RE: [ccp4bb]: STructure question!

[Gerard DVD Kleywegt <gerard@xray.bmc.uu.se>]

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- 9 residue alpha helix, approx 11.5 A from N to C-term CA

- 9 residue beta strand, approx 26.5 A from N to C-term CA
  (in practice, this will about the maximum)

- 9 residue loop - anything from 2.9 A up to the maximum
  (2.9 A occurs for a circular peptide with a cis-peptide
  bond linking nr 9 back to nr 1 ;-)

carugo and pongor use ca(i)-ca(i+N) distances for fold
comparison (j mol biol 315, 887-898 (2002), and j appl
cryst 35, 648-649 (2002)), so they may have database-wide
statistics of the distribution of ca(i)-ca(i+8)

--dvd


> Here is a upper/lower/sloppy case estimate:
> 
> > > If I have a 9 residue peptide, what is the farthest distance
> > > between the 
> > > C-alpha atoms of the 1st and 9th residue. I know that ca-ca 
> > > is 3.8A.  But I am not sure if it is 3.8x9 or is it different 
> > > - can it be longer?
> > 
>  8 times only:
>  
>  *-1-*-2-*-3-*-4-*-5-*-6-*-7-*-8-*
> 
>  9 stars...
> 
>   Then: extended maximally considering no gyration around 
> phi/psi ignoring steric restriction gives about 28A 
> (pulling hard, so to speak) ~ (n/2)*(3.8*cos(30)+3.8)
> (would look bad in ramachandran plot with one cluster
> of overlying verbotens..., the so called torture case by ED)
> 
> for helix you know 3.6 residues/turn and rise of 5.4
> - > low estimate 12A.
>  
> Free gyration is around 18-22 I wager.
>  
> Best, br

******************************************************************
                        Gerard J.  Kleywegt
    [Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
                Biomedical Centre  Box 596
                SE-751 24 Uppsala  SWEDEN

    http://xray.bmc.uu.se/gerard/  mailto:gerard@xray.bmc.uu.se
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