pepwheel

 

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Function

Draw a helical wheel diagram for a protein sequence

Description

pepwheel draws a helical wheel diagram for a protein sequence. This displays the sequence in a helical representation as if looking down the axis of the helix. It is useful for highlighting amphipathicity and other properties of residues around a helix. By default, aliphatic residues are marked with squares, hydrophilic residues are marked with diamonds, and positively charged residues with octagons, although this can be changed.

Usage

Here is a sample session with pepwheel


% pepwheel tsw:hbb_human -send 30 
Draw a helical wheel diagram for a protein sequence
Graph type [x11]: cps

Created pepwheel.ps

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

Command line arguments

Draw a helical wheel diagram for a protein sequence
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   Protein sequence filename and optional
                                  format, or reference (input USA)
   -graph              graph      [$EMBOSS_GRAPHICS value, or x11] Graph type
                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                  tek, tekt, none, data, xterm, png, gif)

   Additional (Optional) qualifiers (* if not always prompted):
   -steps              integer    [18] The number of residues plotted per turn
                                  is this value divided by the 'turns' value.
                                  (Integer from 2 to 100)
   -turns              integer    [5] The number of residues plotted per turn
                                  is the 'steps' value divided by this value.
                                  (Integer from 1 to 100)
*  -squares            string     [ILVM] By default the aliphatic residues
                                  ILVM are marked with squares. (Any string)
*  -diamonds           string     [DENQST] By default the residues DENQST are
                                  marked with diamonds. (Any string)
*  -octags             string     [HKR] By default the positively charged
                                  residues HKR are marked with octagons. (Any
                                  string)

   Advanced (Unprompted) qualifiers:
   -[no]wheel          boolean    [Y] Plot the wheel
   -amphipathic        toggle     If this is true then the residues ACFGILMVWY
                                  are marked as squares and all other
                                  residues are unmarked. This overrides any
                                  other markup that you may have specified
                                  using the qualifiers '-squares', '-diamonds'
                                  and '-octags'.

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of the sequence to be used
   -send1              integer    End of the sequence to be used
   -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
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-graph" associated qualifiers
   -gprompt            boolean    Graph prompting
   -gdesc              string     Graph description
   -gtitle             string     Graph title
   -gsubtitle          string     Graph subtitle
   -gxtitle            string     Graph x axis title
   -gytitle            string     Graph y axis title
   -goutfile           string     Output file for non interactive displays
   -gdirectory         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
[-sequence]
(Parameter 1)
sequence Protein sequence filename and optional format, or reference (input USA) Readable sequence Required
-graph graph Graph type EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif EMBOSS_GRAPHICS value, or x11
Additional (Optional) qualifiers
-steps integer The number of residues plotted per turn is this value divided by the 'turns' value. Integer from 2 to 100 18
-turns integer The number of residues plotted per turn is the 'steps' value divided by this value. Integer from 1 to 100 5
-squares string By default the aliphatic residues ILVM are marked with squares. Any string ILVM
-diamonds string By default the residues DENQST are marked with diamonds. Any string DENQST
-octags string By default the positively charged residues HKR are marked with octagons. Any string HKR
Advanced (Unprompted) qualifiers
-[no]wheel boolean Plot the wheel Boolean value Yes/No Yes
-amphipathic toggle If this is true then the residues ACFGILMVWY are marked as squares and all other residues are unmarked. This overrides any other markup that you may have specified using the qualifiers '-squares', '-diamonds' and '-octags'. Toggle value Yes/No No
Associated qualifiers
"-sequence" associated sequence qualifiers
-sbegin1
-sbegin_sequence
integer Start of the sequence to be used Any integer value 0
-send1
-send_sequence
integer End of the sequence to be used Any integer value 0
-sreverse1
-sreverse_sequence
boolean Reverse (if DNA) Boolean value Yes/No N
-sask1
-sask_sequence
boolean Ask for begin/end/reverse Boolean value Yes/No N
-snucleotide1
-snucleotide_sequence
boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein1
-sprotein_sequence
boolean Sequence is protein Boolean value Yes/No N
-slower1
-slower_sequence
boolean Make lower case Boolean value Yes/No N
-supper1
-supper_sequence
boolean Make upper case Boolean value Yes/No N
-sformat1
-sformat_sequence
string Input sequence format Any string  
-sdbname1
-sdbname_sequence
string Database name Any string  
-sid1
-sid_sequence
string Entryname Any string  
-ufo1
-ufo_sequence
string UFO features Any string  
-fformat1
-fformat_sequence
string Features format Any string  
-fopenfile1
-fopenfile_sequence
string Features file name Any string  
"-graph" associated graph qualifiers
-gprompt boolean Graph prompting Boolean value Yes/No N
-gdesc string Graph description Any string Helical wheel
-gtitle string Graph title Any string  
-gsubtitle string Graph subtitle Any string  
-gxtitle string Graph x axis title Any string $(sequence.name)
-gytitle string Graph y axis title Any string  
-goutfile string Output file for non interactive displays Any string  
-gdirectory 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

Input file format

pepwheel reads any protein sequence USA.

