pairs describes bridge pairs as assigned by DSSP.'
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_category.id dssp_struct_bridge_pairs
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_category.mandatory_code no
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#
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_category_key.name '_dssp_struct_bridge_pairs.id'
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loop_
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_category_group.id 'inclusive_group'
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'struct_group'
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#
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loop_
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_category_examples.detail
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_category_examples.case
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# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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;
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Example taken from 1cbs, first bridge pair
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;
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;
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_dssp_struct_bridge_pairs.id 2
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_dssp_struct_bridge_pairs.label_comp_id ASN
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_dssp_struct_bridge_pairs.label_seq_id 2
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_dssp_struct_bridge_pairs.label_asym_id A
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_dssp_struct_bridge_pairs.auth_seq_id 2
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_dssp_struct_bridge_pairs.auth_asym_id A
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_dssp_struct_bridge_pairs.pdbx_PDB_ins_code ?
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_dssp_struct_bridge_pairs.acceptor_1_label_comp_id PHE
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_dssp_struct_bridge_pairs.acceptor_1_label_seq_id 3
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_dssp_struct_bridge_pairs.acceptor_1_label_asym_id A
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_dssp_struct_bridge_pairs.acceptor_1_auth_seq_id 3
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_dssp_struct_bridge_pairs.acceptor_1_auth_asym_id A
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_dssp_struct_bridge_pairs.acceptor_1_pdbx_PDB_ins_code ?
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_dssp_struct_bridge_pairs.acceptor_1_energy -0.1
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_dssp_struct_bridge_pairs.acceptor_2_label_comp_id SER
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_dssp_struct_bridge_pairs.acceptor_2_label_seq_id 4
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_dssp_struct_bridge_pairs.acceptor_2_label_asym_id A
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_dssp_struct_bridge_pairs.acceptor_2_auth_seq_id 4
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_dssp_struct_bridge_pairs.acceptor_2_auth_asym_id A
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_dssp_struct_bridge_pairs.acceptor_2_pdbx_PDB_ins_code ?
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_dssp_struct_bridge_pairs.acceptor_2_energy -0.1
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_dssp_struct_bridge_pairs.donor_1_label_comp_id ASN
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_dssp_struct_bridge_pairs.donor_1_label_seq_id 91
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_dssp_struct_bridge_pairs.donor_1_label_asym_id A
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_dssp_struct_bridge_pairs.donor_1_auth_seq_id 91
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_dssp_struct_bridge_pairs.donor_1_auth_asym_id A
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_dssp_struct_bridge_pairs.donor_1_pdbx_PDB_ins_code ?
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_dssp_struct_bridge_pairs.donor_1_energy -0.0
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_dssp_struct_bridge_pairs.donor_2_label_comp_id GLU
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_dssp_struct_bridge_pairs.donor_2_label_seq_id 46
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_dssp_struct_bridge_pairs.donor_2_label_asym_id A
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_dssp_struct_bridge_pairs.donor_2_auth_seq_id 46
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_dssp_struct_bridge_pairs.donor_2_auth_asym_id A
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_dssp_struct_bridge_pairs.donor_2_pdbx_PDB_ins_code ?
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_dssp_struct_bridge_pairs.donor_2_energy -0.0
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;
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save_
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#
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save__dssp_struct_bridge_pairs.id
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_item.description
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; The value of _dssp_struct_bridge_pairs.id must uniquely identify a record in the
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dssp_struct_bridge_pairs list.
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;
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_item.name '_dssp_struct_bridge_pairs.id'
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_item.category_id dssp_struct_bridge_pairs
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_item.mandatory_code yes
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_item_type.code code
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save_
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save__dssp_struct_bridge_pairs.label_comp_id
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_item.description
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; A component of the identifier for this monomer.
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This data item is a pointer to _chem_comp.id in the CHEM_COMP
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category.
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;
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_item.name '_dssp_struct_bridge_pairs.label_comp_id'
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_item.category_id dssp_struct_bridge_pairs
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_item.mandatory_code yes
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_item_type.code ucode
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save_
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save__dssp_struct_bridge_pairs.label_seq_id
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_item.description
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; A component of the identifier for this monomer.
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;
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_item.name '_dssp_struct_bridge_pairs.label_seq_id'
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_item.category_id dssp_struct_bridge_pairs
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_item.mandatory_code yes
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_item_type.code int
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save_
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save__dssp_struct_bridge_pairs.label_asym_id
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_item.description
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; A component of the identifier for this monomer
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;
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_item.name '_dssp_struct_bridge_pairs.label_asym_id'
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_item.category_id dssp_struct_bridge_pairs
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_item.mandatory_code yes
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_item_type.code code
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save_
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save__dssp_struct_bridge_pairs.auth_seq_id
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_item.description
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; A component of the identifier for this monomer
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;
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_item.name '_dssp_struct_bridge_pairs.auth_seq_id'
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_item.category_id dssp_struct_bridge_pairs
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_item.mandatory_code no
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_item_type.code int
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save_
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save__dssp_struct_bridge_pairs.auth_asym_id
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_item.description
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; A component of the identifier for this monomer
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;
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_item.name '_dssp_struct_bridge_pairs.auth_asym_id'
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_item.category_id dssp_struct_bridge_pairs
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_item.mandatory_code no
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_item_type.code code
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save_
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save__dssp_struct_bridge_pairs.pdbx_PDB_ins_code
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_item.description
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; A component of the identifier for this monomer
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;
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_item.name '_dssp_struct_bridge_pairs.pdbx_PDB_ins_code'
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_item.category_id dssp_struct_bridge_pairs
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_item.mandatory_code no
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_item_type.code code
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save_
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save__dssp_struct_bridge_pairs.acceptor_1_label_comp_id
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_item.description
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; A component of the identifier of the first residue that forms a bridge pair
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with this monomer where this monomer is the donor.
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;
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_item.name '_dssp_struct_bridge_pairs.acceptor_1_label_comp_id'
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_item.category_id dssp_struct_bridge_pairs
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_item.mandatory_code no
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_item_type.code ucode
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save_
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save__dssp_struct_bridge_pairs.acceptor_1_label_seq_id
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_item.description
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; A component of the identifier of the first residue that forms a bridge pair
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with this monomer where this monomer is the donor.
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;
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_item.name '_dssp_struct_bridge_pairs.acceptor_1_label_seq_id'
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_item.category_id dssp_struct_bridge_pairs
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_item.mandatory_code no
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_item_type.code int
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save_
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save__dssp_struct_bridge_pairs.acceptor_1_label_asym_id
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_item.description
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; A component of the identifier of the first residue that forms a bridge pair
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with this monomer where this monomer is the donor.
