Ramachandran plot

A peptidic bond has two degree of freedom, the dihedral angles named φ and ψ by Ramachandran.

A Ramachandran plot generated from the protein PCNA, a human DNA clamp protein that is composed of both beta sheets and alpha helices (PDB ID 1AXC). Points that lie on the axes indicate N- and C-terminal residues for each subunit. The green regions show possible angle formations that include Glycine, while the blue areas are for formations that don't include Glycine.

The classical version of the Ramachandran plot for (a) alanine (but often taken as typical for all non-glycines) and (b) glycine according to Ramachandran & Sasisekharan (1968). The fully allowed regions are shaded; the partially allowed regions are enclosed by a solid line. The connecting regions enclosed by the dashed lines are permissible with slight flexibility of bond angles. These plots were arrived at by stereo-chemical modelling. Although some overall features of these plots are correct, the details differ from the experimentally observed Ramachandran plots for (c) all 19 non-glycines and (d) glycine. The most remarkable differences are that most regions show a 45 degree slope rather than being parallel to any of the axes, the beta sheet region is split into two distinct maxima and the two most populated regions (red) for glycine seen in (d) were predicted to be only just permissible as shown in (b). There are five areas in the glycine plot; two with psi 0 and three with psi 180. Referenced from Hovmöller (2002)

A Ramachandran plot (also known as a Ramachandran map or a Ramachandran diagram or a [φ,ψ] plot), developed by Gopalasamudram Narayana Ramachandran and Viswanathan Sasisekharan is a way to visualize dihedral angles φ against ψ of amino acid residues in protein structure.^[1] It shows the possible conformations of φ and ψ angles for a polypeptide.

Mathematically, the Ramachandran plot is the visualization of a function . The domain of this function is the torus. Hence, the conventional Ramachandran plot is a projection of the torus on the plane, resulting in a distorted view and the presence of discontinuities.

One would expect that larger side chains would result in more restrictions and consequently a smaller allowable region in the Ramachandran plot. In practice this does not appear to be the case; only the methylene group at the β position has an influence. Glycine has a hydrogen atom, with a smaller van der Waals radius, instead of a methyl group at the β position. Hence it is least restricted and this is apparent in the Ramachandran plot for Glycine for which the allowable area is considerably larger.

In contrast, the Ramachandran plot for proline shows only a very limited number of possible combinations of ψ and φ.

The Ramachandran plot was calculated just before the first protein structures at atomic resolution were determined. Forty years later there were tens of thousands of high-resolution protein structures determined by X-ray crystallography and deposited in the Protein Data Bank (PDB). From one thousand different protein chains, Ramachandran plots of over 200 000 amino acids were plotted, showing some significant differences, especially for glycine (Hovmöller et al. 2002). The upper left region was found to be split into two; one to the left containing amino acids in beta sheets and one to the right containing the amino acids in random coil of this conformation.

One can also plot the dihedral angles in polysaccharides and other polymers in this fashion. For the first two protein side-chain dihedral angles a similar plot is the Janin Plot.

Software

• Web-based tool showing Ramachandran plot of any PDB entry
• STING
• Pymol with the DynoPlot extension
• VMD, distributed with dynamic Ramachandran plot plugin
• Sirius
• Swiss PDB Viewer
• TALOS

See also PDB for a list of similar software.

References

• S. Hovmöller, T. Zhou & T. Ohlson (2002) Conformations of amino acids in proteins. In: Acta Cryst. vol. D58, p. 768-776.

External links

• DynoPlot in PyMOL wiki
• Link to Ramachandran Plot Map of alpha-helix and beta-sheet locations
• Link to Ramachandran plot calculated from protein structures determined by X-ray crystallography compared to the original Ramachan.
• Proteopedia Ramachandran Plot