Protein surfaces by definition?

Stefek Borkowski stefek at killspam.edu
Fri Oct 1 18:36:18 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?

Regards,
Stefek




More information about the Microbio mailing list