CONTACTS documentation |
XX Intra-chain residue-residue contact data. XX TY INTRA XX EX THRESH 1.0; IGNORE 20.0; NMOD 1; NCHA 1 XX NE 1 XX EN [1] XX ID PDB 1cs4; DOM .; LIG . XX CN MO 1; CN1 1; CN2 .; ID1 A; ID2 .; NRES1 52; NRES2 . XX S1 SEQUENCE 52 AA; 5817 MW; D8CCAE0E1FC0849A CRC64; ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS XX NC SM 163; LI . XX SM ASP 2 ; ILE 3 SM ASP 2 ; GLU 4 SM ASP 2 ; ASP 46 SM ASP 2 ; CYS 47 SM ILE 3 ; GLU 4 SM ILE 3 ; GLY 5 SM ILE 3 ; PHE 6 SM ILE 3 ; LEU 9 SM ILE 3 ; LEU 25 SM ILE 3 ; ASP 46 SM GLU 4 ; GLY 5 SM GLU 4 ; PHE 6 SM GLY 5 ; PHE 6 SM GLY 5 ; THR 7 SM GLY 5 ; SER 8 SM GLY 5 ; LEU 9 SM PHE 6 ; THR 7 SM PHE 6 ; SER 8 SM PHE 6 ; LEU 9 SM PHE 6 ; ALA 10 SM PHE 6 ; LEU 18 SM PHE 6 ; LEU 22 SM PHE 6 ; GLY 45 SM PHE 6 ; ASP 46 SM THR 7 ; SER 8 SM THR 7 ; LEU 9 SM THR 7 ; ALA 10 SM THR 7 ; SER 11 SM SER 8 ; LEU 9 SM SER 8 ; ALA 10 SM SER 8 ; SER 11 [Part of this file has been deleted for brevity] SM PHE 29 ; LYS 31 SM PHE 29 ; LEU 32 SM PHE 29 ; ALA 33 SM ASP 30 ; LYS 31 SM ASP 30 ; LEU 32 SM ASP 30 ; ALA 33 SM ASP 30 ; ALA 34 SM ASP 30 ; ARG 40 SM LYS 31 ; LEU 32 SM LYS 31 ; ALA 33 SM LYS 31 ; ALA 34 SM LYS 31 ; GLU 35 SM LEU 32 ; ALA 33 SM LEU 32 ; ALA 34 SM LEU 32 ; GLU 35 SM LEU 32 ; ASN 36 SM ALA 33 ; ALA 34 SM ALA 33 ; GLU 35 SM ALA 33 ; ASN 36 SM ALA 33 ; HIS 37 SM ALA 33 ; CYS 38 SM ALA 34 ; GLU 35 SM ALA 34 ; ASN 36 SM ALA 34 ; HIS 37 SM GLU 35 ; ASN 36 SM GLU 35 ; HIS 37 SM ASN 36 ; HIS 37 SM ASN 36 ; CYS 38 SM HIS 37 ; CYS 38 SM HIS 37 ; LEU 39 SM CYS 38 ; LEU 39 SM CYS 38 ; ARG 40 SM LEU 39 ; ARG 40 SM LEU 39 ; ILE 41 SM ARG 40 ; ILE 41 SM ARG 40 ; LYS 42 SM ARG 40 ; ILE 43 SM ILE 41 ; LYS 42 SM LYS 42 ; ILE 43 SM LYS 42 ; LEU 44 SM LYS 42 ; CYS 47 SM ILE 43 ; LEU 44 SM ILE 43 ; GLY 45 SM ILE 43 ; CYS 47 SM LEU 44 ; GLY 45 SM LEU 44 ; ASP 46 SM LEU 44 ; CYS 47 SM GLY 45 ; ASP 46 SM GLY 45 ; CYS 47 SM ASP 46 ; CYS 47 // |
XX Intra-chain residue-residue contact data. XX TY INTRA XX EX THRESH 1.0; IGNORE 20.0; NMOD 1; NCHA 1 XX NE 1 XX EN [1] XX ID PDB 1ii7; DOM .; LIG . XX CN MO 1; CN1 1; CN2 .; ID1 A; ID2 .; NRES1 65; NRES2 . XX S1 SEQUENCE 65 AA; 7395 MW; 75FBE75B22FD3678 CRC64; MKFAHLADIH LGYEQFHKPQ REEEFAEAFK NALEIAVQEN VDFILIAGDL FHSSRPSPGT LKKAI XX NC SM 151; LI . XX SM ASP 8 ; ILE 9 SM ASP 8 ; HIS 10 SM ASP 8 ; GLY 48 SM ASP 8 ; ASP 49 SM ILE 9 ; HIS 10 SM ILE 9 ; LEU 11 SM ILE 9 ; PHE 25 SM ILE 9 ; PHE 29 SM ILE 9 ; ILE 46 SM ILE 9 ; ASP 49 SM ILE 9 ; LEU 50 SM HIS 10 ; LEU 11 SM HIS 10 ; GLY 12 SM HIS 10 ; TYR 13 SM HIS 10 ; PHE 25 SM HIS 10 ; ASP 49 SM HIS 10 ; LEU 50 SM LEU 11 ; GLY 12 SM LEU 11 ; TYR 13 SM LEU 11 ; ALA 26 SM LEU 11 ; PHE 29 SM LEU 11 ; LEU 50 SM GLY 12 ; TYR 13 SM GLY 12 ; GLU 14 SM GLY 12 ; GLU 22 SM TYR 13 ; GLU 14 SM TYR 13 ; GLN 15 SM TYR 13 ; GLU 22 SM TYR 13 ; PHE 25 SM GLU 14 ; GLN 15 [Part of this file has been deleted for brevity] SM ASN 31 ; ILE 35 SM ALA 32 ; LEU 33 SM ALA 32 ; GLU 34 SM ALA 32 ; ILE 35 SM ALA 32 ; ALA 36 SM LEU 33 ; GLU 34 SM LEU 33 ; ILE 35 SM LEU 33 ; ALA 36 SM LEU 33 ; VAL 37 SM LEU 33 ; ILE 44 SM GLU 34 ; ILE 35 SM GLU 34 ; ALA 36 SM GLU 34 ; VAL 37 SM GLU 34 ; GLN 38 SM ILE 35 ; ALA 36 SM ILE 35 ; VAL 37 SM ILE 35 ; GLN 38 SM ILE 35 ; GLU 39 SM ALA 36 ; VAL 37 SM ALA 36 ; GLN 38 SM ALA 36 ; GLU 39 SM ALA 36 ; ASN 40 SM ALA 36 ; VAL 41 SM ALA 36 ; ILE 44 SM VAL 37 ; GLN 38 SM VAL 37 ; GLU 39 SM VAL 37 ; ASN 40 SM GLN 38 ; GLU 39 SM GLN 38 ; ASN 40 SM GLU 39 ; ASN 40 SM GLU 39 ; VAL 41 SM ASN 40 ; VAL 41 SM ASN 40 ; ASP 42 SM VAL 41 ; ASP 42 SM VAL 41 ; PHE 43 SM VAL 41 ; ILE 44 SM ASP 42 ; PHE 43 SM PHE 43 ; ILE 44 SM PHE 43 ; LEU 45 SM ILE 44 ; LEU 45 SM ILE 44 ; ILE 46 SM LEU 45 ; ILE 46 SM LEU 45 ; ALA 47 SM ILE 46 ; ALA 47 SM ILE 46 ; GLY 48 SM ILE 46 ; LEU 50 SM ALA 47 ; GLY 48 SM GLY 48 ; ASP 49 SM GLY 48 ; LEU 50 SM ASP 49 ; LEU 50 // |
