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.
On Thu, Jun 23, 2011 at 2:49 AM, Paul Pillot <
[email protected]> wrote:
> Thanks Bob,
> this is indeed a great addition to Jmol !
> The canonical example of hydrophobic interaction I use in my teaching with
> students is the HbS/HbS polymerization. I've just tried it on the PDB web
> site using the strategy you provided in your previous email with the pdb
> file 2HBS (asymetric unit)
> It gave the following results : the hydrophobic contacts between Val6:H and
> Ala70:B, Asp73:B has been found. The PDBsum website under the Prot/Prot tab
> reports the same contact plus an extra involving Thr84 (although stated as
> weaker).
> Several websites report Phe85:B and Leu88:B as being the amino acids
> involved in the hydrophobic pocket, but here no contact with val6 are shown
> (and I don't know if they indeed exist).
>
> The command contact hydrophobic connect {val6:B} I used, also shows bubbly
> patches with other amino acids from the same chain (:H) as Val6.
>
> A png file (including the state script) is available here :
> hydrophobic_2HBS.png<http://librairiedemolecules.education.fr/divers/hydrophobic_2HBS.png>
>
> <http://librairiedemolecules.education.fr/divers/hydrophobic_2HBS.png>
> Paul
>
>
>
>
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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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