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

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

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> 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

well, that's all fine and dandy of course, but this tacitly assumes that you
believe your coordinates to the N-th decimal place. for your average 2.5-3.5 A
resolution complex, the errors in your distances may be 1 A or more, so all
arguments about atom-specific radii suggest that you are willing to
over-interpret your model (one cannot draw any valid "1 A" conclusions from a
3 A model !). it's like seeing hydrogen-bonding distances for a 3 A structures
listed with an apparent precision of 0.01 A (think about it !) and surface
areas with a precision of 1 A2 ... what i mean is - (1) an ounce of
"reflection" can save you a ton of pointless computing [of course, a ton of
*reflections* can save you an ounce of reflection ;-), and (2) the accuracy of
a measurement is *not* determined by the format statement of a computer
program.

to come back to the xplor lines - they were used in the analysis of the
ache-fas complex (1fss). since the resolution was less than 3 A we reasoned
that there was no point in calculating hydrogen bonding. instead we called
every contact between polar atoms shorter than 3.5 A a polar interaction, and
every contact between apolar atoms shorter than 4 A a hydrophobic interaction
(not sure about the exact cut-offs - am writing this at home). i seem to
recall that we also did something fairly 'low-resolution-ish' with the buried
surface areas but would have to check the paper again

--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
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