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;
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_item.name '_dssp_struct_bridge_pairs.acceptor_1_label_asym_id'
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_item.category_id dssp_struct_bridge_pairs
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_item.mandatory_code no
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_item_type.code code
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save_
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save__dssp_struct_bridge_pairs.acceptor_1_auth_seq_id
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_item.description
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; A component of the identifier of the first residue that forms a bridge pair
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with this monomer where this monomer is the donor.
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;
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_item.name '_dssp_struct_bridge_pairs.acceptor_1_auth_seq_id'
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_item.category_id dssp_struct_bridge_pairs
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_item.mandatory_code no
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_item_type.code int
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save_
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save__dssp_struct_bridge_pairs.acceptor_1_auth_asym_id
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_item.description
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; A component of the identifier of the first residue that forms a bridge pair
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with this monomer where this monomer is the donor.
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;
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_item.name '_dssp_struct_bridge_pairs.acceptor_1_auth_asym_id'
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_item.category_id dssp_struct_bridge_pairs
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_item.mandatory_code no
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_item_type.code code
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save_
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save__dssp_struct_bridge_pairs.acceptor_1_pdbx_PDB_ins_code
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_item.description
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; A component of the identifier of the first residue that forms a bridge pair
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with this monomer where this monomer is the donor.
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;
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_item.name '_dssp_struct_bridge_pairs.acceptor_1_pdbx_PDB_ins_code'
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_item.category_id dssp_struct_bridge_pairs
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_item.mandatory_code no
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_item_type.code code
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save_
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save__dssp_struct_bridge_pairs.acceptor_1_energy
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_item.description
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; The calculated energy for the H-bond between this residue and the first
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acceptor.
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;
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_item.name '_dssp_struct_bridge_pairs.acceptor_1_energy'
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_item.category_id dssp_struct_bridge_pairs
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_item.mandatory_code no
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_item_type.code float
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save_
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save__dssp_struct_bridge_pairs.acceptor_2_label_comp_id
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|
_item.description
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|
; A component of the identifier of the second residue that forms a bridge pair
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with this monomer where this monomer is the donor.
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;
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_item.name '_dssp_struct_bridge_pairs.acceptor_2_label_comp_id'
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_item.category_id dssp_struct_bridge_pairs
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_item.mandatory_code no
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_item_type.code ucode
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save_
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save__dssp_struct_bridge_pairs.acceptor_2_label_seq_id
|
|
_item.description
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|
; A component of the identifier of the second residue that forms a bridge pair
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with this monomer where this monomer is the donor.
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;
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_item.name '_dssp_struct_bridge_pairs.acceptor_2_label_seq_id'
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_item.category_id dssp_struct_bridge_pairs
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_item.mandatory_code no
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_item_type.code int
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|
save_
|
|
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|
save__dssp_struct_bridge_pairs.acceptor_2_label_asym_id
|
|
_item.description
|
|
; A component of the identifier of the second residue that forms a bridge pair
|
|
with this monomer where this monomer is the donor.
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;
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_item.name '_dssp_struct_bridge_pairs.acceptor_2_label_asym_id'
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_item.category_id dssp_struct_bridge_pairs
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_item.mandatory_code no
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_item_type.code code
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|
save_
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|
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|
save__dssp_struct_bridge_pairs.acceptor_2_auth_seq_id
|
|
_item.description
|
|
; A component of the identifier of the second residue that forms a bridge pair
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with this monomer where this monomer is the donor.
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;
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_item.name '_dssp_struct_bridge_pairs.acceptor_2_auth_seq_id'
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_item.category_id dssp_struct_bridge_pairs
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_item.mandatory_code no
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_item_type.code int
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save_
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save__dssp_struct_bridge_pairs.acceptor_2_auth_asym_id
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|
_item.description
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; A component of the identifier of the second residue that forms a bridge pair
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with this monomer where this monomer is the donor.
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;
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_item.name '_dssp_struct_bridge_pairs.acceptor_2_auth_asym_id'
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_item.category_id dssp_struct_bridge_pairs
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_item.mandatory_code no
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_item_type.code code
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|
save_
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|
save__dssp_struct_bridge_pairs.acceptor_2_pdbx_PDB_ins_code
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|
_item.description
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; A component of the identifier of the second residue that forms a bridge pair
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with this monomer where this monomer is the donor.
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;
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_item.name '_dssp_struct_bridge_pairs.acceptor_2_pdbx_PDB_ins_code'
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_item.category_id dssp_struct_bridge_pairs
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_item.mandatory_code no
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_item_type.code code
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save_
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save__dssp_struct_bridge_pairs.acceptor_2_energy
|
|
_item.description
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; The calculated energy for the H-bond between this residue and the second
|
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acceptor.
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;
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_item.name '_dssp_struct_bridge_pairs.acceptor_2_energy'
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_item.category_id dssp_struct_bridge_pairs
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_item.mandatory_code no
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_item_type.code float
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|
save_
|
|
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|
save__dssp_struct_bridge_pairs.donor_1_label_comp_id
|
|
_item.description
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|
; A component of the identifier of the first residue that forms a bridge pair
|
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with this monomer where this monomer is the acceptor.
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|
;
|
|
_item.name '_dssp_struct_bridge_pairs.donor_1_label_comp_id'
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|
_item.category_id dssp_struct_bridge_pairs
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|
_item.mandatory_code no
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|
_item_type.code ucode
|
|
save_
|
|
|
|
save__dssp_struct_bridge_pairs.donor_1_label_seq_id
|
|
_item.description
|
|
; A component of the identifier of the first residue that forms a bridge pair
|
|
with this monomer where this monomer is the acceptor.
|
|
;
|
|
_item.name '_dssp_struct_bridge_pairs.donor_1_label_seq_id'
|
|
_item.category_id dssp_struct_bridge_pairs
|
|
_item.mandatory_code no
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_struct_bridge_pairs.donor_1_label_asym_id
|
|
_item.description
|
|
; A component of the identifier of the first residue that forms a bridge pair
|
|
with this monomer where this monomer is the acceptor.
|
|
;
|
|
_item.name '_dssp_struct_bridge_pairs.donor_1_label_asym_id'
|
|
_item.category_id dssp_struct_bridge_pairs
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_bridge_pairs.donor_1_auth_seq_id
|
|
_item.description
|
|
; A component of the identifier of the first residue that forms a bridge pair
|
|
with this monomer where this monomer is the acceptor.
|
|
;
|
|
_item.name '_dssp_struct_bridge_pairs.donor_1_auth_seq_id'
|
|
_item.category_id dssp_struct_bridge_pairs
|
|
_item.mandatory_code no
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_struct_bridge_pairs.donor_1_auth_asym_id
|
|
_item.description
|
|
; A component of the identifier of the first residue that forms a bridge pair
|
|
with this monomer where this monomer is the acceptor.
