Re: [ccp4bb]: list of residues buried in an interface

["Gerard \"DVD\" Kleywegt" <gerard@xray.bmc.uu.se>]

***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***

> Is there some program around that takes a number of coordinate files
> (understand: PDB files) corresponding to an "aggregate" (e.g. a dimer)
> and to the separate subunits, and provides a table of the residues
> buried in the subunit-subunit interface(s)?

if you just want the inter-molecular contacts, you can
do it simply in xplor/cns. i used something like this
(ages ago though, so this is xplor syntax):

{ find contacts between ACHE and FAS }
distance from=( SEGID="AAAA" and not hydrogen )
           to=( SEGID="BBBB" and not hydrogen ) cutoff=4.0 end

if you want to look for possible h-bonds, salt-links etc:

distance from=( SEGID="AAAA" and (chemical O* or chemical N*) )
           to=( SEGID="BBBB" and (chemical O* or chemical N*) )
       cutoff=3.6 end

if you are interested in hydrophobic interactions:

distance from=( SEGID="AAAA" and (chemical C* or chemical S*) )
           to=( SEGID="BBBB" and (chemical C* or chemical S*) )
       cutoff=4.0 end

--dvd

******************************************************************
                        Gerard J.  Kleywegt
    [Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
                Biomedical Centre  Box 596
                SE-751 24 Uppsala  SWEDEN

    http://xray.bmc.uu.se/gerard/  mailto:gerard@xray.bmc.uu.se
******************************************************************
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
******************************************************************