[Chimera-users] Maximum surface areas for each amino acid
goddard at sonic.net
Mon Dec 13 18:08:11 PST 2010
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.
> 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.
> 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.
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