On Wed, May 05, 2004, anshul.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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Received on Wed May 05 2004 - 17:53:00 PDT