|
|
;
|
|
_item.name '_dssp_struct_bridge_pairs.donor_1_auth_asym_id'
|
|
_item.category_id dssp_struct_bridge_pairs
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_bridge_pairs.donor_1_pdbx_PDB_ins_code
|
|
_item.description
|
|
; A component of the identifier of the first residue that forms a bridge pair
|
|
with this monomer where this monomer is the acceptor.
|
|
;
|
|
_item.name '_dssp_struct_bridge_pairs.donor_1_pdbx_PDB_ins_code'
|
|
_item.category_id dssp_struct_bridge_pairs
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_bridge_pairs.donor_1_energy
|
|
_item.description
|
|
; The calculated energy for the H-bond between this residue and the first
|
|
donor.
|
|
;
|
|
_item.name '_dssp_struct_bridge_pairs.donor_1_energy'
|
|
_item.category_id dssp_struct_bridge_pairs
|
|
_item.mandatory_code no
|
|
_item_type.code float
|
|
save_
|
|
|
|
save__dssp_struct_bridge_pairs.donor_2_label_comp_id
|
|
_item.description
|
|
; A component of the identifier of the second residue that forms a bridge pair
|
|
with this monomer where this monomer is the acceptor.
|
|
;
|
|
_item.name '_dssp_struct_bridge_pairs.donor_2_label_comp_id'
|
|
_item.category_id dssp_struct_bridge_pairs
|
|
_item.mandatory_code no
|
|
_item_type.code ucode
|
|
save_
|
|
|
|
save__dssp_struct_bridge_pairs.donor_2_label_seq_id
|
|
_item.description
|
|
; A component of the identifier of the second residue that forms a bridge pair
|
|
with this monomer where this monomer is the acceptor.
|
|
;
|
|
_item.name '_dssp_struct_bridge_pairs.donor_2_label_seq_id'
|
|
_item.category_id dssp_struct_bridge_pairs
|
|
_item.mandatory_code no
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_struct_bridge_pairs.donor_2_label_asym_id
|
|
_item.description
|
|
; A component of the identifier of the second residue that forms a bridge pair
|
|
with this monomer where this monomer is the acceptor.
|
|
;
|
|
_item.name '_dssp_struct_bridge_pairs.donor_2_label_asym_id'
|
|
_item.category_id dssp_struct_bridge_pairs
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_bridge_pairs.donor_2_auth_seq_id
|
|
_item.description
|
|
; A component of the identifier of the second residue that forms a bridge pair
|
|
with this monomer where this monomer is the acceptor.
|
|
;
|
|
_item.name '_dssp_struct_bridge_pairs.donor_2_auth_seq_id'
|
|
_item.category_id dssp_struct_bridge_pairs
|
|
_item.mandatory_code no
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_struct_bridge_pairs.donor_2_auth_asym_id
|
|
_item.description
|
|
; A component of the identifier of the second residue that forms a bridge pair
|
|
with this monomer where this monomer is the acceptor.
|
|
;
|
|
_item.name '_dssp_struct_bridge_pairs.donor_2_auth_asym_id'
|
|
_item.category_id dssp_struct_bridge_pairs
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_bridge_pairs.donor_2_pdbx_PDB_ins_code
|
|
_item.description
|
|
; A component of the identifier of the second residue that forms a bridge pair
|
|
with this monomer where this monomer is the acceptor.
|
|
;
|
|
_item.name '_dssp_struct_bridge_pairs.donor_2_pdbx_PDB_ins_code'
|
|
_item.category_id dssp_struct_bridge_pairs
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_bridge_pairs.donor_2_energy
|
|
_item.description
|
|
; The calculated energy for the H-bond between this residue and the second
|
|
donor.
|
|
;
|
|
_item.name '_dssp_struct_bridge_pairs.donor_2_energy'
|
|
_item.category_id dssp_struct_bridge_pairs
|
|
_item.mandatory_code no
|
|
_item_type.code float
|
|
save_
|
|
|
|
########################################
|
|
## Category dssp_struct_ladder ##
|
|
########################################
|
|
|
|
save_dssp_struct_ladder
|
|
#
|
|
_category.description 'dssp_struct_ladder describes ladders as assigned by DSSP.'
|
|
_category.id dssp_struct_ladder
|
|
_category.mandatory_code no
|
|
#
|
|
_category_key.name '_dssp_struct_ladder.id'
|
|
loop_
|
|
_category_group.id 'inclusive_group'
|
|
'struct_group'
|
|
#
|
|
loop_
|
|
_category_examples.detail
|
|
_category_examples.case
|
|
|
|
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
|
|
;
|
|
Example taken from 1cbs, first ladder
|
|
;
|
|
;
|
|
_dssp_struct_ladder.id A
|
|
_dssp_struct_ladder.sheet_id A
|
|
_dssp_struct_ladder.range_id_1 A
|
|
_dssp_struct_ladder.range_id_2 B
|
|
_dssp_struct_ladder.type anti-parallel
|
|
_dssp_struct_ladder.beg_1_label_comp_id GLY
|
|
_dssp_struct_ladder.beg_1_label_asym_id A
|
|
_dssp_struct_ladder.beg_1_label_seq_id 5
|
|
_dssp_struct_ladder.pdbx_beg_1_PDB_ins_code ?
|
|
_dssp_struct_ladder.end_1_label_comp_id TRP
|
|
_dssp_struct_ladder.end_1_label_asym_id A
|
|
_dssp_struct_ladder.end_1_label_seq_id 7
|
|
_dssp_struct_ladder.pdbx_end_1_PDB_ins_code ?
|
|
_dssp_struct_ladder.beg_1_auth_comp_id GLY
|
|
_dssp_struct_ladder.beg_1_auth_asym_id A
|
|
_dssp_struct_ladder.beg_1_auth_seq_id 5
|
|
_dssp_struct_ladder.end_1_auth_comp_id TRP
|
|
_dssp_struct_ladder.end_1_auth_asym_id A
|
|
_dssp_struct_ladder.end_1_auth_seq_id 7
|
|
_dssp_struct_ladder.beg_2_label_comp_id ILE
|
|
_dssp_struct_ladder.beg_2_label_asym_id A
|
|
_dssp_struct_ladder.beg_2_label_seq_id 43
|
|
_dssp_struct_ladder.pdbx_beg_2_PDB_ins_code ?
|
|
_dssp_struct_ladder.end_2_label_comp_id VAL
|
|
_dssp_struct_ladder.end_2_label_asym_id A
|
|
_dssp_struct_ladder.end_2_label_seq_id 41
|
|
_dssp_struct_ladder.pdbx_end_2_PDB_ins_code ?
