Ramachandran plot
A Ramachandran plot (also known as a Rama plot, a Ramachandran diagram or a [φ,ψ] plot), originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, is a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino a…
Full Answer
What is Ramachandran plot analysis?
Ramachandran plot analysis. Volume, Area, Dihedral Angle Reporter. Includes excluded volume, accessible surface area, backbone and side chain dihedral angles, secondary structure, hydrogen bonding partners, hydrogen bond energies, steric quality, solvation free energy as well as local and overall fold quality.
How many plots are there in Rampage?
This even more beautiful figure is from RAMPAGE, and shows the four plots combined. It was extracted from this output which also contains the data as four separate figures:
How do side chains affect the Ramachandran plot?
Either case is usually shown against outlines for the theoretically favored regions. One might expect that larger side chains would result in more restrictions and consequently a smaller allowable region in the Ramachandran plot, but the effect of side chains is small.
What is the percentage of residues in Ramachandran plot?
From Ramachandran plot analysis the portion of residues falling into the most favored regions is calculated to be 69.5%. The 3-D model so designed may be further characterized, analyzed and illustrated using other modeling techniques. Join ResearchGate to access over 30 million figures and 135+ million publications – all in one place.
What does Ramachandran plot tell you?
The Ramachandran plot shows the statistical distribution of the combinations of the backbone dihedral angles ϕ and ψ. In theory, the allowed regions of the Ramachandran plot show which values of the Phi/Psi angles are possible for an amino acid, X, in a ala-X-ala tripeptide (Ramachandran et al., 1963).
What is Ramachandran plot and write its significance?
The Ramachandran plot is a plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in a peptide. In sequence order, φ is the N(i-1),C(i),Ca(i),N(i) torsion angle and ψ is the C(i),Ca(i),N(i),C(i+1) torsion angle. The plot was developed in 1963 by G. N. Ramachandran, et.
How do you plot a Ramachandran plot?
Instructions:Select a protein structure file in PDB format from your hard disk.Select Amino Acid type to show.Check the boxes for Glycine, Verbosity, and Labels as desired.Click the GO! button.
What does the Ramachandran plot say about Proline?
The proline Ramachandran plot is severely restricted by the pyrrolidine ring, where the flexibility in the pyrrolidine ring couples to the backbone [14]. The observed glycine Ramachandran plot has a distinctive distribution (Figure 1A) quite different to the generic Ramachandran plot.
What are the principles underlying the formation of the Ramachandran plot?
Answer : The Ramachandran principle says that alpha helices, beta strands and turns are the most likely conformations for a polypeptide chain to adopt because most other conformations are impossible due to steric collisions between atoms.
Which is the first quadrant in Ramachandran plot?
The Ramachandran Plot helps with determination of secondary structures of proteins. Quadrant I shows a region where some conformations are allowed. This is where rare left-handed alpha helices lie.
Which is correct regarding the peptides in the Ramachandran plot?
Peptides that are unstructured will have all the backbone dihedral angles in the. disallowed regions.
What is Ramachandran plot PDF?
Ramachandran plot provides a simple two-dimensional graphic. representation of all possible protein structures in terms of torsion angles. Although the plot was developed using theoretical. methods, mathematical calculations and models building, once the protein structure began to discover, the importance.
What are allowed and disallowed regions in Ramachandran plot?
The 3(10) helix occurs close to the upper right of the alpha-helical region and is on the edge of allowed region indicating lower stability. Disallowed regions generally involve steric hindrance between the side chain C-beta methylene group and main chain atoms.
Why do Ramachandran plots exclude glycine and proline?
The quick answer I always give is that they exist at the two extreme ends of the spectrum in terms of phi/psi rotation (which is what the Ramachandran plot shows). Gly is the least restricted, Pro is the most restricted. Thus Gly can appear anywhere & Pro only in certain places.
What is the one amino acid that is found in more places in the Ramachandran plot than any other amino acid?
Glycine – has no Beta carbon atom, i.e. no side chain. Therefore it is the least sterically hindered as compared to other amino acids. This fact permits it to cover a large range of area in the plot.