Input files for usage example

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

Database entry: tsw:hbb_human

ID   HBB_HUMAN               Reviewed;         147 AA.
AC   P68871; A4GX73; B2ZUE0; P02023; Q13852; Q14481; Q14510; Q45KT0;
AC   Q549N7; Q6FI08; Q6R7N2; Q8IZI1; Q9BX96; Q9UCD6; Q9UCP8; Q9UCP9;
DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT   23-JAN-2007, sequence version 2.
DT   16-JUN-2009, entry version 76.
DE   RecName: Full=Hemoglobin subunit beta;
DE   AltName: Full=Hemoglobin beta chain;
DE   AltName: Full=Beta-globin;
DE   Contains:
DE     RecName: Full=LVV-hemorphin-7;
GN   Name=HBB;
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC   Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   MEDLINE=77126403; PubMed=1019344;
RA   Marotta C., Forget B., Cohen-Solal M., Weissman S.M.;
RT   "Nucleotide sequence analysis of coding and noncoding regions of human
RT   beta-globin mRNA.";
RL   Prog. Nucleic Acid Res. Mol. Biol. 19:165-175(1976).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   MEDLINE=81064667; PubMed=6254664; DOI=10.1016/0092-8674(80)90428-6;
RA   Lawn R.M., Efstratiadis A., O'Connell C., Maniatis T.;
RT   "The nucleotide sequence of the human beta-globin gene.";
RL   Cell 21:647-651(1980).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANT LYS-7.
RX   PubMed=16175509; DOI=10.1086/491748;
RA   Wood E.T., Stover D.A., Slatkin M., Nachman M.W., Hammer M.F.;
RT   "The beta-globin recombinational hotspot reduces the effects of strong
RT   selection around HbC, a recently arisen mutation providing resistance
RT   to malaria.";
RL   Am. J. Hum. Genet. 77:637-642(2005).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA   Lu L., Hu Z.H., Du C.S., Fu Y.S.;
RT   "DNA sequence of the human beta-globin gene isolated from a healthy
RT   Chinese.";
RL   Submitted (JUN-1997) to the EMBL/GenBank/DDBJ databases.
RN   [5]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANT ARG-113.
RA   Cabeda J.M., Correia C., Estevinho A., Cardoso C., Amorim M.L.,
RA   Cleto E., Vale L., Coimbra E., Pinho L., Justica B.;
RT   "Unexpected patterns of globin mutations in thalassemia patients from
RT   north of Portugal.";


  [Part of this file has been deleted for brevity]

