Ramachandran plots

The angle pairs iji and <)/ are usually plotted against each other in a diagram called a Ramachandran plot after the Indian biophysicist G.N. Ramachandran who first made calculations of sterically allowed regions. Figure 1.7 shows the results of such calculations and also a plot for all amino... 

Ramachandran plot (see Figure 1.7a). The a helix has 3.6 residues per turn with hydrogen bonds between C =0 of residue n and NH of residue n + 4 (Figure 2.2). Thus all NH and C O groups are joined with hydrogen bonds except the first NH groups and the last C O groups at the ends of the a helix. As a consequence, the ends of a helices are polar and are almost always at the surface of protein molecules. 

G. N. Ramachandran and his coworkers in Madras, India, first showed that it was convenient to plot (p values against i/t values to show the distribution of allowed values in a protein or in a family of proteins. A typical Ramachandran plot is shown in Figure 6.4. Note the clustering of (p and i/t values in a few regions of the plot. Most combinations of (p and i/t are sterically forbidden, and the corresponding regions of the Ramachandran plot are sparsely populated. The combinations that are sterically allowed represent the subclasses of structure described in the remainder of this section. 

Choose any three regions in the Ramachandran plot and discuss the likelihood of observing that combination of [Pg.207]

Make a plot of / (vertical axis) vs. (j) (horizontal axis) with /=0, ( )=0 in the middle and ranging from -180° to 180° for both variables. Put a point on your plot for each dihedral angle (in each conformer). You have constructed what is now known as a Ramachandran plot. 

Fig. 8. A Ramachandran plot (37) indicating the overall geometrical quality of the structure of the Fepr protein from D. vulgaris at 1.7 A resolution. Some 94% of the residues lie within the most favored regions, 5.5% in the additional allowed regions, and only one residue, N303 on the border of a disallowed region. The electron density of this residue is very well defined (see text).

Regions of ordered secondary structure arise when a series of aminoacyl residues adopt similar phi and psi angles. Extended segments of polypeptide (eg, loops) can possess a variety of such angles. The angles that define the two most common types of secondary structure, the a helix and the (5 sheet, fall within the lower and upper left-hand quadrants of a Ramachandran plot, respectively (Figure 5-1). 

Figure 5-1. Ramachandran plot of the main chain phi (< ) and psi (T) angles for approximately 1000 nonglycine residues in eight proteins whose structures were solved at high resolution. The dots represent allowable combinations and the spaces prohibited combinations of phi and psi angles. (Reproduced, with permission, from Richardson JS The anatomy and taxonomy of protein structures. Adv Protein Chem 1981 34 167.)...

A detailed quantitative analysis of the preferences of amino acids in folded proteins for different regions of the Ramachandran plot reveals that the 18 nonglycine, nonproline residues exhibit different preferences (Shortle, 2002). Figure 5 shows the range of relative propensities displayed by these 18 amino acids for a somewhat arbitrary subdivision... 

Fig. 44. Distribution of Ala in the Ramachandran plot when using (A) all secondary structure conformations in the protein database or (B) only those Ala residues in a coil conformation. (From Serrano, 1995. 1995, with permission from Academic Press.)...

Fig. 4. Ramachandran plots of glutamines (A) making side chain-to-backbone hydrogen bonds with the next residue in sequence (B). Filled circles denote residues where the glutamine is in the PPII conformation. Open circles denote all residues where the glutamine is not in the PPII conformation.

Fig. 6. Ramachandran plots for simulated Ac-Ala-Xaa-Ala-Ala-NMe peptides with Xaa = glutamine or asparagine, with a constrained side chain-to-backbone hydrogen bond. Conformational distribution for glutamine i (A) and for the residue i +1 to which the glutamine is hydrogen-bonded (B). Conformational distribution for asparagine i (C) and for the residue i +1 to which it is hydrogen-bonded (D).

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