Why are proline and glycine helix breakers?
Proline lacks an amide proton when found within proteins. This precludes hydrogen bonding between it and hydrogen bond acceptors, and thus often restricts the Pro residue to the first four positions of an α helix.
What is Ramachandran plot Wikipedia?
Ramachandran, C. Ramakrishnan, and V. Sasisekharan, is a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure. The figure on the left illustrates the definition of the φ and ψ backbone dihedral angles (called φ and φ' by Ramachandran).
What is Ramachandran plot PDF?
Ramachandran plot provides a simple two-dimensional graphic. representation of all possible protein structures in terms of torsion angles. Although the plot was developed using theoretical. methods, mathematical calculations and models building, once the protein structure began to discover, the importance.
What is Ramachandran plot Slideshare?
The Ramachandran Plot • The two torsion angles of the polypeptide chain, describe the rotations of the polypeptide backbone around the bonds between N-Cα (called Phi, φ) and Cα-C (called Psi, ψ) • It provides an easy way to view the distribution of torsion angles of a protein structure.
Who discovered Ramachandran plot?
Gopalasamudram Narayanan RamachandranGopalasamudram Narayanan Ramachandran, or G.N. Ramachandran, FRS (8 October 1922 – 7 April 2001) was an Indian physicist who was known for his work that led to his creation of the Ramachandran plot for understanding peptide structure. He was the first to propose a triple-helical model for the structure of collagen.
When was the Ramachandran plot first calculated?
The first Ramachandran plot was calculated just after the first protein structure at atomic resolution was determined ( myoglobin, in 1960 ), although the conclusions were based on small-molecule crystallography of short peptides.
What is the angle of a Ramachandran plot?
All three angles are at 180° in the conformation shown. In biochemistry, a Ramachandran plot (also known as a Rama plot, a Ramachandran diagram or a [φ,ψ] plot ), originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, is a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ ...
Overview
In biochemistry, a Ramachandran plot (also known as a Rama plot, a Ramachandran diagram or a [φ,ψ] plot), originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, is a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure. The figure on the left illustrates the definitio…
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 (as at right, here) in usage for structure validation, or else in a database of many structures (as in the lower 3 plots at left). Either case is usually shown against outlines for the th…
Amino-acid preferences
One might expect that larger side chains would result in more restrictions and consequently a smaller allowable region in the Ramachandran plot, but the effect of side chains is small. In practice, the major effect seen is that of the presence or absence of the methylene group at Cβ. Glycine has only a hydrogen atom for its side chain, with a much smaller van der Waals radius than the CH3, CH2, or CH group that starts the side chain of all other amino acids. Hence it is least re…
More recent updates
The first Ramachandran plot was calculated just after the first protein structure at atomic resolution was determined (myoglobin, in 1960 ), although the conclusions were based on small-molecule crystallography of short peptides. Now, many decades later, there are tens of thousands of high-resolution protein structures determined by X-ray crystallography and deposited in the Protein Data Bank (PDB). Many studies have taken advantage of this data to produce more detai…
Related conventions
One can also plot the dihedral angles in polysaccharides (e.g. with CARP).
Gallery
• Ramachandran plot for the general case; data from Lovell 2003
• Ramachandran plot for Glycine
• Ramachandran plot for Proline
• Ramachandran plot for pre-Proline
Software
• Web-based Structural Analysis tool for any uploaded PDB file, producing Ramachandran plots, computing dihedral angles and extracting sequence from PDB
• Web-based tool showing Ramachandran plot of any PDB entry
• MolProbity web service that produces Ramachandran plots and other validation of any PDB-format file
Further reading
• Richardson, J.S. (1981). "The Anatomy and Taxonomy of Protein Structure". Anatomy and Taxonomy of Protein Structures. Advances in Protein Chemistry. Vol. 34. pp. 167–339. doi:10.1016/S0065-3233(08)60520-3. ISBN 9780120342341. PMID 7020376., available on-line at Anatax
• Branden, C.-I.; Tooze, J. (1991), Introduction to Protein Structure, Garland Publishing, NY, ISBN 0-8153-0344-0