Protein surface interpretation - help

Stefek Borkowski stefek at killspam.edu
Sun Oct 3 13:24:30 EST 2004

Could someone tell me whether I am right or wrong in understanding the idea
of different protein surfaces, please? Do the values of the surfaces area
that I have managed to calculate for a 15 kD protein seem reasonable?
1. van der Waals surface - the bigest area (covers van der Waals atomic
surfaces), eg. 14,000 squared Angstroms
2. molecular surface or contact surface covered by a rolling molecule of the
solvent, eg. 2,000 squared Angstroms
3. (solvent) accessible surface - described by the trace of the central
point of a solvent molecule rolling over the protein contact surface, eg.
7,000 squared Angstroms.

Are the values calculated for a 15 kD protein probable? Is the below true
for a typical protein:
molecular surface < accessible surface < van der Waals surface?

Which surface area is best to calculate in order to consider the geometry of
interacting surfaces
of proteinous antigen and an immunoglobulin? I would like to calculate
potential binding sites on a surface of an antigen assuming that the average
antigen surface covered by a monovalent antibody binding site is approx.
1500 squared Angstroms.
Thanks in advance for all your help.


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