INTERFACE documentation |
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 7; NE 0; XX SQ SEQUENCE 141 AA; 15126 MW; 34D13618E62A33C1 CRC64; 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 8; NE 0; XX SQ SEQUENCE 146 AA; 15867 MW; EACBC707CFD466A1 CRC64; 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 7; NE 0; XX SQ SEQUENCE 141 AA; 15126 MW; 34D13618E62A33C1 CRC64; 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 8; NE 0; XX SQ SEQUENCE 146 AA; 15867 MW; EACBC707CFD466A1 CRC64; VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK EFTPPVQAAY QKVVAGVANA LAHKYH XX RE 1 1 1 1 V VAL . . . . . C 360.00 130.57 137.00 142.86 94.30 113.45 99.30 29.40 79.10 113.56 98.30 29.29 81.40 RE 1 1 2 2 L LEU . . . . . C -80.50 121.94 16.80 18.20 10.20 7.73 5.50 10.48 27.90 7.73 5.40 10.48 28.80 RE 1 1 3 3 S SER 1 AA H 1 . C -71.32 164.78 44.40 44.59 38.30 44.42 56.90 0.17 0.40 39.26 80.90 5.34 7.90 RE 1 1 4 4 P PRO 1 AA H 1 1 H -62.31 -35.05 99.60 105.25 77.30 103.02 85.90 2.23 13.70 103.65 85.70 1.60 10.50 RE 1 1 5 5 A ALA 1 AA H 1 1 H -65.00 -41.52 59.80 65.59 60.80 64.35 92.70 1.24 3.20 64.35 90.20 1.24 3.40 RE 1 1 6 6 D ASP 1 AA H 1 1 H -56.29 -42.84 13.60 13.83 9.90 13.80 13.40 0.03 0.10 0.44 0.90 13.39 14.70 [Part of this file has been deleted for brevity] AT 1 . . . 174 . HOH W O -4.764 -6.228 5.515 8.00 40.89 AT 1 . . . 175 . HOH W O 23.809 19.925 1.758 8.00 39.37 AT 1 . . . 176 . HOH W O -7.871 -9.078 2.406 8.00 43.37 AT 1 . . . 177 . HOH W O 4.693 12.083 7.558 8.00 40.24 AT 1 . . . 178 . HOH W O 8.775 -23.438 16.055 8.00 42.33 AT 1 . . . 179 . HOH W O -7.480 -10.898 17.998 8.00 38.06 AT 1 . . . 180 . HOH W O -4.731 16.453 2.295 8.00 36.37 AT 1 . . . 181 . HOH W O -1.055 11.866 -0.448 8.00 43.19 AT 1 . . . 182 . HOH W O -27.610 -10.991 5.353 8.00 43.46 AT 1 . . . 183 . HOH W O 26.015 11.766 5.159 8.00 40.95 AT 1 . . . 184 . HOH W O -18.517 -8.355 15.267 8.00 35.55 AT 1 . . . 185 . HOH W O -14.034 2.806 -30.367 8.00 41.77 AT 1 . . . 186 . HOH W O -32.905 -9.033 0.480 8.00 43.68 AT 1 . . . 187 . HOH W O -28.749 -13.315 1.938 8.00 45.36 AT 1 . . . 188 . HOH W O 0.516 -8.074 -26.354 8.00 41.53 AT 1 . . . 189 . HOH W O -20.080 -9.873 -22.862 8.00 36.25 AT 1 . . . 190 . HOH W O -13.442 9.778 -13.572 8.00 39.70 AT 1 . . . 191 . HOH W O -24.804 -2.608 -15.488 8.00 37.79 AT 1 . . . 192 . HOH W O 6.547 9.706 16.296 8.00 41.86 AT 1 . . . 193 . HOH W O 0.029 22.606 14.164 8.00 43.02 AT 1 . . . 194 . HOH W O -11.367 0.306 28.463 8.00 44.30 AT 1 . . . 195 . HOH W O -19.950 -10.635 14.301 8.00 40.17 AT 1 . . . 196 . HOH W O -7.047 -6.324 20.098 8.00 36.98 AT 1 . . . 197 . HOH W O -23.876 1.108 14.102 8.00 33.31 AT 1 . . . 198 . HOH W O -34.199 8.033 11.037 8.00 40.72 AT 1 . . . 199 . HOH W O -14.173 13.393 -8.778 8.00 43.21 AT 1 . . . 200 . HOH W O 11.388 -11.044 24.763 8.00 39.34 AT 1 . . . 201 . HOH W O 3.735 -3.643 2.734 8.00 42.17 AT 1 . . . 202 . HOH W O 3.149 -0.692 2.083 8.00 41.40 AT 1 . . . 203 . HOH W O 4.511 -25.886 13.006 8.00 39.83 AT 1 . . . 204 . HOH W O 8.712 -21.655 3.577 8.00 43.08 AT 1 . . . 205 . HOH W O 22.926 -4.304 24.079 8.00 38.10 AT 1 . . . 206 . HOH W O 11.435 9.654 20.618 8.00 40.23 AT 1 . . . 207 . HOH W O 18.099 5.542 27.744 8.00 39.03 AT 1 . . . 208 . HOH W O 12.174 9.951 9.804 8.00 44.34 AT 1 . . . 209 . HOH W O 24.745 -2.501 15.270 8.00 39.78 AT 1 . . . 210 . HOH W O 24.231 0.100 14.764 8.00 42.94 AT 1 . . . 211 . HOH W O 23.324 -18.136 10.981 8.00 53.60 AT 1 . . . 212 . HOH W O 25.576 -22.211 6.309 8.00 45.18 AT 1 . . . 213 . HOH W O 14.639 24.823 -4.300 8.00 41.35 AT 1 . . . 214 . HOH W O 14.903 5.393 -23.047 8.00 37.45 AT 1 . . . 215 . HOH W O 16.650 -5.137 -16.717 8.00 39.12 AT 1 . . . 216 . HOH W O 7.424 -6.700 -20.085 8.00 38.62 AT 1 . . . 217 . HOH W O -1.263 -2.837 -21.251 8.00 45.10 AT 1 . . . 218 . HOH W O 23.120 -3.118 -12.992 8.00 37.05 AT 1 . . . 219 . HOH W O 23.664 0.968 -14.389 8.00 36.25 AT 1 . . . 220 . HOH W O 25.698 7.981 -15.362 8.00 35.85 AT 1 . . . 221 . HOH W O 30.009 16.347 -6.794 8.00 37.62 AT 1 . . . 222 . HOH W O 27.728 16.677 -1.376 8.00 42.54 AT 1 . . . 223 . HOH W O 8.142 18.836 1.041 8.00 39.90 // |
