EMBOSS: pepcoil

Program 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
Input sequence: sw:gcn4_yeast
Window size [28]: 
Output file [gcn4_yeast.pepcoil]:

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           bool       Report coiled coil regions
   -frame              bool       Show coil frameshifts
   -[no]other          bool       Report non coiled coil regions

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose

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 Yes/No Yes
-frame Show coil frameshifts Yes/No Yes if -coil is true
-[no]other Report non coiled coil regions Yes/No Yes

Input file format

It reads in a protein sequence.

Output file format

Here is the output file from the example run. 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. 

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 nameDescription
antigenicFinds antigenic sites in proteins
digestProtein proteolytic enzyme or reagent cleavage digest
fuzzproProtein pattern search
fuzztranProtein pattern search after translation
garnierPredicts protein secondary structure
helixturnhelixReport nucleic acid binding motifs
hmomentHydrophobic moment calculation
oddcompFinds protein sequence regions with a biased composition
patmatdbSearch a protein sequence with a motif
patmatmotifsSearch a PROSITE motif database with a protein sequence
pepnetDisplays proteins as a helical net
pepwheelShows protein sequences as helices
pregRegular expression search of a protein sequence
pscanScans proteins using PRINTS
sigcleaveReports protein signal cleavage sites
tmapDisplays membrane spanning regions

Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.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.

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