Hi all,
Another solution to calculate the polar vs. non-polar portions of
the ASA at the interface is, as suggested by Susan Crennel,
to use the server: http://www.biochem.ucl.ac.uk/bsm/PP/server/
(actually before posting my question I tried that server which I used
before, but I received no results for the submitted job! now it is working).
The server reports the ASA at the interface for each chain as well
as the % of polar and apolar atoms. The % then can be used to
determine the fractions of polar and non-polar (roughly) for the ASA
at the interface.
Also, Edwin Pozharski suggested the following:
Try Surface Racer or CNS - both programs will give you the output
file with ASA per atom, and you can use that for your polar/apolar
calculation (just add up everything for carbons and rest of the
protein atoms separately - you would need a simple script for that).
Ed.
thanks for all who replied,
Ibrahim
Ibrahim M.Moustafa, Ph.D.
Pennsylvania State University
Biochemistry & Molecular Biology Dept.
201 Althouse Lab.
University Park, PA16802
Tel (814) 863 8703
Fax (814) 865 7927
