[BiO BB] Ramachandran plot.

[Vivek Philip]

But isn't it true that the ramachandarn plot is a plot of phi psi angles per
residue and that should agree with the properties of alpha helices and beta
sheet angles. That was our understanding of the problem.and that's why we
thought it was interesting.
Vivek


On 3/30/06, Boris Steipe <boris.steipe at utoronto.ca> wrote:
>
> This is not misclassification: helices and strands have >>repeating<<
> residues with certain (phi,psi) values. The Ramachandran plot shows
> you a value for >>single<< residues. To classify a structural segment
> as belonging to a certain type you need more information than
> individual (phi,psi) values.
>
> HTH,
> Boris
>
>
>
> On 30 Mar 2006, at 10:57, Vivek Philip wrote:
>
> > Hi,
> >   While analyzing the plot of phi and psi angles on the
> > Ramachandran plot, we found out that there was a lot of overlap
> > between the alpha-helix and beta-sheet regions. By this we mean
> > that just based on the phi and psi angles alpha helices are meant
> > to be both negative, while for beta sheets phi angles take negative
> > values and psi positive. The results we used for generating these
> > plots were obtained from STRIDE and DSSP for top 500 high
> > resolution pdb structures.
> >   Does anyone have an idea as to what the reason for such an
> > overlap could be? Moreover on further analysis we did see a lot of
> > misclassification particularly related to the pi-helix region (Only
> > about 38% of the residues were classified correctly).We are talking
> > about approximately 40% overlap between the two regions.
> >   Any feedback on this would be greatly appreciated.
> >   Thank you,
> > Vivek
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--
Vivek M. Philip
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