Structural Biology Glossary
Ramachandran plot
The Ramachandran plot is a graph of the protein backbone torsional angles psi (Calpha-C bond) versus phi (N-Calpha bond). The definition of backbone torsional angles is given here (GIF, VRML). The psi and phi angles cover the ranges from -180 to +180°.
By a systematic variation of these angles it was first found by Ramachandran and coworkers that not all angle combinations are allowed. This is due to van-der-Waals clashes and leads to allowed core regions and forbidden angle combinations. Moreover, different secondary structure elements cover different regions in the plot.
An example for the protein crambin (PDB code: 1crn) is shown here. This Ramachandran plot is part of the general analysis tool WHAT_CHECK devoted to the quality assessment of biopolymer structures. An analogous plot generated by the Uppsala University Ramachandran Server is shown here (PDF format). Finally, an interactive analysis of the Ramachandran plot is possible with Webmol. After the program has launched click on Rama. Then you can either click on the points in the Ramachandran plot or on amino acids in the structure image. In this way direct information on the psi/phi values for single amino acids is provided.
All these plots show the following allowed angle combinations:
right-handed alpha helix: -60° < psi < +30°
-120° < phi < -30°
beta sheet +90° < psi < +180°
(parallel / antiparallel): -180° < phi < -60°
left-handed alpha helix: 0° < psi < +60°
+45° < phi < +90°
The angle ranges given depend on the tolerable limits of the steric strain and should thus be viewed as a rather crude information. To our knowledge a left-handed alpha helix has thus far not obeserved in experimentally determined protein structures. More information on protein secondary structure elements can be obtained here.
Note that Ramachandran plots for individual amino acid types can be generated as well (singe structures, structure sets). Glycine is unique as it lacks a side chain (to be more precise the side chain is a hydrogen atom). It can, therefore, occur in all four quadrants of the Ramachandran plot. On the other hand, in proline phi is restricted to a value around -60°. In general, larger side chains result in more severe restrictions as compared to small ones. Mor information on amino acids can be obtained from the The Amino Acid Repository.