pepwheel

Function

Description

pepwheel displays peptide sequences in a helical representation.

This gives a view of a helix from a protein sequence looking down the axis of the helix.

It is useful for highlighting amphipathicity and other properties of residues around a helix.

Usage

Command line arguments


Input file format

pepwheel reads any protein sequence USA.

Output file format

An image is output to the specified graphics device.

Data files

None.

Notes

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.

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.

Author(s)

History

Target users

Comments