[CHEKAL]

Could someone please explain what information you gain about a protein from its Ramachandran plot. I understand its a plot of its dihedral angles of amino acid rotations, but how can you critically analyse the quality of its crystal structure from it?

Also, I thought a Ramachandran plot was a single plot. I don't understand the different types of plot for general case, pre-proline, glycine, cis- and trans- proline....

Thanks a lot

[Babcock_Hall]

There is a recent educational article that has references to some research done in this area over the last twenty years or so:  Using Molecular Models To Show Steric Clash in Peptides: An Illustration of Two Disallowed Regions in the Ramachandran Diagram, Halkides, Christopher J., Journal of Chemical Education, vol. 90, issue 6, pp. 760-762.  P. Andrew Karplus has done some work in this area, as has Bosco Ho:  http://www.biomedcentral.com/1472-6807/5/14  Ho has a website which is worth checking out.

Because glycine has only a hydrogen, not an R-group of any size, it has a larger allowed area in a Ramachandran plot than other amino acids.  It is also achiral.  Proline has a very limited allowed region, because its R group links back to its amino nitrogen.  Pre-proline residues also are more limited (see the link and also Figure 5-11 in Volume 1 of Cantor and Schimmel's Biophysical Chemistry).  The main issue in pre-proline may be the methylene group directly attached to the proline nitrogen interfering with one or two atoms of the pre-proline residue.  Amino acids that have branching at the beta-carbon also have some special restrictions, but I cannot recall the details at the moment.

At the end of the refinement process, one checks to see whether or not the new protein model has dihedral angles that (mostly) fall within the allowed regions of the Ramachandran diagram.  Some known structural features, such as the gamma-turn, fall a little bit outside of allowed region.  But if there are many outliers, the structure may need further refinement.