AMBER Archive (2004)Subject: Re: AMBER: H Bonds
From: anshul_at_imtech.res.in
Date: Thu May 06 2004  18:01:33 CDT
Dear David
Eventhough, the distance in case of of nn+3 is less then nn+4,
indicating the weak nature of this bond but it shows an angle of 48.65 which is much
higher then that for nn+4(17.69). I would like to know if there is any
kind of angle criteria which allows the bonds to form in a specific
angle range.
I mean to say that if the donor and acceptor groups are some distance
apart which can form strong hydrogen bonds but the angle between them is
not in the favourable region, will carnal show a hydrogen bond in this
case also??
With regards
Anshul
On Wed, 5 May 2004, David A. Case wrote:
> On Wed, May 05, 2004, anshul_at_imtech.res.in wrote:
>
> > I am ttrying to analyse the H. bond pattern in various peptides. I am
> > using a right handed helix of a decapeptide. when i use carnal to find the
> > possible h bonds it gives a total of 13 H.Bonds. Insted of giving H bonds
> > between residue n and n+4 it also gives the same between residues n and
> > n+3. Is it normal or I am doing something wrong.
>
> It is quite a common to have both n>n+4 and n>n+3 hydrogen bonds in a
> helical peptide. In you example, as in many structures, the n>n+3 bonds are
> systematically longer (and therefore weaker) than the n>n+4 hydrogen bonds.
> >
> > 1 ( ALA 4 N )( ALA 1 O ) 3.335977 50.016235
> > 1 ( ALA 5 N )( ALA 1 O ) 3.096780 18.832615
> > 1 ( ALA 5 N )( ALA 2 O ) 3.336197 50.021879
> > 1 ( ALA 6 N )( ALA 2 O ) 3.096576 18.820264
> > 1 ( ALA 6 N )( ALA 3 O ) 3.335950 50.016080
> > 1 ( ALA 7 N )( ALA 3 O ) 3.097679 18.839666
> > 1 ( ALA 7 N )( ALA 4 O ) 3.336395 49.991904
> > 1 ( ALA 8 N )( ALA 4 O ) 3.096568 18.858349
> > 1 ( ALA 8 N )( ALA 5 O ) 3.336350 49.972242
> > 1 ( ALA 9 N )( ALA 5 O ) 3.097235 18.838018
> > 1 ( ALA 9 N )( ALA 6 O ) 3.336560 49.998391
> > 1 ( ALA 10 N )( ALA6 O ) 3.096918 18.815361
> > 1 ( ALA 10 N )( ALA 7 O ) 3.335742 50.034458
> >
>
> ...dac
> 
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