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