On Tue, Jun 18, 2002 at 01:43:17PM +0300, Dan Thomas Major wrote: > Hi, > I'm modelling G-protein coupled receptors using rhodopsin as a template. > > When I compare the Ramachandran plot of the models vs that of rhodopsin, > > the models have much more ideal helices than the rhodopsin X-ray > structure (2.8 A).

I am also modelling a GPCR using rhodopsin as a template. There is a kink in one of the helices in rhodopsin caused by met308-met309-asn310-lys311. Because the kink isn't caused by something like proline, dihedral angles must probably incur some violations.

> Is this because: > 1) The homology is relatively low (20-30%) and the distance constraints > receive a low weight in the pdf function?? > 2) The helices in rhodopsin are less regular than the globular proteins > used in the pdf parametrization?? > 3) None of the above... > > Sincerely, > Dan > > -- > Dan Thomas Major (at Dr. B. Fischer's lab) > Bar-Ilan University > Ramat-Gan, Israel > Phone: 972-3-5317785 > Fax: 972-3-5348730 > >