Another question also linked with the non-covalent interaction.

In particular I wounder to know how i Could represent all hydrophobic ( Ley Ile Val etc) sidechains in my proteins in most trivial manner? I'd like to represent the hydrophobic core of the proteins made from those residues.


Thanks,

James

2011/11/27 Edward A. Berry <BerryE@upstate.edu>
Yes i think the strongest H-bonds are single acceptor and straight
(angle at H = 180*). but these other bonds have significant
strength also.
Sorry, I'm a complete beginner at pymol. I have no idea how to
do these things.

ed


James Starlight wrote:
Thanks Edward

but recently I've studied generation of the Hbond in the water crystalls ( ice ) where H
could be as the donor of only one H-bond. It seems that I need to refresh my protein
physics course again :)

By the way as I understtod the mode=2 way shows not only H-bonds but also others
electrostatic bonds ( e.g as the salt bridges)
1- Is there any way to make clear difference betwen two distinguished electostatic contacts?

2- Also I'm looking for the most trivial way to show S-S bonds ( between 2 Cys resiudes)
in the specified chain as well as between differen chains ( as in the inslulin for instance ).


Thanks again,

James

2011/11/26 Edward A. Berry <BerryE@upstate.edu <mailto:BerryE@upstate.edu>>


   While the single acceptor H-bond is most common, bifurcated (or three-centred) H-bods
   are not uncommon in crystal structures, as described starting page 22 of GA Jeffrey's
   book:
   http://www.amazon.com/__Introduction-Hydrogen-Bonding-__Physical-Chemistry/dp/__0195095499/ref=sr_1_2?ie=UTF8&__qid=1322331503&sr=8-2

   <http://www.amazon.com/Introduction-Hydrogen-Bonding-Physical-Chemistry/dp/0195095499/ref=sr_1_2?ie=UTF8&qid=1322331503&sr=8-2>

   James Starlight wrote:

       Thomas, thank you for so detailed explanation.

       This way works good but I'd like to ask you about possibe Hbonds in the protein chain.

       As I remember for protein physics courses the H atom is always donor for only ONE
       H-bond (
       and O or N atoms could be akceptors for 1 or 2 Hbonds)

       But In my case there are some cases where H atom ( white ) is donor for the 2
       Hbonds.  By
       the way I found the same on the picture in WIKI too.

       How it could be explaned ?

       James


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