XX Intra-chain residue-residue contact data. XX TY INTRA XX EX THRESH 1.0; IGNORE 20.0; NMOD 1; NCHA 4 XX NE 4 XX EN [1] XX ID PDB 2hhb; DOM .; LIG . XX CN MO 1; CN1 1; CN2 .; ID1 A; ID2 .; NRES1 141; NRES2 . XX S1 SEQUENCE 141 AA; 15126 MW; 34D13618E62A33C1 CRC64; VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA VHASLDKFLA SVSTVLTSKY R XX NC SM 643; LI . XX SM VAL 1 ; LEU 2 SM VAL 1 ; SER 3 SM VAL 1 ; LYS 127 SM LEU 2 ; SER 3 SM LEU 2 ; PRO 4 SM LEU 2 ; ASP 6 SM LEU 2 ; LYS 7 SM LEU 2 ; VAL 73 SM LEU 2 ; MET 76 SM LEU 2 ; LYS 127 SM LEU 2 ; PHE 128 SM LEU 2 ; SER 131 SM SER 3 ; PRO 4 SM SER 3 ; ALA 5 SM SER 3 ; ASP 6 SM SER 3 ; LYS 7 SM SER 3 ; LYS 127 SM PRO 4 ; ALA 5 SM PRO 4 ; ASP 6 SM PRO 4 ; LYS 7 SM PRO 4 ; THR 8 SM ALA 5 ; ASP 6 SM ALA 5 ; LYS 7 SM ALA 5 ; THR 8 SM ALA 5 ; ASN 9 SM ASP 6 ; LYS 7 SM ASP 6 ; THR 8 SM ASP 6 ; ASN 9 SM ASP 6 ; VAL 10 [Part of this file has been deleted for brevity] SM GLN 131 ; LYS 132 SM GLN 131 ; VAL 133 SM GLN 131 ; VAL 134 SM GLN 131 ; ALA 135 SM LYS 132 ; VAL 133 SM LYS 132 ; VAL 134 SM LYS 132 ; ALA 135 SM LYS 132 ; GLY 136 SM VAL 133 ; VAL 134 SM VAL 133 ; ALA 135 SM VAL 133 ; GLY 136 SM VAL 133 ; VAL 137 SM VAL 134 ; ALA 135 SM VAL 134 ; GLY 136 SM VAL 134 ; VAL 137 SM VAL 134 ; ALA 138 SM ALA 135 ; GLY 136 SM ALA 135 ; VAL 137 SM ALA 135 ; ALA 138 SM ALA 135 ; ASN 139 SM GLY 136 ; VAL 137 SM GLY 136 ; ALA 138 SM GLY 136 ; ASN 139 SM GLY 136 ; ALA 140 SM VAL 137 ; ALA 138 SM VAL 137 ; ASN 139 SM VAL 137 ; ALA 140 SM VAL 137 ; LEU 141 SM ALA 138 ; ASN 139 SM ALA 138 ; ALA 140 SM ALA 138 ; LEU 141 SM ALA 138 ; ALA 142 SM ASN 139 ; ALA 140 SM ASN 139 ; LEU 141 SM ASN 139 ; ALA 142 SM ASN 139 ; HIS 143 SM ALA 140 ; LEU 141 SM ALA 140 ; ALA 142 SM ALA 140 ; HIS 143 SM LEU 141 ; ALA 142 SM LEU 141 ; HIS 143 SM LEU 141 ; TYR 145 SM ALA 142 ; HIS 143 SM ALA 142 ; LYS 144 SM ALA 142 ; TYR 145 SM HIS 143 ; LYS 144 SM HIS 143 ; TYR 145 SM LYS 144 ; TYR 145 SM LYS 144 ; HIS 146 SM TYR 145 ; HIS 146 // |
1cs4 1ii7 2hhb |
Generate intra-chain CON files from CCF files. Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-cpdbdir] dirlist [./] This option specifies the location of CCF files (clean coordinate files) (input). A 'clean cordinate file' contains protein coordinate and derived data for a single PDB file ('protein clean coordinate file') or a single domain from SCOP or CATH ('domain clean coordinate file'), in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. -vdwfile datafile [Evdw.dat] This option specifies the name of the data file with van der Waals radii of atoms for different amino acid residues. -threshold float [1.0] Contact between two residues is defined as when the van der Waals surface of any atom of the first residue comes within the threshold contact distance of the van der Waals surface of any atom of the second residue. The threshold