The Ramachandran Plot

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]

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.)...

NNN (normal face, thin underline) residues in core //- or allowed //-region of the Ramachandran plot. 

Yes. These values put the right-handed a helix into a particularly favorable area of the Ramachandran plot, indicated in Fig. 4-5 with the symbol aR. 

What is meant by the statement that a particular conformation of an amino acid residue lies in an unfavorable region of the Ramachandran plot ... 

The average of these converged structures is taken as the protein structure, whose precision can be assessed by the deviations of the individual structures from the average. The quality of the final structure can be described in terms of this root mean square deviation, for both the peptide backbone and side chains, and to some extent by the extent to which it conforms to limitations of dihedral bond angles and interatomic contacts anticipated from thousands of previously known structures (the Ramachandran plot ). By all criteria, NMR structures of proteins that are determined in this way are comparable to structures determined by x-ray crystallography. In addition, NMR methods can be applied to evaluate the... 

Hruby VJ, Nikiforovich GV (1991) The Ramachandran Plot and Beyond Conformational and Topographical Considerations in the Design of Peptides and Proteins. In Molecular Conformation and Biological Interactions (Balaram P and Ramasehan S, eds) pp 429 45. Bangalore Indian Academy of Sciences. 

Sasisekharan, first performed such an analysis. The Ramachandran plot in Figure 12.27 shows peptide torsion angles for D-xylose isomerase. " ... 

R denotes the region of the conformational space of the Ramachandran plot occupied by the given residue ne, nonallowed for nonglycine residues. 

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