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 <ber...@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 <ber...@upstate.edu <mailto:ber...@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>
>>
>> <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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