|
|
_dssp_struct_ladder.beg_2_auth_comp_id ILE
|
|
_dssp_struct_ladder.beg_2_auth_asym_id A
|
|
_dssp_struct_ladder.beg_2_auth_seq_id 43
|
|
_dssp_struct_ladder.end_2_auth_comp_id VAL
|
|
_dssp_struct_ladder.end_2_auth_asym_id A
|
|
_dssp_struct_ladder.end_2_auth_seq_id 41
|
|
;
|
|
save_
|
|
|
|
save__dssp_struct_ladder.id
|
|
_item.description
|
|
; The value of _dssp_struct_ladder.id must uniquely identify a record in the
|
|
dssp_struct_ladder list.
|
|
;
|
|
_item.name '_dssp_struct_ladder.id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code yes
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_ladder.sheet_id
|
|
_item.description
|
|
; This data item is a pointer to _struct_sheet.id in the
|
|
STRUCT_SHEET category.
|
|
;
|
|
_item.name '_dssp_struct_ladder.sheet_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code yes
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_ladder.range_id_1
|
|
_item.description
|
|
; This data item is a pointer to _struct_sheet_range.id in
|
|
the STRUCT_SHEET_RANGE category.
|
|
;
|
|
_item.name '_dssp_struct_ladder.range_id_1'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code yes
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_ladder.range_id_2
|
|
_item.description
|
|
; This data item is a pointer to _struct_sheet_range.id in
|
|
the STRUCT_SHEET_RANGE category.
|
|
;
|
|
_item.name '_dssp_struct_ladder.range_id_2'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code yes
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_ladder.type
|
|
_item.description
|
|
; The type of the ladder, be it parallel or anti-parallel
|
|
;
|
|
_item.name '_dssp_struct_ladder.type'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code yes
|
|
_item_type.code code
|
|
loop_
|
|
_item_enumeration.value
|
|
_item_enumeration.detail
|
|
parallel 'The strands forming a ladder are oriented parallel'
|
|
anti-parallel 'The strands forming a ladder are oriented anti-parallel'
|
|
save_
|
|
|
|
save__dssp_struct_ladder.beg_1_label_comp_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
first ladder segment begins.
|
|
;
|
|
_item.name '_dssp_struct_ladder.beg_1_label_comp_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code yes
|
|
_item_type.code ucode
|
|
save_
|
|
|
|
save__dssp_struct_ladder.beg_1_label_asym_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
first ladder segment begins.
|
|
;
|
|
_item.name '_dssp_struct_ladder.beg_1_label_asym_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code yes
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_ladder.beg_1_label_seq_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
first ladder segment begins.
|
|
;
|
|
_item.name '_dssp_struct_ladder.beg_1_label_seq_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_struct_ladder.pdbx_beg_1_PDB_ins_code
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
first ladder segment begins.
|
|
;
|
|
_item.name '_dssp_struct_ladder.pdbx_beg_1_PDB_ins_code'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_ladder.end_1_label_comp_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
first ladder segment ends.
|
|
;
|
|
_item.name '_dssp_struct_ladder.end_1_label_comp_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code yes
|
|
_item_type.code ucode
|
|
save_
|
|
|
|
save__dssp_struct_ladder.end_1_label_asym_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
first ladder segment ends.
|
|
;
|
|
_item.name '_dssp_struct_ladder.end_1_label_asym_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code yes
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_ladder.end_1_label_seq_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
first ladder segment ends.
|
|
;
|
|
_item.name '_dssp_struct_ladder.end_1_label_seq_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_struct_ladder.pdbx_end_1_PDB_ins_code
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
first ladder segment ends.
|
|
;
|
|
_item.name '_dssp_struct_ladder.pdbx_end_1_PDB_ins_code'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_ladder.beg_1_auth_comp_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
first ladder segment begins.
|
|
;
|
|
_item.name '_dssp_struct_ladder.beg_1_auth_comp_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code no
|
|
_item_type.code ucode
|
|
save_
|
|
|
|
save__dssp_struct_ladder.beg_1_auth_asym_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
first ladder segment begins.
|
|
;
|
|
_item.name '_dssp_struct_ladder.beg_1_auth_asym_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_ladder.beg_1_auth_seq_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
first ladder segment begins.
|
|
;
|
|
_item.name '_dssp_struct_ladder.beg_1_auth_seq_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code no
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_struct_ladder.end_1_auth_comp_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
first ladder segment ends.
|
|
;
|
|
_item.name '_dssp_struct_ladder.end_1_auth_comp_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code no
|
|
_item_type.code ucode
|
|
save_
|
|
|
|
save__dssp_struct_ladder.end_1_auth_asym_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
first ladder segment ends.
|
|
;
|
|
_item.name '_dssp_struct_ladder.end_1_auth_asym_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_ladder.end_1_auth_seq_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
first ladder segment ends.
|
|
;
|
|
_item.name '_dssp_struct_ladder.end_1_auth_seq_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code no
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_struct_ladder.beg_2_label_comp_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
second ladder segment begins.
|
|
;
|
|
_item.name '_dssp_struct_ladder.beg_2_label_comp_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code yes
|
|
_item_type.code ucode
|
|
save_
|
|
|
|
save__dssp_struct_ladder.beg_2_label_asym_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
second ladder segment begins.
|
|
;
|
|
_item.name '_dssp_struct_ladder.beg_2_label_asym_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code yes
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_ladder.beg_2_label_seq_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
second ladder segment begins.
|
|
;
|
|
_item.name '_dssp_struct_ladder.beg_2_label_seq_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_struct_ladder.pdbx_beg_2_PDB_ins_code
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
second ladder segment begins.
|
|
;
|
|
_item.name '_dssp_struct_ladder.pdbx_beg_2_PDB_ins_code'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_ladder.end_2_label_comp_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
second ladder segment ends.
|
|
;
|
|
_item.name '_dssp_struct_ladder.end_2_label_comp_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code yes
|
|
_item_type.code ucode
|
|
save_
|
|
|
|
save__dssp_struct_ladder.end_2_label_asym_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
second ladder segment ends.
|
|
;
|
|
_item.name '_dssp_struct_ladder.end_2_label_asym_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code yes
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_ladder.end_2_label_seq_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
second ladder segment ends.
|
|
;
|
|
_item.name '_dssp_struct_ladder.end_2_label_seq_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_struct_ladder.pdbx_end_2_PDB_ins_code
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
second ladder segment ends.
|
|
;
|
|
_item.name '_dssp_struct_ladder.pdbx_end_2_PDB_ins_code'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_ladder.beg_2_auth_comp_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
second ladder segment begins.
|
|
;
|
|
_item.name '_dssp_struct_ladder.beg_2_auth_comp_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code no
|
|
_item_type.code ucode
|
|
save_
|
|
|
|
save__dssp_struct_ladder.beg_2_auth_asym_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
second ladder segment begins.
|
|
;
|
|
_item.name '_dssp_struct_ladder.beg_2_auth_asym_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_ladder.beg_2_auth_seq_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
second ladder segment begins.
