Subject: accessible atom or residues on protein surface

From: "Jerry Song" <[email-masked]>
Date: Tue, 31 Jul 2001 15:12:14 -0400

Hello,
Firstly, thanks for the replies from Kumar and Gert.

I am sorry that I didn't make my question very clear in my previous email.

I had tried the several softwares to calculate the solvent accesible area or
relative %area of per atom or residue.
But in order to pick out those groups on the protein surface, I also have to
define a threthod value for the surface area.
(for example, let is say, if the surface area of one certain residue is
larger than 30%, we can assume the residue is on
the protein surface.) So my question will turn into :
    how large will this reasonable value roughly be? ( from the view of
biochemistry and chemistry)

Of course I can try some arbitrary values, select out the assumed suface
group and finally check them by comparing with some general-used
softwares.But since I just began my work, so I am very interested in know
whether any previous works/references about  this question or are there any
other methods instead of calculating solvent accesible areas.

Thanks,
Minghu