## CONTACTS 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 intra-chain residue-residue contact data. Generate intra-chain CON files from CCF files

## 2.0 INPUTS & OUTPUTS

CONTACTS reads a directory of domain or protein CCF files (clean coordinate files) and writes a CON file (contacts file) of intra-chain residue-residue contact data for each file in the input directory. Each CON file contains residue contact data for every chain of every model in a protein coordinate file, or for a single domain where a domain CCF file is read. The user is prompted for the paths for the CCF (input) and CON (output) files and the file extensions are specified in the ACD file. The domain identifier code or pdb identifier code is used as appropriate to name the output files. A log file is also written.

## 3.0 INPUT FILE FORMAT

The format of the clean coordinate file is described in the PDBPARSE documentation.

## 4.0 OUTPUT FILE FORMAT

The CON format used for the contact files (Figure 1) is similar to EMBL format and uses the following records:

- XX - used for spacing and comments. The first line is bibliographic information and contains the text "XX Intra-chain residue-residue contact data".
- TY - type of contact. For CON files generated by CONTACTS, 'INTRA' 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 CONTACTS, the threshold ignore distance is given after 'THRESH'. 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 (chains) in the file. For CON files generated by CONTACTS this is the number of chains, equal to the number of models multiplied by the number of unique chains. 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) and number of contacts (NC), that together define the chain and its contacts.
- EN - entry number. The number in brackets indicates the start of an entry (chain).
- 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. (3) CN2: Not used by CONTACTS, a '.' is given. (4) ID1: PDB chain identifier (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: Not used by CONTACTS, a '.' is given. (6) NRES1: number of amino acid residues in the chain or domain. (7) NRES2: Not used by SITES, a '.' is given.
- NC - number of contacts: (1) SM: Number of residue-residue contacts; between the side-chain or main-chain atoms of different amino acid residues in the same chain (2) LI: Not used by CONTACTS, a '.' is given.
- ID - identifier codes: (1) PDB: 4-character PDB identifier code. (2) DOM: 7-character domain identifier code from SCOP or CATH (where domain CCF files were read). (3) LIG: Not used by CONTACTS, a '.' is given.
- S1 - polypeptide chain sequence for domain or protein. The number of residues is given before AA on the first line. The sequece is given on subsequent lines.
- SM - Line of residue contact data. Pairs of amino acid identifiers and residue numbers are delimited by a ';'. Residue numbers are taken from the CCF file and give a correct index into the sequence (i.e. they are not necessarily the same as the original PDB file). This sequence is given in the CON file itself (S1 record).
- // - delimiter for individual entries in the file and also given on the last line of the file.

### Output files for usage example

### File: 1cs4.con

    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
    //

### File: 1ii7.con

    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
    //

### File: 2hhb.con

    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
    //

### File: contacts.log

    1cs4
    1ii7
    2hhb

## 5.0 DATA FILES

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

## 6.0 USAGE

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

       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:

       "-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

[-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
"-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 CONTACTS is shown below. Here is a sample session with contacts

    % 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

## 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.
Skip option
Two residues that are adjacent in the sequence will always be in contact through their peptide bond, therefore it is not normally necessary to calculate such contacts directly. Furthermore, some analyses require such contacts to be omitted. The skip option determines whether contacts between residue adjacent in sequence are calculated and written to the output file.

### 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 within a protein or domain make with one another is required for several different analyses. CONTACTS calculates intra-chain residue-residue contact data from protein and domain CCF files (clean coordinate files).

## 10.0 ALGORITHM

Contact between two residues is defined 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
--- | ---
domainalign | Generate alignments (DAF file) for nodes in a DCF file
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
libgen | Generate discriminating elements from alignments
matgen3d | Generate a 3D-1D scoring matrix from CCF files
psiphi | Calculates phi and psi torsion angles from protein coordinates
rocon | Generates a hits file from comparing two DHF files
rocplot | Performs ROC analysis on hits files
seqalign | Extend alignments (DAF file) with sequences (DHF file)
seqfraggle | Removes fragment sequences from DHF files
seqsearch | Generate PSI-BLAST hits (DHF file) from a DAF file
seqsort | Remove ambiguous classified sequences from DHF files
seqwords | Generates DHF files from keyword search of UniProt
siggen | Generates a sparse protein signature from an alignment
siggenlig | Generates ligand-binding signatures from a CON file
sigscan | Generates hits (DHF file) from a signature search
sigscanlig | Searches ligand-signature library & writes hits (LHF file)

## 12.0 DIAGNOSTIC ERROR MESSAGES

CONTACTS generates a log file an excerpt of which is shown (Figure 2). If there is a problem in processing a CCF file, three lines containing the record '//', the domain or 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 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