How To Charecterize A Residue In A Protein Based On It'S Asa

Question

[Suk211]

How can we characterize a residue in a protein as a buried, exposed or intermediate based on it's accessible surface area(ASA)?

I came across a paper in which they are taking the ratio between the residue's ASA at a particular position to the maximum ASA observed for that residue in the whole protein.Further they apply a cut off on these ratios to characterize a residue as buried , exposed or intermediate. I am not sure about the basis of these cut offs.

Can any one validate or provide a better approach for doing this?

[Istvan Albert]

It might probably help if you gave the full reference to the paper that you mention.

Answer 1

[Ryan]

Yeah, the better answer is not to use surface area to calculate depth. use depth. http://dx.doi.org/10.1016/j.tibs.2003.09.004

Answer 2

[Nir London]

ASA-view is a server that can help you visualize the burial of each amino acid in your protein

Answer 3

[Khader Shameer]

This depends on the program you use, I have calculated surface accessibility using PSA from JOY package. Another programs which I have seen frequently in literature is NACCESS.