FT   VARIANT     141    141       A -> V (in Puttelange; polycythemia; O(2)
FT                                affinity up).
FT                                /FTId=VAR_003082.
FT   VARIANT     142    142       L -> R (in Olmsted; unstable).
FT                                /FTId=VAR_003083.
FT   VARIANT     143    143       A -> D (in Ohio; O(2) affinity up).
FT                                /FTId=VAR_003084.
FT   VARIANT     144    144       H -> D (in Rancho Mirage).
FT                                /FTId=VAR_003085.
FT   VARIANT     144    144       H -> P (in Syracuse; O(2) affinity up).
FT                                /FTId=VAR_003087.
FT   VARIANT     144    144       H -> Q (in Little Rock; O(2) affinity
FT                                up).
FT                                /FTId=VAR_003086.
FT   VARIANT     144    144       H -> R (in Abruzzo; O(2) affinity up).
FT                                /FTId=VAR_003088.
FT   VARIANT     145    145       K -> E (in Mito; O(2) affinity up).
FT                                /FTId=VAR_003089.
FT   VARIANT     146    146       Y -> C (in Rainier; O(2) affinity up).
FT                                /FTId=VAR_003090.
FT   VARIANT     146    146       Y -> H (in Bethesda; O(2) affinity up).
FT                                /FTId=VAR_003091.
FT   VARIANT     147    147       H -> D (in Hiroshima; O(2) affinity up).
FT                                /FTId=VAR_003092.
FT   VARIANT     147    147       H -> L (in Cowtown; O(2) affinity up).
FT                                /FTId=VAR_003093.
FT   VARIANT     147    147       H -> P (in York; O(2) affinity up).
FT                                /FTId=VAR_003094.
FT   VARIANT     147    147       H -> Q (in Kodaira; O(2) affinity up).
FT                                /FTId=VAR_003095.
FT   CONFLICT     26     26       Missing (in Ref. 15; ACD39349).
FT   CONFLICT     42     42       F -> L (in Ref. 13; AAR96398).
FT   HELIX         6     16
FT   TURN         21     23
FT   HELIX        24     35
FT   HELIX        37     42
FT   HELIX        44     46
FT   HELIX        52     57
FT   HELIX        59     77
FT   TURN         78     80
FT   HELIX        82     94
FT   TURN         95     97
FT   HELIX       102    119
FT   HELIX       120    122
FT   HELIX       125    142
FT   HELIX       144    146
SQ   SEQUENCE   147 AA;  15998 MW;  A31F6D621C6556A1 CRC64;
     MVHLTPEEKS AVTALWGKVN VDEVGGEALG RLLVVYPWTQ RFFESFGDLS TPDAVMGNPK
     VKAHGKKVLG AFSDGLAHLD NLKGTFATLS ELHCDKLHVD PENFRLLGNV LVCVLAHHFG
     KEFTPPVQAA YQKVVAGVAN ALAHKYH
//

Output file format

An image is output to the specified graphics device.

Output files for usage example

Graphics File: pepwheel.ps

[pepwheel results]

Data files

None.

Notes

The number of residues plotted per turn is the specified "steps" value (-steps) divided by the specified "turns" value (-turns).

The default settings for turn (5) and steps (18) apply to alpha helices. For other possible secondary structures, see the following table:

helix       phi   psi  omega  res/turn  transl.  turns  steps
alpha       -57   -47    180       3.6     1.50      5     18
3-10        -49   -26    180       3.0     2.00      1      3
pi          -57   -70    180       4.4     1.15      5     22
PP I        -83   158      0       3.33    1.9       3     10
PP II       -78   149    180       3.0     3.12      1      3
PG II       -80   150    180       3.0     3.1       1      3
anti Beta  -139   135   -178       2.0     3.4       4      9
para Beta  -119   113    180       2.0     3.2       4      9

PP is polyproline
PG II is polyGlycine.

When you specify the number of turns and steps, be aware that you should remove common factors from these two numbers. For example, if you (for some improbable reason) wished to plot a wheel with 8 turns in 18 steps (2.25 residues per turn) you should remove the common factor (i.e. 2) and specify 4 turns in 9 steps.

References

  1. Rachamandran and Sasisekharan, Adv. Protein Chem. 23:283-437, 1968
  2. IUPAC-IUB Commission on biochemical nomenclature, Biochemistry 9:3471-3479, 1970

Warnings

When you specify the number of turns and steps, be aware that you should remove common factors from these two numbers. For example, if you (for some improbable reason) wished to plot a wheel with 8 turns in 18 steps (2.25 residues per turn) you should remove the common factor (i.e. 2) and specify 4 turns in 9 steps.

Diagnostic Error Messages

None.

Exit status

0 upon successful completion.

Known bugs

None.

See also

Program name Description
abiview Display the trace in an ABI sequencer file
cirdna Draws circular maps of DNA constructs
garnier Predicts protein secondary structure using GOR method
helixturnhelix Identify nucleic acid-binding motifs in protein sequences
hmoment Calculate and plot hydrophobic moment for protein sequence(s)
lindna Draws linear maps of DNA constructs
pepcoil Predicts coiled coil regions in protein sequences
pepnet Draw a helical net for a protein sequence
prettyplot Draw a sequence alignment with pretty formatting
prettyseq Write a nucleotide sequence and its translation to file
remap Display restriction enzyme binding sites in a nucleotide sequence
seealso Finds programs with similar function to a specified program
showalign Display a multiple sequence alignment in pretty format
showdb Displays information on configured databases
showfeat Display features of a sequence in pretty format
showpep Displays protein sequences with features in pretty format
showseq Displays sequences with features in pretty format
sixpack Display a DNA sequence with 6-frame translation and ORFs
textsearch Search the textual description of sequence(s)
tmap Predict and plot transmembrane segments in protein sequences

Author(s)

Alan Bleasby (ajb © ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

History

Written (March 1999) - Alan Bleasby

Target users

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

Comments

None