Protein surface interpretation - help

Dr Engelbert Buxbaum engelbert_buxbaum at hotmail.com
Tue Oct 5 08:31:33 EST 2004


Stefek Borkowski wrote:

> Hi,
> 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.

If you told us how you calculated these values, we could comment on the
methods used rather than the results, which would probably be more
useful to you.



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