[Chimera-users] Solvent Exposure of Amino Acids HELP
narinevapuryan at hotmail.com
Wed Jul 15 13:03:56 PDT 2020
Thank you so much for your help! This clears things up.
> On Jul 15, 2020, at 12:51 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Narine,
> No, it is the opposite: lower relSESA means less exposed, higher means more exposed.
> You can see in the page that the calculation is simply normalizing the surface area (in your specific structure) by the surface area of the same residue type in a tripeptide representing the unfolded state. If the surface area of residue is 10 in your structure and 100 in the exposed state, then relSESA is 10/100 = 0.10 exposed, same as 10% exposed (90% buried).
> The normalization is just because some amino acid types are bigger than others.
> I hope this helps,
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Jul 15, 2020, at 12:14 PM, Narine Vapuryan <narinevapuryan at hotmail.com> wrote:
>> I hope this email finds you well and healthy. I have a question regarding relative solvent excluded surface area (relSESA) calculations using Chimera. I am able to calculate the relative solvent excluded surface areas of residues using the following Chimera guide: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html. Although I am able to perform the calculations and get an output, I am having trouble understanding those values. I would have expected lower relSESA values to mean more residue exposure to solvent (surface residues), and high relSESA to mean less residue exposure to solvent (buried residues). Is my interpretation incorrect? Are lower relSESA values are to be interpreted as lower exposure to solvent (buried residues) and higher relSESA values as more exposed to the solvent (surface residues)?
>> I would really appreciate any help or insight on this matter considering that I have been trying to figure this out for the past week. Please feel free to reach out to me if you need clarification on my question.
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