| pepcoil

## Function

Predicts coiled coil regions

## Description

Coiled coils are formed by two or three alpha helices in parallel and in register that cross at an angle of approximately 20 degrees, are strongly amphipathic and display a pattern of hydrophilic and hydrophobic residues that is repeated every seven residues. The seven positions of the heptad repeat are designated a through g, a and d being generally hydrophobic, while the others are hydrophilic.

The parallel two-stranded alpha-helical coiled coil is the most frequently encountered subunit-oligomerization motif in proteins.

pepcoil calculates the probability of a coiled-coil structure for windows of 28 residues through a protein sequence using the method of Lupas A, van Dyke M & Stock J (1991); Science 252:1162-4

## Usage

Here is a sample session with pepcoil

    % pepcoil
    Predicts coiled coil regions
    Input sequence(s): tsw:gcn4_yeast
    Window size [28]:
    Output file [gcn4_yeast.pepcoil]:

Go to the input files for this example
Go to the output files for this example

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          seqall     Sequence database USA
       -window             integer    Window size
      [-outfile]           outfile    Output file name

       Optional qualifiers: (none)
       Advanced qualifiers:
       -[no]coil           boolean    Report coiled coil regions
       -frame              boolean    Show coil frameshifts
       -[no]other          boolean    Report non coiled coil regions

       Associated qualifiers:
      "-sequence" related qualifiers
       -sbegin1             integer    First base used
       -send1               integer    Last base used, def=seq length
       -sreverse1           boolean    Reverse (if DNA)
       -sask1               boolean    Ask for begin/end/reverse
       -snucleotide1        boolean    Sequence is nucleotide
       -sprotein1           boolean    Sequence is protein
       -slower1             boolean    Make lower case
       -supper1             boolean    Make upper case
       -sformat1            string     Input sequence format
       -sopenfile1          string     Input filename
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name
      "-outfile" related qualifiers
       -odirectory2         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 required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -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

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence database USA | Readable sequence(s) | Required
-window | Window size | Integer from 7 to 28 | 28
[-outfile] (Parameter 2) | Output file name | Output file | <sequence>.pepcoil
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
-[no]coil | Report coiled coil regions | Boolean value Yes/No | Yes
-frame | Show coil frameshifts | Boolean value Yes/No | Yes if -coil is true
-[no]other | Report non coiled coil regions | Boolean value Yes/No | Yes

## Input file format

pepcoil reads in a protein sequence USA.

### Input files for usage example

'tsw:gcn4_yeast' is a sequence entry in the example protein database 'tsw'

### Database entry: tsw:gcn4_yeast

    ID   GCN4_YEAST     STANDARD;      PRT;   281 AA.
    AC   P03069; P03068;
    DT   21-JUL-1986 (Rel. 01, Created)
    DT   21-JUL-1986 (Rel. 01, Last sequence update)
    DT   15-JUL-1999 (Rel. 38, Last annotation update)
    DE   GENERAL CONTROL PROTEIN GCN4 (AMINO ACID BIOSYNTHESIS REGULATORY
    DE   PROTEIN).
    GN   GCN4 OR ARG9 OR AAS3 OR YEL009C.
    OS   Saccharomyces cerevisiae (Baker's yeast).
    OC   Eukaryota; Fungi; Ascomycota; Hemiascomycetes; Saccharomycetales;
    OC   Saccharomycetaceae; Saccharomyces.
    RN   [1]
    RP   SEQUENCE FROM N.A.
    RX   MEDLINE; 85038531.
    RA   HINNEBUSCH A.G.;
    RT   "Evidence for translational regulation of the activator of general
    RT   amino acid control in yeast.";
    RL   Proc. Natl. Acad. Sci. U.S.A. 81:6442-6446(1984).
    RN   [2]
    RP   SEQUENCE FROM N.A.
    RX   MEDLINE; 84298088.
    RA   THIREOS G., PENN M.D., GREER H.;
    RT   "5' untranslated sequences are required for the translational control
    RT   of a yeast regulatory gene.";
    RL   Proc. Natl. Acad. Sci. U.S.A. 81:5096-5100(1984).
    RN   [3]
    RP   SEQUENCE FROM N.A.
    RC   STRAIN=S288C / AB972;
    RA   DIETRICH F.S., MULLIGAN J.T., HENNESSEY K.M., ALLEN E., ARAUJO R.,
    RA   AVILES E., BERNO A., BRENNAN T., CARPENTER J., CHEN E., CHERRY J.M.,
    RA   CHUNG E., DUNCAN M., GUZMAN E., HARTZELL G., HUNICKE-SMITH S.,
    RA   HYMAN R., KAYSER A., KOMP C., LASHKARI D., LEW H., LIN D.,
    RA   MOSEDALE D., NAKAHARA K., NAMATH A., NORGREN R., OEFNER P., OH C.,
    RA   PETEL F.X., ROBERTS D., SEHL P., SCHRAMM S., SHOGREN T., SMITH V.,
    RA   TAYLOR P., WEI Y., YELTON M., BOTSTEIN D., DAVIS R.W.;
    RL   Submitted (DEC-1994) to the EMBL/GenBank/DDBJ databases.
    RN   [4]
    RP   DOMAINS.
    RX   MEDLINE; 87002456.
    RA   HOPE I.A., STRUHL K.;
    RT   "Functional dissection of a eukaryotic transcriptional activator
    RT   protein, GCN4 of yeast.";
    RL   Cell 46:885-894(1986).
    RN   [5]
    RP   X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 250-281.
    RX   MEDLINE; 92054531.
    RA   O'SHEA E.K., KLEMM J.D., KIM P.S., ALBER T.;
    RT   "X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel
    RT   coiled coil.";
    RL   Science 254:539-544(1991).

