how find relative solvent accesibility

Question

[gbahramali]

I have a question about relative solvent accessibility. I have two peptide groups including many peptides in each group. I want the first :find absolute solvent accessibility in DSSP and then for finding absolute solvent accessibility, add every number of solvent accessibility of every peptide for example I have peptide "abcdef" with solvent "102-34-89-67-89-99" :103+34+89+67+89+99 is it true?

And after do this method for all of peptide then calculate mean (average) of solvent accessibility for two groups, is it true?

And then how find relative solvent accessibility? and how compare two groups?

Answer 1

[João Rodrigues]

You might consider using NACCESS or STRIDE, which should give you the RSA value directly.

I don't really understand the rest of the question, but in principle you could sum the accessibilities of several parts of a group to get an idea of the overall accessibility, but consider that you might have several conformations of the peptide and this value might deviate a lot. Tricky business if not done right.

[gbahramali]

Thanks for your reply

I have absolute solvent accessibility from DSSP AND selected only my region(peptide) but in this format have solvent accessibility for every residue ,could you please tell me for finding solvent accessibility of one peptide can I sum every solvent of residue in my peptide?

And also I want to know that NACCESS give me relative or same dssp?

For finding relative solvent accessibility(RSA) I want absolute solvent divide To maximum solvent is it true?

And could you please tell me any tools have this option

Thanks again

[João Rodrigues]

Relative SA is relative to a GLY-X-GLY peptide if I recall correctly. That's why you always have >100% RSAs at termini.

I already replied: NACCESS will give you the relative accessibility. It will also give the absolute accessibility.

[gbahramali]

Thanks again for your helping

I have many peptide and I wrote program for parsing the ASA from DSSP program AND I want to calculate RSA using manually .

Now for calculating RSA, I need MAXIMUM ASA. Could you please tell me how can find maximum RSA

[João Rodrigues]

It's in the README of NACCESS:

A residue accessibility (.rsa) file containing summed atomic accessible surface areas over each protein or nucleic acid residue, as well as the relative accessibility of each residue calculated as the %accessiblity compared to the accessibility of that residue type in an extended ALA-x-ALA tripeptide (for amino acids). See Hubbard, Campbell & Thornton (1991) J.Mol.Biol.220,507-530. You can prevent this file from being calculated if you don't need it.