|
|
;
|
|
_item.name '_dssp_struct_ladder.beg_2_auth_seq_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code no
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_struct_ladder.end_2_auth_comp_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
second ladder segment ends.
|
|
;
|
|
_item.name '_dssp_struct_ladder.end_2_auth_comp_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code no
|
|
_item_type.code ucode
|
|
save_
|
|
|
|
save__dssp_struct_ladder.end_2_auth_asym_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
second ladder segment ends.
|
|
;
|
|
_item.name '_dssp_struct_ladder.end_2_auth_asym_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_ladder.end_2_auth_seq_id
|
|
_item.description
|
|
; A component of the identifier for the residue at which the
|
|
second ladder segment ends.
|
|
;
|
|
_item.name '_dssp_struct_ladder.end_2_auth_seq_id'
|
|
_item.category_id dssp_struct_ladder
|
|
_item.mandatory_code no
|
|
_item_type.code int
|
|
save_
|
|
|
|
|
|
########################################
|
|
## Category dssp_statistics ##
|
|
########################################
|
|
|
|
save_dssp_statistics
|
|
#
|
|
_category.description 'dssp_statistics contains secondary structure statistics as calculated by DSSP.'
|
|
_category.id dssp_statistics
|
|
_category.mandatory_code no
|
|
#
|
|
_category_key.name '_dssp_statistics.entry_id'
|
|
loop_
|
|
_category_group.id 'inclusive_group'
|
|
'struct_group'
|
|
#
|
|
loop_
|
|
_category_examples.detail
|
|
_category_examples.case
|
|
|
|
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
|
|
;
|
|
Example taken from 1cbs
|
|
;
|
|
;
|
|
_dssp_statistics.entry_id 1CBS
|
|
_dssp_statistics.nr_of_residues 137
|
|
_dssp_statistics.nr_of_chains 1
|
|
_dssp_statistics.nr_of_ss_bridges_total 0
|
|
_dssp_statistics.nr_of_ss_bridges_intra_chain 0
|
|
_dssp_statistics.nr_of_ss_bridges_inter_chain 0
|
|
_dssp_statistics.accessible_surface_of_protein 7905.01
|
|
;
|
|
save_
|
|
|
|
save__dssp_statistics.entry_id
|
|
_item.description
|
|
; The entry ID for which these statistics are calculated.
|
|
;
|
|
_item.name '_dssp_statistics.entry_id'
|
|
_item.category_id dssp_statistics
|
|
_item.mandatory_code yes
|
|
_item_type.code code
|
|
#
|
|
_item_linked.child_name "_dssp_statistics.entry_id"
|
|
_item_linked.parent_name "_entry.id"
|
|
#
|
|
save_
|
|
|
|
save__dssp_statistics.nr_of_residues
|
|
_item.description
|
|
; The total number of residues to which secondary structure information was assigned.
|
|
;
|
|
_item.name '_dssp_statistics.nr_of_residues'
|
|
_item.category_id dssp_statistics
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics.nr_of_chains
|
|
_item.description
|
|
; The number of chains used
|
|
;
|
|
_item.name '_dssp_statistics.nr_of_chains'
|
|
_item.category_id dssp_statistics
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics.nr_of_ss_bridges_total
|
|
_item.description
|
|
; The number of sulfur-sulfur bridges assigned.
|
|
;
|
|
_item.name '_dssp_statistics.nr_of_ss_bridges_total'
|
|
_item.category_id dssp_statistics
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics.nr_of_ss_bridges_intra_chain
|
|
_item.description
|
|
; The number of intra-chain sulfur-sulfur bridges assigned.
|
|
;
|
|
_item.name '_dssp_statistics.nr_of_ss_bridges_intra_chain'
|
|
_item.category_id dssp_statistics
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics.nr_of_ss_bridges_inter_chain
|
|
_item.description
|
|
; The number of inter-chain sulfur-sulfur bridges assigned.
|
|
;
|
|
_item.name '_dssp_statistics.nr_of_ss_bridges_inter_chain'
|
|
_item.category_id dssp_statistics
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics.accessible_surface_of_protein
|
|
_item.description
|
|
; The total accessible surface of the protein in square Angstroms.
|
|
;
|
|
_item.name '_dssp_statistics.accessible_surface_of_protein'
|
|
_item.category_id dssp_statistics
|
|
_item.mandatory_code yes
|
|
_item_type.code float
|
|
save_
|
|
|
|
########################################
|
|
## Category dssp_statistics_hbond ##
|
|
########################################
|
|
|
|
save_dssp_statistics_hbond
|
|
#
|
|
_category.description 'dssp_statistics_hbond contains statistics for the collection of h-bond variants calculated by DSSP.'
|
|
_category.id dssp_statistics_hbond
|
|
_category.mandatory_code no
|
|
#
|
|
loop_
|
|
_category_key.name '_dssp_statistics_hbond.entry_id'
|
|
'_dssp_statistics_hbond.type'
|
|
loop_
|
|
_category_group.id 'inclusive_group'
|
|
'struct_group'
|
|
#
|
|
loop_
|
|
_category_examples.detail
|
|
_category_examples.case
|
|
|
|
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
|
|
;
|
|
Example taken from 1cbs
|
|
;
|
|
;
|
|
_dssp_statistics_hbond.entry_id 1CBS
|
|
_dssp_statistics_hbond.type O(I)-->H-N(J)
|
|
_dssp_statistics_hbond.count 94
|
|
_dssp_statistics_hbond.count_per_100 68.6
|
|
;
|
|
save_
|
|
|
|
save__dssp_statistics_hbond.entry_id
|
|
_item.description
|
|
; The entry ID for which these statistics are calculated.