      [Part of this file has been deleted for brevity]

    CC   -!- SUBCELLULAR LOCATION: NUCLEAR.
    CC   -!- SIMILARITY: TO OTHER BZIP PROTEINS.
    CC   --------------------------------------------------------------------------
    CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
    CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
    CC   the European Bioinformatics Institute.  There are no  restrictions on  its
    CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
    CC   modified and this statement is not removed.  Usage  by  and for commercial
    CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
    CC   or send an email to license@isb-sib.ch).
    CC   --------------------------------------------------------------------------
    DR   EMBL; K02205; AAA34640.1; -.
    DR   EMBL; K02649; AAA65521.1; -.
    DR   EMBL; U18530; AAB64486.1; -.
    DR   PIR; A03604; RGBYA1.
    DR   PIR; A03605; RGBYA2.
    DR   PDB; 1ZTA; 15-APR-93.
    DR   PDB; 2ZTA; 15-OCT-92.
    DR   PDB; 1YSA; 31-OCT-93.
    DR   PDB; 1DGC; 22-JUN-94.
    DR   PDB; 2DGC; 08-MAR-96.
    DR   PDB; 1GCL; 03-JUN-95.
    DR   PDB; 1GCM; 29-JAN-96.
    DR   PDB; 1SWI; 08-NOV-96.
    DR   PDB; 1ZII; 07-JUL-97.
    DR   PDB; 1ZIJ; 07-JUL-97.
    DR   PDB; 1ZIK; 07-JUL-97.
    DR   PDB; 1ZIL; 07-JUL-97.
    DR   PDB; 1ZIM; 07-JUL-97.
    DR   PDB; 1PIQ; 30-SEP-98.
    DR   PDB; 1CE9; 25-MAR-99.
    DR   TRANSFAC; T00321; -.
    DR   SGD; L0000683; GCN4.
    DR   PFAM; PF00170; bZIP; 1.
    DR   PROSITE; PS00036; BZIP_BASIC; 1.
    KW   Amino-acid biosynthesis; Transcription regulation; Activator;
    KW   DNA-binding; Nuclear protein; 3D-structure.
    FT   DOMAIN      106    125       REQUIRED FOR TRANSCRIPTIONAL ACTIVATION.
    FT   DNA_BIND    231    249       BASIC MOTIF.
    FT   DOMAIN      253    274       LEUCINE-ZIPPER.
    FT   CONFLICT    239    281       ARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLVG
    FT                                ER -> PGVLVRESCKE (IN REF. 2).
    FT   HELIX       227    276
    FT   TURN        277    277
    SQ   SEQUENCE   281 AA;  31310 MW;  A2155238 CRC32;
         MSEYQPSLFA LNPMGFSPLD GSKSTNENVS ASTSTAKPMV GQLIFDKFIK TEEDPIIKQD
         TPSNLDFDFA LPQTATAPDA KTVLPIPELD DAVVESFFSS STDSTPMFEY ENLEDNSKEW
         TSLFDNDIPV TTDDVSLADK AIESTEEVSL VPSNLEVSTT SFLPTPVLED AKLTQTRKVK
         KPNSVVKKSH HVGKDDESRL DHLGVVAYNR KQRSIPLSPI VPESSDPAAL KRARNTEAAR
         RSRARKLQRM KQLEDKVEEL LSKNYHLENE VARLKKLVGE R
    //

## Output file format

### Output files for usage example

The SwissProt annotation marks the true leucine zipper motif as from 253 to 274. The leucine zipper is a special case of a coiled-coil region.

### File: gcn4_yeast.pepcoil

    PEPCOIL of GCN4_YEAST
       using a window of 28 residues

    Other structures from 1 to 232 (232 residues)
       Max score: 1.283 (probability 0.21)

    Prediction starts at 233
    Probable coiled-coil from 233 to 281 (49 residues)
       Max score: 1.910 (probability 1.00)

## Data files

None.

## Notes

None.

## References

1. Lupas A, van Dyke M & Stock J; Predicting Coiled Coils from Protein Sequences. Science 252:1162-4 (1991)

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with a status of 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
antigenic | Finds antigenic sites in proteins
digest | Protein proteolytic enzyme or reagent cleavage digest
fuzzpro | Protein pattern search
fuzztran | Protein pattern search after translation
garnier | Predicts protein secondary structure
helixturnhelix | Report nucleic acid binding motifs
hmoment | Hydrophobic moment calculation
oddcomp | Finds protein sequence regions with a biased composition
patmatdb | Search a protein sequence with a motif
patmatmotifs | Search a PROSITE motif database with a protein sequence
pepnet | Displays proteins as a helical net
pepwheel | Shows protein sequences as helices
pestfind | Finds PEST motifs as potential proteolytic cleavage sites
preg | Regular expression search of a protein sequence
pscan | Scans proteins using PRINTS
sigcleave | Reports protein signal cleavage sites
tmap | Displays membrane spanning regions

## Author(s)

Alan Bleasby (ableasby © hgmp.mrc.ac.uk)
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

Original program "PEPCOIL" by Peter Rice (EGCG 1991)

## History

Written (1999) - Alan Bleasby

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments