It's just saying that at that van der Waals size, those two atoms have
intersecting van der Waals radii. Not something we usually think about, but
it appears to be true.
On Thu, Jun 23, 2011 at 4:31 PM, Paul Pillot <
[email protected]> wrote:
> Thanks Bob for the extensive explanation of the parameters. It's very
> exciting to find that the tool you designed can predict the very same
> results as the ones from books/articles.
> I have a question regarding one of the interactions figured in the last
> example (106%) : a second contact ties Val6:B to Asp73, involving Carbon
> Gamma. But this last contact "goes through" an oxygen atom from the
> carboxylate which sounds strange to me ? Am I missing something there ?
> -Paul
>
> Le 23 juin 2011 à 18:39, Robert Hanson a écrit :
>
> Paul -- the parameters that are helpful here include the van der Waals
> radius to use and the second (target) atom set:
>
> contact ID "contact1" hydrophobic {val6:H} {!:H} 100%
>
> My analysis is here:
> http://stolaf.edu/people/hansonr/jmol/contact/2hbs.htm
>
> Looks like 100% gives you the strongest two Ala70 and Asp73,
> then changing that a bit more gives you:
>
> 101% Phe85
> 104% Leu88
> 106% Thr84
>
> I think the fact that we can even discuss this so succinctly proves my
> point that the CONTACT command with the CONNECT option could be useful.
>
>
>
>
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>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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