|
|
;
|
|
_item.name '_dssp_statistics_hbond.entry_id'
|
|
_item.category dssp_statistics_hbond
|
|
_item.mandatory_code yes
|
|
_item_type.code code
|
|
#
|
|
_item_linked.child_name "_dssp_statistics_hbond.entry_id"
|
|
_item_linked.parent_name "_entry.id"
|
|
#
|
|
save_
|
|
|
|
save__dssp_statistics_hbond.type
|
|
_item.description
|
|
; The type of the h-bond
|
|
;
|
|
_item.name '_dssp_statistics_hbond.type'
|
|
_item.category dssp_statistics_hbond
|
|
_item.mandatory_code yes
|
|
_item_type.code text
|
|
loop_
|
|
_item_enumeration.value
|
|
_item_enumeration.detail
|
|
O(I)-->H-N(J) 'non-bridge h-bond with residue further away than 5 residues'
|
|
'PARALLEL BRIDGES' 'h-bond forming a parallel bridge'
|
|
'ANTIPARALLEL BRIDGES' 'h-bond forming a anti-parallel bridge'
|
|
O(I)-->H-N(I-5) 'h-bond with residue five residues before the current one'
|
|
O(I)-->H-N(I-4) 'h-bond with residue four residues before the current one'
|
|
O(I)-->H-N(I-3) 'h-bond with residue three residues before the current one'
|
|
O(I)-->H-N(I-2) 'h-bond with residue two residues before the current one'
|
|
O(I)-->H-N(I-1) 'h-bond with residue one residue before the current one'
|
|
O(I)-->H-N(I+0) 'h-bond with current residue itself'
|
|
O(I)-->H-N(I+1) 'h-bond with residue one residues after the current one'
|
|
O(I)-->H-N(I+2) 'h-bond with residue two residues after the current one'
|
|
O(I)-->H-N(I+3) 'h-bond with residue three residues after the current one'
|
|
O(I)-->H-N(I+4) 'h-bond with residue four residues after the current one'
|
|
O(I)-->H-N(I+5) 'h-bond with residue five residues after the current one'
|
|
save_
|
|
|
|
save__dssp_statistics_hbond.count
|
|
_item.description
|
|
; Absolute number of h-bonds of this type
|
|
;
|
|
_item.name '_dssp_statistics_hbond.count'
|
|
_item.category dssp_statistics_hbond
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_hbond.count_per_100
|
|
_item.description
|
|
; Number of h-bonds of this type per hundred residues in the entire structure
|
|
;
|
|
_item.name '_dssp_statistics_hbond.count_per_100'
|
|
_item.category dssp_statistics_hbond
|
|
_item.mandatory_code yes
|
|
_item_type.code float
|
|
save_
|
|
|
|
########################################
|
|
## Category dssp_statistics_histogram ##
|
|
########################################
|
|
|
|
save_dssp_statistics_histogram
|
|
#
|
|
_category.description 'dssp_statistics_histogram contains the statistics for the ladders and helices in the form of a histogram as calculated by DSSP.'
|
|
_category.id dssp_statistics_histogram
|
|
_category.mandatory_code no
|
|
#
|
|
loop_
|
|
_category_key.name '_dssp_statistics_histogram.entry_id'
|
|
'_dssp_statistics_histogram.type'
|
|
loop_
|
|
_category_group.id 'inclusive_group'
|
|
'struct_group'
|
|
#
|
|
loop_
|
|
_category_examples.detail
|
|
_category_examples.case
|
|
|
|
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
|
|
;
|
|
Example taken from 1cbs
|
|
;
|
|
;
|
|
_dssp_statistics_histogram.entry_id 1CBS
|
|
_dssp_statistics_histogram.type antiparallel_bridges_per_ladder
|
|
_dssp_statistics_histogram.1 0
|
|
_dssp_statistics_histogram.2 0
|
|
_dssp_statistics_histogram.3 1
|
|
_dssp_statistics_histogram.4 1
|
|
_dssp_statistics_histogram.5 1
|
|
_dssp_statistics_histogram.6 1
|
|
_dssp_statistics_histogram.7 4
|
|
_dssp_statistics_histogram.8 1
|
|
_dssp_statistics_histogram.9 0
|
|
_dssp_statistics_histogram.10 0
|
|
_dssp_statistics_histogram.11 0
|
|
_dssp_statistics_histogram.12 0
|
|
_dssp_statistics_histogram.13 0
|
|
_dssp_statistics_histogram.14 0
|
|
_dssp_statistics_histogram.15 0
|
|
_dssp_statistics_histogram.16 0
|
|
_dssp_statistics_histogram.17 0
|
|
_dssp_statistics_histogram.18 0
|
|
_dssp_statistics_histogram.19 0
|
|
_dssp_statistics_histogram.20 0
|
|
_dssp_statistics_histogram.21 0
|
|
_dssp_statistics_histogram.22 0
|
|
_dssp_statistics_histogram.23 0
|
|
_dssp_statistics_histogram.24 0
|
|
_dssp_statistics_histogram.25 0
|
|
_dssp_statistics_histogram.26 0
|
|
_dssp_statistics_histogram.27 0
|
|
_dssp_statistics_histogram.28 0
|
|
_dssp_statistics_histogram.29 0
|
|
_dssp_statistics_histogram.30 0
|
|
;
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.entry_id
|
|
_item.description
|
|
; The entry ID for which these statistics are calculated.
|
|
;
|
|
_item.name '_dssp_statistics_histogram.entry_id'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code code
|
|
#
|
|
_item_linked.child_name "_dssp_statistics_histogram.entry_id"
|
|
_item_linked.parent_name "_entry.id"
|
|
#
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.type
|
|
_item.description
|
|
; The type for which this histogram contains data
|
|
;
|
|
_item.name '_dssp_statistics_histogram.type'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code code
|
|
loop_
|
|
_item_enumeration.value
|
|
_item_enumeration.detail
|
|
residues_per_alpha_helix 'residues per alpha helix'
|
|
parallel_bridges_per_ladder 'parallel bridges per ladder'
|
|
antiparallel_bridges_per_ladder 'antiparallel bridges per ladder'
|
|
ladders_per_sheet 'ladders per sheet'
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.1
|
|
_item.description
|
|
; The count of this type of ladder with a length of 1 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.1'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.2
|
|
_item.description
|
|
; The count of this type of ladder with a length of 2 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.2'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.3
|
|
_item.description
|
|
; The count of this type of ladder with a length of 3 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.3'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.4
|
|
_item.description
|
|
; The count of this type of ladder with a length of 4 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.4'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.5
|
|
_item.description
|
|
; The count of this type of ladder with a length of 5 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.5'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.6
|
|
_item.description
|
|
; The count of this type of ladder with a length of 6 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.6'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.7
|
|
_item.description
|
|
; The count of this type of ladder with a length of 7 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.7'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.8
|
|
_item.description
|
|
; The count of this type of ladder with a length of 8 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.8'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.9
|
|
_item.description
|
|
; The count of this type of ladder with a length of 9 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.9'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.10
|
|
_item.description
|
|
; The count of this type of ladder with a length of 10 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.10'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.11
|
|
_item.description
|
|
; The count of this type of ladder with a length of 11 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.11'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.12
|
|
_item.description
|
|
; The count of this type of ladder with a length of 12 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.12'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.13
|
|
_item.description
|
|
; The count of this type of ladder with a length of 13 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.13'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.14
|
|
_item.description
|
|
; The count of this type of ladder with a length of 14 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.14'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.15
|
|
_item.description
|
|
; The count of this type of ladder with a length of 15 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.15'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.16
|
|
_item.description
|
|
; The count of this type of ladder with a length of 16 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.16'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.17
|
|
_item.description
|
|
; The count of this type of ladder with a length of 17 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.17'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.18
|
|
_item.description
|
|
; The count of this type of ladder with a length of 18 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.18'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.19
|
|
_item.description
|
|
; The count of this type of ladder with a length of 19 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.19'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.20
|
|
_item.description
|
|
; The count of this type of ladder with a length of 20 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.20'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.21
|
|
_item.description
|
|
; The count of this type of ladder with a length of 21 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.21'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.22
|
|
_item.description
|
|
; The count of this type of ladder with a length of 22 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.22'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.23
|
|
_item.description
|
|
; The count of this type of ladder with a length of 23 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.23'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.24
|
|
_item.description
|
|
; The count of this type of ladder with a length of 24 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.24'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.25
|
|
_item.description
|
|
; The count of this type of ladder with a length of 25 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.25'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.26
|
|
_item.description
|
|
; The count of this type of ladder with a length of 26 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.26'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.27
|
|
_item.description
|
|
; The count of this type of ladder with a length of 27 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.27'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.28
|
|
_item.description
|
|
; The count of this type of ladder with a length of 28 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.28'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.29
|
|
_item.description
|
|
; The count of this type of ladder with a length of 29 residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.29'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_statistics_histogram.30
|
|
_item.description
|
|
; The count of this type of ladder with a length of 30 or more residues
|
|
;
|
|
_item.name '_dssp_statistics_histogram.30'
|
|
_item.category dssp_statistics_histogram
|
|
_item.mandatory_code yes
|
|
_item_type.code int
|
|
save_
|
|
|
|
########################################
|
|
## Category dssp_struct_summary ##
|
|
########################################
|
|
|
|
save_dssp_struct_summary
|
|
#
|
|
_category.description 'dssp_struct_summary contains the extra secondary structure information per residue as calculated by DSSP.'
