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
-
Rachamandran and Sasisekharan, Adv. Protein Chem.
23:283-437, 1968
-
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