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interface |
Knowledge of the physical contacts that amino acid residues in two different polypeptide chains of a protein make with one another is required for several different analyses. interface calculates inter-chain residue-residue contact data from clean protein coordinate files.
interface reads a protein coordinate file and writes a file of inter-chain residue-residue contact data in embl-like format. The file contains residue contact data for all pairs of chains in each model in the coordinate file. The input and output files are specified by the user. A log file is also written.
% interface Reads CCF files (clean coordinate files) and writes CON files (contact files) of inter-chain residue-residue contact data. Name of protein CCF file (clean coordinate file) (input): interface/2hhb.ccf Threshold contact distance [1.0]: 1 Name of CON file (contact file) (output) [test.con]: 2hhb.con Name of log file for the build [interface.log]: 2hhb |
Go to the input files for this example
Go to the output files for this example
Standard (Mandatory) qualifiers: [-infile] infile This option specifies the name of the protein CCF file (clean coordinate file) (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. -thresh float This option specifies the threshold contact distance. 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. [-outfile] outfile This option specifies the name of CON file (contact file) (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 FUNKY. -conerrfile outfile This option specifies the name of the log file for the build. The log file contains messages about any errors arising while INTERFACE ran. Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -vdwfile datafile This option specifies the name of data file with van der Waals radii. The file of van der Waals radii for atoms in amino acid residues is part of the emboss distribution. -ignore float This option specifies the threshold ignore distance. 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. Associated qualifiers: "-outfile" associated qualifiers -odirectory2 string Output directory "-conerrfile" associated qualifiers -odirectory string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write standard output -filter boolean Read standard input, write 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. 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 deaths |
Standard (Mandatory) qualifiers | Allowed values | Default | |
---|---|---|---|
[-infile] (Parameter 1) |
This option specifies the name of the protein CCF file (clean coordinate file) (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. | Input file | Required |
-thresh | This option specifies the threshold contact distance. 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 |
[-outfile] (Parameter 2) |
This option specifies the name of CON file (contact file) (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 FUNKY. | Output file | test.con |
-conerrfile | This option specifies the name of the log file for the build. The log file contains messages about any errors arising while INTERFACE ran. | Output file | interface.log |
Additional (Optional) qualifiers | Allowed values | Default | |
(none) | |||
Advanced (Unprompted) qualifiers | Allowed values | Default | |
-vdwfile | This option specifies the name of data file with van der Waals radii. The file of van der Waals radii for atoms in amino acid residues is part of the emboss distribution. | Data file | Evdw.dat |
-ignore | This option specifies the threshold ignore distance. 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 |
ID 2hhb XX DE HEMOGLOBIN (DEOXY) XX OS HUMAN (HOMO SAPIENS) XX EX METHOD xray; RESO 1.74; NMOD 1; NCHN 4; NGRP 0; XX CN [1] XX IN ID A; NR 141; NL 1; NH 0; NE 0; XX SQ SEQUENCE 141 AA; 15127 MW; 5EC7DB1E CRC32; VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA VHASLDKFLA SVSTVLTSKY R XX CN [2] XX IN ID B; NR 146; NL 1; NH 0; NE 0; XX SQ SEQUENCE 146 AA; 15868 MW; EC9744C9 CRC32; VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK EFTPPVQAAY QKVVAGVANA LAHKYH XX CN [3] XX IN ID C; NR 141; NL 1; NH 0; NE 0; XX SQ SEQUENCE 141 AA; 15127 MW; 5EC7DB1E CRC32; VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA VHASLDKFLA SVSTVLTSKY R XX CN [4] XX IN ID D; NR 146; NL 2; NH 0; NE 0; XX SQ SEQUENCE 146 AA; 15868 MW; EC9744C9 CRC32; VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK EFTPPVQAAY QKVVAGVANA LAHKYH XX CO 1 1 . P 1 1 . . . . . . V VAL N 6.130 16.559 4.905 7.00 41.29 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 1 1 . . . . . . V VAL CA 6.870 17.784 4.702 6.00 41.33 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 1 1 . . . . . . V VAL C 8.377 17.548 4.913 6.00 31.64 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 1 1 . . . . . . V VAL O 8.820 16.980 5.922 8.00 38.31 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 1 1 . . . . . . V VAL CB 6.345 18.763 5.731 6.00 52.26 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 1 . P 1 1 . . . . . . V VAL CG1 6.745 20.188 5.356 6.00 52.75 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 [Part of this file has been deleted for brevity] CO 1 . . W . 