|
|
_category.id dssp_struct_summary
|
|
_category.mandatory_code no
|
|
#
|
|
loop_
|
|
_category_key.name '_dssp_struct_summary.entry_id'
|
|
'_dssp_struct_summary.label_asym_id'
|
|
'_dssp_struct_summary.label_seq_id'
|
|
'_dssp_struct_summary.label_comp_id'
|
|
loop_
|
|
_category_group.id 'inclusive_group'
|
|
'struct_group'
|
|
#
|
|
loop_
|
|
_category_examples.detail
|
|
_category_examples.case
|
|
|
|
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
|
|
;
|
|
Example taken from 1cbs
|
|
;
|
|
;
|
|
_dssp_struct_summary.entry_id 1CBS
|
|
_dssp_struct_summary.label_comp_id PHE
|
|
_dssp_struct_summary.label_asym_id A
|
|
_dssp_struct_summary.label_seq_id 15
|
|
_dssp_struct_summary.secondary_structure H
|
|
_dssp_struct_summary.ss_bridge .
|
|
_dssp_struct_summary.helix_3_10 .
|
|
_dssp_struct_summary.helix_alpha >
|
|
_dssp_struct_summary.helix_pi .
|
|
_dssp_struct_summary.helix_pp .
|
|
_dssp_struct_summary.bend S
|
|
_dssp_struct_summary.chirality +
|
|
_dssp_struct_summary.sheet .
|
|
_dssp_struct_summary.strand .
|
|
_dssp_struct_summary.ladder_1 .
|
|
_dssp_struct_summary.ladder_2 .
|
|
_dssp_struct_summary.accessibility 23.1
|
|
_dssp_struct_summary.TCO 0.940
|
|
_dssp_struct_summary.kappa 73.9
|
|
_dssp_struct_summary.alpha 44.8
|
|
_dssp_struct_summary.phi -66.9
|
|
_dssp_struct_summary.psi -48.6
|
|
_dssp_struct_summary.x_ca 22.4
|
|
_dssp_struct_summary.y_ca 17.2
|
|
_dssp_struct_summary.z_ca 17.7
|
|
;
|
|
save_
|
|
|
|
save__dssp_struct_summary.entry_id
|
|
_item.description
|
|
; The entry ID for which these statistics are calculated.
|
|
;
|
|
_item.name '_dssp_struct_summary.entry_id'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code yes
|
|
_item_type.code code
|
|
#
|
|
_item_linked.child_name "_dssp_struct_summary.entry_id"
|
|
_item_linked.parent_name "_entry.id"
|
|
#
|
|
save_
|
|
|
|
save__dssp_struct_summary.label_comp_id
|
|
_item.description
|
|
; A component of the identifier for this monomer.
|
|
|
|
This data item is a pointer to _chem_comp.id in the CHEM_COMP
|
|
category.
|
|
;
|
|
_item.name '_dssp_struct_summary.label_comp_id'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code yes
|
|
_item_type.code ucode
|
|
save_
|
|
|
|
save__dssp_struct_summary.label_asym_id
|
|
_item.description
|
|
; A component of the identifier for this monomer
|
|
;
|
|
_item.name '_dssp_struct_summary.label_asym_id'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code yes
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_summary.label_seq_id
|
|
_item.description
|
|
; A component of the identifier for this monomer
|
|
;
|
|
_item.name '_dssp_struct_summary.label_seq_id'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code yes
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_summary.secondary_structure
|
|
_item.description
|
|
; The secondary structure assigned to this residue in a single letter code
|
|
|
|
The value for this field may be empty in which case the assigned
|
|
secondary structure is Loop.
|
|
;
|
|
_item.name '_dssp_struct_summary.secondary_structure'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
loop_
|
|
_item_enumeration.value
|
|
_item_enumeration.detail
|
|
H Alphahelix
|
|
B Betabridge
|
|
E Strand
|
|
G Helix_3
|
|
I Helix_5
|
|
P Helix_PPII
|
|
T Turn
|
|
S Bend
|
|
save_
|
|
|
|
save__dssp_struct_summary.ss_bridge
|
|
_item.description
|
|
; Identifier for the SS-Bridge formed by this residue
|
|
;
|
|
_item.name '_dssp_struct_summary.ss_bridge'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code no
|
|
_item_type.code int
|
|
save_
|
|
|
|
save__dssp_struct_summary.helix_3_10
|
|
_item.description
|
|
; In case this residue is a candidate to form a 3_10 helix, this
|
|
field contains the position of the residue in the helix.
|
|
;
|
|
_item.name '_dssp_struct_summary.helix_3_10'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
loop_
|
|
_item_enumeration.value
|
|
_item_enumeration.detail
|
|
'>' 'The residue has h-bond(s) is a candidate to start a 3_10 helix'
|
|
'3' 'The residue has h-bond(s) is a candidate to be within a 3_10 helix'
|
|
'<' 'The residue has h-bond(s) is a candidate to end a 3_10 helix'
|
|
'X' 'The residue has h-bond(s) is a candidate for both a start and an end of a 3_10 helix'
|
|
save_
|
|
|
|
save__dssp_struct_summary.helix_alpha
|
|
_item.description
|
|
; In case this residue is a candidate to form a alpha helix, this
|
|
field contains the position of the residue in the helix.