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; 15126 MW; 34D13618E62A33C1 CRC64; VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA VHASLDKFLA SVSTVLTSKY R XX S2 SEQUENCE 146 AA; 15867 MW; EACBC707CFD466A1 CRC64; 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 |
Generate inter-chain CON files from CCF files. Version: EMBOSS:6.4.0.0 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 [1.0] 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) [-outfile] outfile [test.con] 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 SITES. -conlogfile outfile [interface.log] 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 [Evdw.dat] 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 [20.0] 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) Associated qualifiers: "-outfile" associated qualifiers -odirectory2 string Output directory "-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 | ||||
[-infile] (Parameter 1) |
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. | Input file | Required |
-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. | Any numeric value | 1.0 |
[-outfile] (Parameter 2) |
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 SITES. | Output file | test.con |
-conlogfile | 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. | Output file | interface.log |
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. | Data file | Evdw.dat |
-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. | Any numeric value | 20.0 |
Associated qualifiers | ||||
"-outfile" associated outfile qualifiers | ||||
-odirectory2 -odirectory_outfile |
string | Output directory | Any string | |
"-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 |
% interface Generate inter-chain CON files from CCF files. Clean protein structure coordinates file: ../pdbplus-keep/2hhb.ccf Threshold contact distance [1.0]: 1 Structure contacts output file [test.con]: 2hhb.con Domainatrix log output file [interface.log]: 2hhb |
Go to the input files for this example
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 |
---|---|
aaindexextract | Extract amino acid property data from AAINDEX |
allversusall | Sequence similarity data from all-versus-all comparison |
cathparse | Generates DCF file from raw CATH files |
cutgextract | Extract codon usage tables from CUTG database |
domainer | Generates domain CCF files from protein CCF files |
domainnr | Removes redundant domains from a DCF file |
domainseqs | Adds sequence records to a DCF file |
domainsse | Add secondary structure records to a DCF file |
hetparse | Converts heterogen group dictionary to EMBL-like format |
jaspextract | Extract data from JASPAR |
pdbplus | Add accessibility and secondary structure to a CCF file |
pdbtosp | Convert swissprot:PDB codes file to EMBL-like format |
printsextract | Extract data from PRINTS database for use by pscan |
prosextract | Processes the PROSITE motif database for use by patmatmotifs |
rebaseextract | Process the REBASE database for use by restriction enzyme applications |
scopparse | Generate DCF file from raw SCOP files |
seqnr | Removes redundancy from DHF files |
sites | Generate residue-ligand CON files from CCF files |
ssematch | Search a DCF file for secondary structure matches |
tfextract | Process TRANSFAC transcription factor database for use by tfscan |
See also http://emboss.sourceforge.net/