contact distance is a user-defined distance with a default value of 1 Angstrom. (Any numeric value) [-conoutdir] outdir [./] This option specifies the location of CON files (contact files) (output). A 'contact file' contains contact data for a protein or a domain from SCOP or CATH, in the CON format (EMBL-like). The contacts may be intra-chain residue-residue, inter-chain residue-residue or residue-ligand. The files are generated by using CONTACTS, INTERFACE and SITES. -conlogfile outfile [contacts.log] The log file contains messages about any errors arising while contacts ran. Additional (Optional) qualifiers: -[no]ccfnaming boolean [Y] This option specifies whether to use pdbid code to name the output files. If set, the PDB identifier code (from the PDB file) is used to name the file. Otherwise, the output files have the same names as the input files. -skip boolean [N] Whether to calculate contacts between residue adjacent in sequence. -ignore float [20.0] If any two atoms from two different residues are at least this distance apart then no futher inter-atomic contacts will be checked for for that residue pair . This speeds the calculation up considerably. (Any numeric value) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-cpdbdir" associated qualifiers -extension1 string Default file extension "-conoutdir" associated qualifiers -extension2 string Default file extension "-conlogfile" associated qualifiers -odirectory string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit |
Qualifier | Type | Description | Allowed values | Default |
---|---|---|---|---|
Standard (Mandatory) qualifiers | ||||
[-cpdbdir] (Parameter 1) |
dirlist | This option specifies the location of CCF files (clean coordinate files) (input). A 'clean cordinate file' contains protein coordinate and derived data for a single PDB file ('protein clean coordinate file') or a single domain from SCOP or CATH ('domain clean coordinate file'), in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. | Directory with files | ./ |
-vdwfile | datafile | This option specifies the name of the data file with van der Waals radii of atoms for different amino acid residues. | Data file | Evdw.dat |
-threshold | float | Contact between two residues is defined as when the van der Waals surface of any atom of the first residue comes within the threshold contact distance of the van der Waals surface of any atom of the second residue. The threshold contact distance is a user-defined distance with a default value of 1 Angstrom. | Any numeric value | 1.0 |
[-conoutdir] (Parameter 2) |
outdir | This option specifies the location of CON files (contact files) (output). A 'contact file' contains contact data for a protein or a domain from SCOP or CATH, in the CON format (EMBL-like). The contacts may be intra-chain residue-residue, inter-chain residue-residue or residue-ligand. The files are generated by using CONTACTS, INTERFACE and SITES. | Output directory | ./ |
-conlogfile | outfile | The log file contains messages about any errors arising while contacts ran. | Output file | contacts.log |
Additional (Optional) qualifiers | ||||
-[no]ccfnaming | boolean | This option specifies whether to use pdbid code to name the output files. If set, the PDB identifier code (from the PDB file) is used to name the file. Otherwise, the output files have the same names as the input files. | Boolean value Yes/No | Yes |