174 . . . . . . . HOH O -4.764 -6.228 5.515 8.00 40.89 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 175 . . . . . . . HOH O 23.809 19.925 1.758 8.00 39.37 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 176 . . . . . . . HOH O -7.871 -9.078 2.406 8.00 43.37 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 177 . . . . . . . HOH O 4.693 12.083 7.558 8.00 40.24 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 178 . . . . . . . HOH O 8.775 -23.438 16.055 8.00 42.33 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 179 . . . . . . . HOH O -7.480 -10.898 17.998 8.00 38.06 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 180 . . . . . . . HOH O -4.731 16.453 2.295 8.00 36.37 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 181 . . . . . . . HOH O -1.055 11.866 -0.448 8.00 43.19 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 182 . . . . . . . HOH O -27.610 -10.991 5.353 8.00 43.46 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 183 . . . . . . . HOH O 26.015 11.766 5.159 8.00 40.95 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 184 . . . . . . . HOH O -18.517 -8.355 15.267 8.00 35.55 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 185 . . . . . . . HOH O -14.034 2.806 -30.367 8.00 41.77 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 186 . . . . . . . HOH O -32.905 -9.033 0.480 8.00 43.68 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 187 . . . . . . . HOH O -28.749 -13.315 1.938 8.00 45.36 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 188 . . . . . . . HOH O 0.516 -8.074 -26.354 8.00 41.53 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 189 . . . . . . . HOH O -20.080 -9.873 -22.862 8.00 36.25 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 190 . . . . . . . HOH O -13.442 9.778 -13.572 8.00 39.70 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 191 . . . . . . . HOH O -24.804 -2.608 -15.488 8.00 37.79 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 192 . . . . . . . HOH O 6.547 9.706 16.296 8.00 41.86 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 193 . . . . . . . HOH O 0.029 22.606 14.164 8.00 43.02 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 194 . . . . . . . HOH O -11.367 0.306 28.463 8.00 44.30 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 195 . . . . . . . HOH O -19.950 -10.635 14.301 8.00 40.17 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 196 . . . . . . . HOH O -7.047 -6.324 20.098 8.00 36.98 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 197 . . . . . . . HOH O -23.876 1.108 14.102 8.00 33.31 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 198 . . . . . . . HOH O -34.199 8.033 11.037 8.00 40.72 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 199 . . . . . . . HOH O -14.173 13.393 -8.778 8.00 43.21 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 200 . . . . . . . HOH O 11.388 -11.044 24.763 8.00 39.34 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 201 . . . . . . . HOH O 3.735 -3.643 2.734 8.00 42.17 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 202 . . . . . . . HOH O 3.149 -0.692 2.083 8.00 41.40 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 203 . . . . . . . HOH O 4.511 -25.886 13.006 8.00 39.83 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 204 . . . . . . . HOH O 8.712 -21.655 3.577 8.00 43.08 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 205 . . . . . . . HOH O 22.926 -4.304 24.079 8.00 38.10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 206 . . . . . . . HOH O 11.435 9.654 20.618 8.00 40.23 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 207 . . . . . . . HOH O 18.099 5.542 27.744 8.00 39.03 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 208 . . . . . . . HOH O 12.174 9.951 9.804 8.00 44.34 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 209 . . . . . . . HOH O 24.745 -2.501 15.270 8.00 39.78 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 210 . . . . . . . HOH O 24.231 0.100 14.764 8.00 42.94 