Hi Dan- There's an online server and program called DPX which will calculate the depth of all the atoms in your PDB file. An atom's depth is defined as the minimum distance it is to the nearest solvent accessible atom, with depth = 0 meaning the atom is not buried at all (most likely at the protein surface) whereas depth > 3 A or higher means the atom is most likely buried. I understand these are not surface area values like you are wanting but it does at least give you some quantitative measure if an atom is buried or not. I've run depth calculations for several protein structures and upon visual inspection of the structures, the depth values seem to be an accurate descriptor of an atom's burial and/or exposure. Maybe this will tell you something about your loop in the 2 states.
Alternatively, the authors of this program may very well have developed a sister program that calculates exactly what you're wanting. HTH- Brad On Fri, Sep 25, 2009 at 3:19 PM, Daniel Bonsor <[email protected]> wrote: > Sorry I should of made this clearer in my original post. Thanks anyway to > people who have responded thus far. > > I am trying to calculate the buried surface area of a loop which folds from > a disordered to an ordered state. > > I am looking for a program that will allow me to calculate; > (1) the buried surface area per atom (not residue) > or > (2) something that returns the buried surface area of apolar and polar > atoms. > > It has to be per atoms and not per residues. > > Thanks again in advance. > > > Dan >