-skip | boolean | Whether to calculate contacts between residue adjacent in sequence. | Boolean value Yes/No | No |
-ignore | float | If any two atoms from two different residues are at least this distance apart then no futher inter-atomic contacts will be checked for for that residue pair . This speeds the calculation up considerably. | Any numeric value | 20.0 |
Advanced (Unprompted) qualifiers | ||||
(none) | ||||
Associated qualifiers | ||||
"-cpdbdir" associated dirlist qualifiers | ||||
-extension1 -extension_cpdbdir |
string | Default file extension | Any string | ccf |
"-conoutdir" associated outdir qualifiers | ||||
-extension2 -extension_conoutdir |
string | Default file extension | Any string | con |
"-conlogfile" associated outfile qualifiers | ||||
-odirectory | string | Output directory | Any string | |
General qualifiers | ||||
-auto | boolean | Turn off prompts | Boolean value Yes/No | N |
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
-warning | boolean | Report warnings | Boolean value Yes/No | Y |
-error | boolean | Report errors | Boolean value Yes/No | Y |
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
-die | boolean | Report dying program messages | Boolean value Yes/No | Y |
-version | boolean | Report version number and exit | Boolean value Yes/No | N |
% contacts Generate intra-chain CON files from CCF files. Clean protein structure coordinates directories [./]: ../pdbplus-keep/ Van der waals radii data file [Evdw.dat]: Threshold contact distance [1.0]: 1 Structure contacts file output directory [./]: Domainatrix log output file [contacts.log]: 1cs4 1ii7 2hhb |
Go to the output files for this example
FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO |
Clean coordinate file (for protein) | CCF format (EMBL-like). | Protein coordinate and derived data for a single PDB file. The data are 'cleaned-up': self-consistent and error-corrected. | PDBPARSE | Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. |
Clean coordinate file (for domain) | CCF format (EMBL-like). | Protein coordinate and derived data for a single domain from SCOP or CATH. The data are 'cleaned-up': self-consistent and error-corrected. | DOMAINER | Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. |
Contact file (intra-chain residue-residue contacts) | CON format (EMBL-like.) | Intra-chain residue-residue contact data for a protein or a domain from SCOP or CATH. | CONTACTS | N.A. |
Contact file (inter-chain residue-residue contacts) | CON format (EMBL-like.) | Inter-chain residue-residue contact data for a protein or a domain from SCOP or CATH. | INTERFACE | N.A. |
Contact file (residue-ligand contacts) | CON format (EMBL-like.) | Residue-ligand contact data for a protein or a domain from SCOP or CATH. | SITES | N.A. |
van der Waals radii | A file of van der Waals radii for atoms in amino acid residues. Part of the emboss distribution. | N.A. | N.A. |
Program name | Description |
---|---|
domainrep | Reorder DCF file to identify representative structures |
domainreso | Remove low resolution domains from a DCF file |
interface | Generate inter-chain CON files from CCF files |
psiphi | Calculates phi and psi torsion angles from protein coordinates |
See also http://emboss.sourceforge.net/