Torsion Angles and the Ramachandran Plot, Allowed

and Disallowed Regions

Next part of this overview will be on torsion angles, which are also called Ramachandran angles (RAMACHANDRAN GN, RAMAKRISHNAN C, SASISEKHARAN
V., J Mol Biol., 7:95-99).
The two torsion angles phi and psi describe the rotation of the polypeptide around the two bonds on both sides of the Ca atom:

Different secondary structure elements have their characteristic torsion angles, which can be visualized using the Ramachandran plot (on the left plot the
region marked alpha is for alpha-helices and the beta is for beta-sheet regions):

Each dot on the Ramachandran plot shows the phi and psi values for an amino acid in the protein in question. The horizontal axis are phi
value, while the vertical shows psi values. Notice that the counting in the left hand corner starts from -180 degrees and extends to +180 for
both axes. This is a convenient presentation and allows clear distinction of the characteristic regions of alpha-helices and beta-sheets. The
regions on the plot with the highest density of dots are the so called allowed regions of the Ramachandran plot, also called low-energy
regions. Some values of phi and psi can be forbidden for an amino acid to adopt. The reason is that for some torsion angles the atoms within
the polypeptide chain will come too close to each other, a so-called "steric clash", which would result in very high energy of the system. On
the Ramachandran plot such regions can be easily distinguished: For a high-quality experimental structure these regions are simply empty or
almost empty. Very few amino acid residues in a protein have their torsion angles within these regions. But there are exclusions from this
rule. Sometimes such values can be found and they most probably will result in some strain in the polypeptide chain. In such cases additional
interactions must be present to stabilize such structures. They may have functional significance and may be conserved within a protein family,
which may be related to possible conformational dynamics of the structure, as suggested by Pal and Chakrabarti, 2002.

Another exception from the principle of clustering around the alpha- and beta-regions can be seen on the right plot of the above figure. In
this case the Ramachandran plot shows torsion angle distribution for one single residue, glycine. Glycine does not have a side chain and, as
mentioned earlier in the discussion of the basics principles of protein structure, it provides high flexibility to the polypeptide chain. By other
words, it may adopt torsion angles, which are normally not allowed for other amino acids. That is why glycines are often found in loop
regions, where the polypeptide chain makes a sharp turn. This is also the reason for the high conservation of glycine residues, since turns are
important for the preservation of the particular fold of the protein structure.

Theoretically, the average phi and psi values for alpha-helices and beta-sheets should be clustered around -57, -47 and -80, +150,
respectively. However, for real experimental structures these values were found to be different. A detailed discussion of the fine structure of
phi- and psi-angle distribution in the Ramachandran plot can be found in the work by Hovmöller at al., 2002.

The Ramachndran plot and the quality of a protein structure

In cases when the protein X-ray structure was not properly refined, and even for bad or wrong homology models, we may find torsion angles
in disallowed regions of the Ramachandran plot. Usually these deviations indicate problems with the structure, suggesting that the
Ramachandran plot may be used in assessing the quality of experimental structures or structures built using homology modeling. The figure
below shows two Ramachandran plots for the same protein structure. Red regions indicate low-energy regions, brown allowed regions, yellow
the so-called generously-allowed regions and pale-yellow marks disallowed regions. The structure used to generate the plot on the left is at
2.9 Å and was not properly refined (it is an old structure from the early days of protein crystallography). The structure used to generate the
plot on the right is more recent and was refined against 1.8 Å resolution X-ray data. You may notice that the torsion angles on the left plot
lack real clustering around secondary structure regions and show a much wider distribution, compared the the plot on the right (also
compared to the left plot on the figure above). There are also many dots in the disallowed regions on the left plot and almost none on the
right (the ones which are seen are for glycine residues):

Thus, the Ramachandran plot provides valuable information on the quality of a protein structure and gives some additional insights into the
relationships between the amino acid sequence and the three-dimensional protein structure.
There will be further discussions of other aspects related to the quality of experimental protein structures, and the quality of homology
models.
In the next section we will move to discuss common motifs. Using the following link you may leave the Ramachandran plot part and return to
the summary of the protein