Ramachandran Plotting

BioCodeKb - Bioinformatics Knowledgebase

The Ramachandran plot was developed in 1963 by G. N. Ramachandran, by plotting the φ values on the x-axis and the ψ values on the y-axis. Plotting the torsional angles in this way graphically shows which combination of angles are possible. The torsional angles of each residue in a peptide define the geometry of its attachment to its two adjacent residues by positioning its planar peptide bond relative to the two adjacent planar peptide bonds, thereby the torsional angles determine the conformation of the residues and the peptide. Many of the angle combinations, and therefore the conformations of residues, are not possible because of steric hindrance. By making a Ramachandran plot, protein structural scientists can determine which torsional angles are permitted and can obtain insight into the structure of peptides.


The two torsion angles of the polypeptide chain, also called Ramachandran angles, describe the rotations of the polypeptide backbone around the bonds between N-Cα (called Phi, φ) and Cα-C (called Psi, ψ). The Ramachandran plot provides an easy way to view the distribution of torsion angles of a protein structure. It also provides an overview of allowed and disallowed regions of torsion angle values, serving as an important factor in the assessment of the quality of protein three-dimensional structures.


Torsion angles are among the most important local structural parameters that control protein folding - essentially, if we would have a way to predict the Ramachandran angles for a particular protein, we would be able to predict its 3D structure. The reason is that these angles provide the flexibility required for folding of the polypeptide backbone, since the third possible torsion angle within the protein backbone (called omega, ω) is essentially flat and fixed to 180 degrees. This is due to the partial double-bond character of the peptide bond, which restricts rotation around the C-N bond, placing two successive alpha-carbons and C, O, N and H between them in one plane. Thus, rotation of the main chain (backbone) of a protein can be described as the rotation of the peptide bond planes relative to each other.


Regions in plot

  • Quadrant I shows a region where some conformations are allowed. This is where rare left-handed alpha helices lie.

  • Quadrant II shows the biggest region in the graph. This region has the most favorable conformations of atoms. It shows the sterically allowed conformations for beta strands.

  • Quadrant III shows the next biggest region in the graph. This is where right-handed alpha helices lie.

  • Quadrant IV has almost no outlined region. This conformation(ψ around -180 to 0 degrees, φ around 0-180 degrees) is disfavored due to steric clash.


Secondary structures of a peptide are segments of the peptide that have ordered and repetitive structure, and the repetitive structure is due to a repetitive conformation of the residues and, ultimately, repetitive values of φ and ψ. The different secondary structures can be distinguished by their range of φ and ψ values with the values of different secondary structures mapping to different regions of the Ramachandran plot.


Uses

A Ramachandran plot can be used in two somewhat different ways. One is to show in theory which values, or conformations, of the ψ and φ angles are possible for an amino-acid residue in a protein (as at top right). A second is to show the empirical distribution of datapoints observed in a single structure in usage for structure validation, or else in a database of many structures. Either case is usually shown against outlines for the theoretically favored regions.

Need to learn more about Ramachandran Plotting and much more?

To learn Bioinformatics, analysis, tools, biological databases, Computational Biology, Bioinformatics Programming in Python & R through interactive video courses and tutorials, Join BioCode.

Get in touch with us

Tel: +92 314 7785980

Email: Contact@BioCode.ltd

  • Black Instagram Icon
  • Facebook

© Copyright 2020 BioCode Ltd. - All rights reserved.