[Chimera-users] Maximum surface areas for each amino acid

Tom Goddard goddard at sonic.net
Mon Dec 13 18:08:11 PST 2010

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.


> 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

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