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
Paul
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