[ccp4bb]: Interaction surface-->GRASP

[Jean-Philippe Cartailler <jp@anx12.bio.uci.edu>]

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> I wonder if there is a simple way to calculate the percentage of
> charged/polar interactions and the percentage of hydrophobic interactions
> in a protein-protein interface (i.e. a dimer interface)?

I don't know of a way of doing it in CCP4, but in GRASP, you can assign
amino acids (i.e.hydrophobic) as "subsets" and perform calculations from
there.  Specifically, you would make one subset per molecule (to separate
the dimer) for those side chains of interest (you have complete freedom in
choosing the ones you want to analyze) and then calculate the interacting
surface area from both subsets and relate to the overall
interaction/surface area for all amino acids.  

In the back of the GRAP manual, you'll have to get acquainted with the
command line syntax of GRASP, since that's where all the GRASP goodies
are.

Good luck,
JP@UCI