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 211 . . . . . . . HOH O 23.324 -18.136 10.981 8.00 53.60 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 212 . . . . . . . HOH O 25.576 -22.211 6.309 8.00 45.18 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 213 . . . . . . . HOH O 14.639 24.823 -4.300 8.00 41.35 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 214 . . . . . . . HOH O 14.903 5.393 -23.047 8.00 37.45 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 215 . . . . . . . HOH O 16.650 -5.137 -16.717 8.00 39.12 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 216 . . . . . . . HOH O 7.424 -6.700 -20.085 8.00 38.62 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 217 . . . . . . . HOH O -1.263 -2.837 -21.251 8.00 45.10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 218 . . . . . . . HOH O 23.120 -3.118 -12.992 8.00 37.05 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 219 . . . . . . . HOH O 23.664 0.968 -14.389 8.00 36.25 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 220 . . . . . . . HOH O 25.698 7.981 -15.362 8.00 35.85 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 221 . . . . . . . HOH O 30.009 16.347 -6.794 8.00 37.62 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 222 . . . . . . . HOH O 27.728 16.677 -1.376 8.00 42.54 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CO 1 . . W . 223 . . . . . . . HOH O 8.142 18.836 1.041 8.00 39.90 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 // |
The format of the clean protein coordinate file is described in pdbparse
XX Inter-chain residue-residue contact data. XX TY INTER XX EX THRESH 1.0; IGNORE 20.0; NMOD 1; NCHA 4 XX NE 6 XX EN [1] XX ID PDB 2hhb; DOM .; LIG . XX CN MO 1; CN1 1; CN2 2; ID1 A; ID2 B; NRES1 141; NRES2 146 XX S1 SEQUENCE 141 AA; 15127 MW; 5EC7DB1E CRC32; VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA VHASLDKFLA SVSTVLTSKY R XX S2 SEQUENCE 146 AA; 15868 MW; EC9744C9 CRC32; VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK EFTPPVQAAY QKVVAGVANA LAHKYH XX NC SM 48; LI . XX SM GLU 30 ; PRO 124 SM ARG 31 ; PHE 122 SM ARG 31 ; THR 123 SM ARG 31 ; PRO 124 SM ARG 31 ; GLN 127 SM LEU 34 ; PRO 124 SM LEU 34 ; PRO 125 SM LEU 34 ; ALA 128 SM SER 35 ; GLN 127 SM SER 35 ; ALA 128 SM SER 35 ; GLN 131 SM PHE 36 ; GLN 131 SM HIS 103 ; ASN 108 SM HIS 103 ; VAL 111 SM HIS 103 ; CYS 112 SM HIS 103 ; GLN 127 SM HIS 103 ; GLN 131 SM CYS 104 ; GLN 127 SM LEU 106 ; CYS 112 SM VAL 107 ; VAL 111 SM VAL 107 ; CYS 112 SM VAL 107 ; ALA 115 SM VAL 107 ; PHE 122 SM VAL 107 ; GLN 127 [Part of this file has been deleted for brevity] SM GLU 27 ; PRO 124 SM GLU 30 ; PRO 124 SM ARG 31 ; PHE 122 SM ARG 31 ; THR 123 SM ARG 31 ; PRO 124 SM ARG 31 ; GLN 127 SM LEU 34 ; PRO 124 SM LEU 34 ; PRO 125 SM LEU 34 ; ALA 128 SM SER 35 ; GLN 127 SM SER 35 ; ALA 128 SM SER 35 ; GLN 131 SM PHE 36 ; GLN 131 SM HIS 103 ; ASN 108 SM HIS 103 ; VAL 111 SM HIS 103 ; CYS 112 SM HIS 103 ; GLN 127 SM HIS 103 ; GLN 131 SM CYS 104 ; GLN 127 SM LEU 106 ; CYS 112 SM VAL 107 ; VAL 111 SM VAL 107 ; CYS 112 SM VAL 107 ; ALA 115 SM VAL 107 ; PHE 122 SM VAL 107 ; GLN 127 SM ALA 110 ; CYS 112 SM ALA 110 ; ALA 115 SM ALA 110 ; HIS 116 SM ALA 111 ; ALA 115 SM ALA 111 ; GLY 119 SM LEU 113 ; HIS 116 SM PRO 114 ; HIS 116 SM PHE 117 ; ARG 30 SM PHE 117 ; CYS 112 SM PHE 117 ; HIS 116 SM THR 118 ; ARG 30 SM PRO 119 ; ARG 30 SM PRO 119 ; VAL 33 SM PRO 119 ; VAL 34 SM PRO 119 ; MET 55 SM ALA 120 ; VAL 33 SM ALA 120 ; PRO 51 SM HIS 122 ; ARG 30 SM HIS 122 ; VAL 34 SM HIS 122 ; VAL 109 SM HIS 122 ; CYS 112 SM ALA 123 ; VAL 33 SM ALA 123 ; VAL 34 SM ASP 126 ; VAL 34 SM ASP 126 ; TYR 35 // |
2hhb |
The embl-like format used for the contact files (below) uses the following records:
(1) ID - the 4-character PDB identifier code.
(2) DE - bibliographic information. The text "Residue-residue contact data" is always given.
(3) EX - experimental information. The value of the threshold contact distance is given as a floating point number after 'THRESH'. The number of models and number of polypeptide chains are given after 'NMOD' and 'NCHA' respectively. domain coordinate files a 1 is always given. Following the EX record, the file will have a section containing a PA, IN and SM records (see below) for each chain pair. The sections for each chain pair of a model are given after the MO record.
(4) MO - model number. The number given in brackets after this record indicates the start of a section of model-specific data.
(5) PA - chain pair number. The numbers given either side of the ':' after this record indicate the start of a section of chain pair-specific data.
