[Chimera-users] Interaction interface between two residues and measure buriedArea

Tom Goddard goddard at sonic.net
Wed Mar 11 16:11:12 PDT 2015


Hi Massimo,

 I think the reason buried solvent accessible area is usually reported is because it is probably better correlated with the solvation energy, how much energy is related to the water / protein interface, then solvent excluded area.  This makes some sense to me because the SAS surface is where the “probe” sphere representing a water molecule is centered so it roughly says how many spheres or water molecules you can pack against the protein.  This is all just my guess.  The only case where I have read literature on this topic is studies that try to identify biologically meaningful protein-protein interfaces in X-ray crystal structures by measuring buried areas.

  A sanity check on your buried area values (after checking that they are positive) is try changing the probe radius by a small bit and see if you get just a small change in buried area.  This will cause different surfaces to be computed but should result in a small area change if the calculation is correct.  The default probe radius is 1.4 Angstroms, so try “measure buried #0 #1 probe 1.45”.

	Tom


> On Mar 11, 2015, at 3:48 PM, ms wrote:
> 
> Hi Tom,
> 
> Thanks for your reply.
> 
> On 11/03/15 23:18, Tom Goddard wrote:
> 
>> I think buried solvent accessible area (SAS) is most often used when
>> buried areas are reported.
> 
> OK, thanks. Any justification in the literature for that, just to be on the safe side?
> 
>> Negative values of buried SAS are
>> impossible, that would be a bug, probably a failure of the surface
>> calculation,
> 
> OK.
> 
>> and if you see a case of that could you send me a
>> Chimera session that demostrates it?
> 
> I will do it tomorrow.
> 
>> Unfortunately with erratic
>> surface calculation (which does not always report when it goes awry)
>> you cannot be certain the numbers are correct.
> 
> Understood. If so, is there any sanity check I can do to see if a calculation has more or less chances of being meaningful?
> 
> thanks,
> Massimo
> 
> -- 
> Massimo Sandal, Ph.D.
> http://devicerandom.org
> 




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