|
|
;
|
|
_item.name '_dssp_struct_summary.helix_alpha'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
loop_
|
|
_item_enumeration.value
|
|
_item_enumeration.detail
|
|
'>' 'The residue has h-bond(s) is a candidate to start a alpha helix'
|
|
'4' 'The residue has h-bond(s) is a candidate to be within a alpha helix'
|
|
'<' 'The residue has h-bond(s) is a candidate to end a alpha helix'
|
|
'X' 'The residue has h-bond(s) is a candidate for both a start and an end of a alpha helix'
|
|
save_
|
|
|
|
save__dssp_struct_summary.helix_pi
|
|
_item.description
|
|
; In case this residue is a candidate to form a pi helix, this
|
|
field contains the position of the residue in the helix.
|
|
;
|
|
_item.name '_dssp_struct_summary.helix_pi'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
loop_
|
|
_item_enumeration.value
|
|
_item_enumeration.detail
|
|
'>' 'The residue has h-bond(s) is a candidate to start a pi helix'
|
|
'5' 'The residue has h-bond(s) is a candidate to be within a pi helix'
|
|
'<' 'The residue has h-bond(s) is a candidate to end a pi helix'
|
|
'X' 'The residue has h-bond(s) is a candidate for both a start and an end of a pi helix'
|
|
save_
|
|
|
|
save__dssp_struct_summary.helix_pp
|
|
_item.description
|
|
; In case this residue is a candidate to form a poly-proline helix, this
|
|
field contains the position of the residue in the helix.
|
|
;
|
|
_item.name '_dssp_struct_summary.helix_pp'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
loop_
|
|
_item_enumeration.value
|
|
_item_enumeration.detail
|
|
'>' 'The residue has h-bond(s) is a candidate to start a poly-proline helix'
|
|
'P' 'The residue has h-bond(s) is a candidate to be within a poly-proline helix'
|
|
'<' 'The residue has h-bond(s) is a candidate to end a poly-proline helix'
|
|
'X' 'The residue has h-bond(s) is a candidate for both a start and an end of a poly-proline helix'
|
|
save_
|
|
|
|
save__dssp_struct_summary.bend
|
|
_item.description
|
|
; If this field contains S this indicates that the assigned secondary structure Turn actually forms a Bend.
|
|
;
|
|
_item.name '_dssp_struct_summary.bend'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
_item_enumeration.value S
|
|
_item_enumeration.detail 'The residue forms a Bend'
|
|
save_
|
|
|
|
save__dssp_struct_summary.chirality
|
|
_item.description
|
|
; The chirality for the virtual torsion angle (dihedral angle) defined by the four C-alpha atoms of residues I-1, I, I+1 and I+2.
|
|
;
|
|
_item.name '_dssp_struct_summary.chirality'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
loop_
|
|
_item_enumeration.value '+'
|
|
'-'
|
|
save_
|
|
|
|
save__dssp_struct_summary.sheet
|
|
_item.description
|
|
; This data item is a pointer to _struct_sheet.id in
|
|
the STRUCT_SHEET category.
|
|
;
|
|
_item.name '_dssp_struct_summary.sheet'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_summary.strand
|
|
_item.description
|
|
; This data item is a pointer to _struct_sheet_range.id in
|
|
the STRUCT_SHEET_RANGE category.
|
|
;
|
|
_item.name '_dssp_struct_summary.strand'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_summary.ladder_1
|
|
_item.description
|
|
; Label for the first beta bridge of which this residue is part.
|
|
;
|
|
_item.name '_dssp_struct_summary.ladder_1'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_summary.ladder_2
|
|
_item.description
|
|
; Label for the second beta bridge of which this residue is part.
|
|
;
|
|
_item.name '_dssp_struct_summary.ladder_2'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code no
|
|
_item_type.code code
|
|
save_
|
|
|
|
save__dssp_struct_summary.accessibility
|
|
_item.description
|
|
; Solvent accessibility for this residue in square Angstroms
|
|
;
|
|
_item.name '_dssp_struct_summary.accessibility'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code no
|
|
_item_type.code float
|
|
save_
|
|
|
|
save__dssp_struct_summary.TCO
|
|
_item.description
|
|
; The cosine of the angle between C=O of residue I and C=O of residue I-1. For alpha-helices, TCO is near +1, for Beta-sheets TCO is near -1.
|
|
|
|
Not used for structure definition.
|
|
;
|
|
_item.name '_dssp_struct_summary.TCO'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code no
|
|
_item_type.code float
|
|
save_
|
|
|
|
save__dssp_struct_summary.kappa
|
|
_item.description
|
|
; The virtual bond angle (bend angle) defined by the three C-alpha atoms of residues I-2, I and I+2.
|
|
|
|
Used to define bend (structure code 'S').
|
|
;
|
|
_item.name '_dssp_struct_summary.kappa'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code no
|
|
_item_type.code float
|
|
save_
|
|
|
|
save__dssp_struct_summary.alpha
|
|
_item.description
|
|
; The virtual torsion angle (dihedral angle) defined by the four C-alpha atoms of residues I-1, I, I+1 and I+2.
|
|
|
|
Used to define chirality (structure code '+' or '-').
|
|
;
|
|
_item.name '_dssp_struct_summary.alpha'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code no
|
|
_item_type.code float
|
|
save_
|
|
|
|
save__dssp_struct_summary.phi
|
|
_item.description
|
|
; IUPAC peptide backbone torsion phi angle
|
|
;
|
|
_item.name '_dssp_struct_summary.phi'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code no
|
|
_item_type.code float
|
|
save_
|
|
|
|
save__dssp_struct_summary.psi
|
|
_item.description
|
|
; IUPAC peptide backbone torsion psi angle
|
|
;
|
|
_item.name '_dssp_struct_summary.psi'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code no
|
|
_item_type.code float
|
|
save_
|
|
|
|
save__dssp_struct_summary.x_ca
|
|
_item.description
|
|
; The x coordinate of the C-alpha atom for this residue
|
|
;
|
|
_item.name '_dssp_struct_summary.x_ca'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code no
|
|
_item_type.code float
|
|
save_
|
|
|
|
save__dssp_struct_summary.y_ca
|
|
_item.description
|
|
; The y coordinate of the C-alpha atom for this residue
|
|
;
|
|
_item.name '_dssp_struct_summary.y_ca'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code no
|
|
_item_type.code float
|
|
save_
|
|
|
|
save__dssp_struct_summary.z_ca
|
|
_item.description
|
|
; The z coordinate of the C-alpha atom for this residue
|
|
;
|
|
_item.name '_dssp_struct_summary.z_ca'
|
|
_item.category dssp_struct_summary
|
|
_item.mandatory_code no
|
|
_item_type.code float
|
|
save_
|