(6) IN - chain specific data. The characters given after ID1 and ID2 are the PDB chain identifiers for the pair taken from the input file, (a '.` given in cases where a chain identifier was not specified in the original pdb file). The number of amino acid residues comprising each chain is given after NR1 and NR2 respectively. The number of residue-residue contacts is given after NSMCON.
(7) SM - Line of residue contact data. Pairs of amino acid identifiers and residue numbers are delimited by a ';'. Residue numbers are taken from the clean coordinate file and give a correct index into the sequence (i.e. they are not necessarily the same as the original pdb file). The first residue belongs to the first partner of the chain-pair, the second residue belongs to the second partner.
(8) XX - used for spacing.
(9) // - given on the last line of the file only.
Note - SM records are used for contacts between either either side-chain or main-chain atoms as defined above. In a future implementation, SS will be used for side-chain only contacts, MM will be used for main-chain only contacts, and there will probably be several other forms of contact too.
Excerpt from interface output file
ID 2hhb XX DE Residue-residue side-chain contact data XX EX THRESH 1.0; IGNORE 20.0; NMOD 1; NCHA 4; XX MO [1] XX PA 1:2 XX IN ID1 A; ID2 B; NR1 141; NR2 146; NSMCON 48; XX SM GLU 30 ; PRO 124 SM ARG 31 ; PHE 122 SM ARG 31 ; THR 123 SM ARG 31 ; PRO 124 SM ARG 31 ; GLN 127 SM LEU 34 ; PRO 124 SM LEU 34 ; PRO 125 ** < data ommitted for clarity > ** SM ALA 123 ; VAL 34 SM ASP 126 ; VAL 34 SM ASP 126 ; TYR 35 XX PA 1:3 XX IN ID1 A; ID2 C; NR1 141; NR2 141; NSMCON 3; XX SM ASP 126 ; ARG 141 SM LYS 127 ; ARG 141 SM ALA 130 ; ARG 141 XX PA 1:4 XX IN ID1 A; ID2 D; NR1 141; NR2 146; NSMCON 25; XX SM PRO 37 ; HIS 146 ** < data ommitted for clarity > ** SM ASP 126 ; VAL 34 SM ASP 126 ; TYR 35 XX //
EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".
The directories are searched in the following order:
contacts uses a data file containing van der Waals radii for atoms in proteins. The file Evdw.dat is such a data file and is part of the emboss distribution.
Excerpt of log file
// DS002__ WARN Could not open for reading cpdb file s002.pxyz //
Program name | Description |
---|---|
contactcount | Counts specific versus non-specific contacts in a directory of cleaned protein chain contact files |
contacts | Reads CCF files (clean coordinate files) and writes CON files (contact files) of intra-chain residue-residue contact data |
domainalign | Generates DAF files (domain alignment files) of structure-based sequence alignments for nodes in a DCF file (domain classification file) |
domainrep | Reorder DCF file (domain classification file) so that the representative structure of each user-specified node is given first |
domainreso | Removes low resolution domains from a DCF file (domain classification file) |
libgen | Generates various types of discriminating elements for each alignment in a directory |
psiphi | Calculates phi and psi torsion angles from cleaned EMBOSS-style protein co-ordinate file |
rocon | Reads a DHF file (domain hits file) of hits (sequences of unknown structural classification) and a DHF file of validation sequences (known classification) and writes a 'hits file' for the hits, which are classified and rank-ordered on the basis of score |
rocplot | Provides interpretation and graphical display of the performance of discriminating elements (e.g. profiles for protein families). rocplot reads file(s) of hits from discriminator-database search(es), performs ROC analysis on the hits, and writes graphs illustrating the diagnostic performance of the discriminating elements |
seqalign | Reads a DAF file (domain alignment file) and a DHF file (domain hits file) and writes a DAF file extended with the hits |
seqfraggle | Removes fragments from DHF files (domain hits files) or other files of sequences |
seqsearch | Generate database hits (sequences) for nodes in a DCF file (domain classification file) by using PSI-BLAST |
seqsort | Reads DHF files (domain hits files) of database hits (sequences) and removes hits of ambiguous classification |
seqwords | Generates DHF files (domain hits files) of database hits (sequences) for nodes in a DCF file (domain classification file) by keyword search of UniProt |
siggen | Generates a sparse protein signature from an alignment and residue contact data |
sigscan | Generates a DHF file (domain hits file) of hits (sequences) from scanning a signature against a sequence database |
A 'protein coordinate file' contains protein coordinate and other data extracted from a single pdb file. The files, generated by pdbparse, are in embl-like format and contain 'cleaned-up' data that is self-consistent and error-corrected.