Hi Ira,
I don't know of any table of maximal solvent accessible surface
areas for each residue type when bounded by glycines. Maybe someone
on the Chimera mailing list will know.
A Chimera Python script could run through the PDB and accumulate
per-residue surface area statistics. One trouble with that would be
that surface calculation fails in Chimera in some percentage of
cases (~5%) due to numerical problems.
Tom
Hi Tom,
Love the software. Do you have a table for calculating the maximum
available surface area for amino acids eg.(Gly-Xxx-Gly) so that I
can get a relative percentage exposed surface area from the
calculations? Do you know how to find one in the literature? Has
anyone written a program that describes the possible surface
exposure for a residue in a particular secondary structure and/or
a particular sequence? This maximal value would certainly be
different depending on the local sequence and structure. For
example, a residue in the middle of a helix would have to be
shielded from the solvent by the i+4 and i-4 residues, and the
size of those residues would matter.
Thanks,
Ira
On 12/10/10 2:41 PM, Tom Goddard wrote:
Hi Sumitro,
I made a Chimera video tutorial showing how to determine which
residues are on the surface.
http://www.cgl.ucsf.edu/chimera/videodoc/surfaceresidues/index.html
Tom