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Protein surface interpretation problem...

Stefek Borkowski stefek at killspam.edu
Tue Oct 5 11:30:25 EST 2004

Hi again,
Could someone tel me whether I am right or wrong in understanding the idea
of different protein surfaces, please?
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 the geometry of interacting surfaces
of proteinous antigen and an immunoglobulin?


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