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

[Phil Jeffrey <phil@xray2.mskcc.org>]

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> > (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):

Back in the days when I used to worry about Fab:antigen contacts an
informal survey of other lab's definitions of "contacts" suggested that a
cutoff of 4.0 or 4.2 is often used, although it might be more appropriate
to use per-atom assignment of radii, since oxygens are quite a lot smaller
than a methyl group, for example.  If you want to use the cutoff method
for buried atoms then something like 5.0-5.4 might not be a bad guess
(basically twice a typical extended-atom-radius of 1.8 plus 1.4 for a
water molecule).

M. Connolly's (sp?) suite of programs to calculate molecular surfaces used
to allow one to calculate the explicit buried surface on one molecule by
another.  I no longer have those programs and don't know where they are to
be found (URL anyone?) but they worked well at the time.  It's worth
pointing out that if you do runs of DSSP on the entire complex and compare
the output with that for the molecules separately, you can get a fairly
good idea of what residues' buried surface areas change upon complex
formation.  Requires a little bit of Fortran/Perl/name-your-language but
nothing too extreme.  Probably not the most accurate method, but.... 

Cheers,
Phil
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| Phil Jeffrey                                  |                             |
| Crystallography Facility Manager              | If you lie to the compiler, |
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