| ## INTERFACE documentation

## CONTENTS

1.0 SUMMARY
2.0 INPUTS & OUTPUTS
3.0 INPUT FILE FORMAT
4.0 OUTPUT FILE FORMAT
5.0 DATA FILES
6.0 USAGE
7.0 KNOWN BUGS & WARNINGS
8.0 NOTES
9.0 DESCRIPTION
10.0 ALGORITHM
11.0 RELATED APPLICATIONS
12.0 DIAGNOSTIC ERROR MESSAGES
13.0 AUTHORS
14.0 REFERENCES

## 1.0 SUMMARY

Reads CCF files (clean coordinate files) and writes CON files (contact files) of inter-chain residue-residue contact data. Generate inter-chain CON files from CCF files

## 2.0 INPUTS & OUTPUTS

INTERFACE reads a protein CCF file (clean coordinate file) and writes a CON file (contacts file) of inter-chain residue-residue contact data. The file contains residue contact data for all pairs of chains in each model in the CCF file. The input and output files are specified by the user. A log file is also written.

## 3.0 INPUT FILE FORMAT

The format of the protein CCF file is described in the PDBPARSE documentation.

### Input files for usage example

### File: ../pdbplus-keep/2hhb.ccf

    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
    //

## 4.0 OUTPUT FILE FORMAT

The CON format used for the contact files (Figure 1) is similar to EMBL format and is described in the CONTACTS documentation. A few of the records differ in the INTERFACE output compared to the CONTACTS output, however, so for the sake of clarity all records are described below.

- XX - used for spacing and comments. The first line is bibliographic information and contains the text "Inter-chain residue-residue contact data".
- TY - type of contact. For CON files generated by CONTACTS, 'INTER' is always given.
- EX - experimental information. The value of the threshold contact distance is given as a floating point number after 'THRESH'. For CON files generated by INTERFACE, a '.' is given after 'THRESH' (this record is used by the CONTACTS application and can be disregarded). The number of models and number of polypeptide chains are given after 'NMOD' and 'NCHA' respectively. For domain CCF files a 1 is always given.
- NE - number of entries (interfaces) in the file. For CON files generated by INTERFACE this is the number of interfaces (pairs of chains), equal to the number of models multiplied by the number of unique interfaces. Following the NE record, the file has a section for each entry containing records for entry number (EN), identifier codes (ID), polypeptide chain-specific data (CN), chain sequence information (S1 & S2) and number of contacts (NC), that together define the interface and its contacts.
- EN - entry number. The number in brackets indicates the start of an entry (interface).
- CN - polypeptide chain-specific data. Tokens delimiting data items are as follow. (1) MO: The model number (from the PDB file). (2) CN1: Chain number (first chain). (3) CN2: Chain number (second chain). (4) ID1: PDB chain identifier (first chain) (a '.` given in cases where a chain identifier was not specified in the original PDB file or, for domain CCF files, the domain is comprised of more than one domain). (5) ID2: Chain identifier (second chain). (6) NRES1: number of residues (first chain). (7) NRES2: number of residues (second chain).
- NC - number of contacts: (1) SM: Number of residue-residue contacts; between side-chain or main-chain atoms of an amino acid residue in one chain and the side- or main-chain atoms of a residue in a different chain. (2) LI: Number of residue-ligand contacts; between side-chain or main-chain atoms of an amino acid residue and a ligand.
- ID - identifier codes: (1) PDB: 4-character PDB identifier code. (2) DOM: SCOP or CATH domain identifier code. (3) LIG: Not used by INTERFACE, a '.' is given.
- S1 - polypeptide chain sequence (first chain). The number of residues is given before AA on the first line. The sequece is given on subsequent lines.
- S2 - polypeptide chain sequence (second chain).
- SM - Line of residue contact data. Pairs of amino acid identifiers and residue numbers are delimited by a ';'. The left-hand term refers to the first chain and the right-hand term the second chain. Residue numbers are taken from the CCF files and give a correct index into the sequences (i.e. they are not necessarily the same as the original PDB file). These sequence is given in the CON file itself (S1 & S2 records).
- // - delimiter for individual entries in the file and also given on the last line of the file.

### Output files for usage example

### File: 2hhb.con

    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
    //

### File: interface.log

    2hhb

## 5.0 DATA FILES

INTERFACE uses a data file containing van der Waals radii for atoms in proteins (see CONTACTS documentation.) The file Evdw.dat is such a data file and is part of the EMBOSS distribution.

## 6.0 USAGE

    Generate inter-chain CON files from CCF files.
    Version: EMBOSS:6.2.0

       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

### 6.1 COMMAND LINE ARGUMENTS

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

### 6.2 EXAMPLE SESSION

An example of interactive use of INTERFACE is shown below. Here is a sample session with interface

    % 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

## 7.0 KNOWN BUGS & WARNINGS

None.

## 8.0 NOTES

Types of contact
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, LI will be used for contacts to ligands, and there will probably be several other forms of contact too.
Threshold ignore distance option
The threshold ignore distance can be adjusted to speed-up the calculation of contacts considerably. 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.

### 8.1 GLOSSARY OF FILE TYPES

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.

None

## 9.0 DESCRIPTION

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 protein CCF files (clean coordinate files).

## 10.0 ALGORITHM

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.

## 11.0 RELATED APPLICATIONS

## See also

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 & 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

## 12.0 DIAGNOSTIC ERROR MESSAGES

INTERFACE generates a log file an excerpt of which is shown below. If there is a problem in processing a CCF file, three lines containing the record '//', the PDB identifier code and an error message respectively are written. The text 'WARN file open error filename' , 'ERROR file read error filename' or 'ERROR file write error filename ' will be reported when an error was encountered during a file open, read or write respectively. Various other error messages may also be given (in case of difficulty email Jon Ison, jison@ebi.ac.uk).

## 13.0 AUTHORS

Jon Ison (jison@ebi.ac.uk)
The European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD UK

## 14.0 REFERENCES

Please cite the authors and EMBOSS.
Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European Molecular Biology Open Software Suite" Trends in Genetics, 15:276-278.

See also http://emboss.sourceforge.net/

### 14.1 Other useful references