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 a 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 acid residues in protein structure.
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 Ramachandran plot for p27 SJ?
The Ramachandran plot for p27 SJ using RAMPAGE software revealed that among the 263 residues, 259 (99.2%) were in favoured region, 2 (0.8%) were in allowed region and 0 (0.0%) were in disallowed region proving that the predicted model is acceptable (Fig. 1).
What is a PCNA Ramachandran plot?
A Ramachandran plot generated from human PCNA, a trimeric DNA clamp protein that contains both β-sheet and α-helix ( PDB ID 1AXC). The red, brown, and yellow regions represent the favored, allowed, and "generously allowed" regions as defined by ProCheck A Ramachandran plot can be used in two somewhat different ways.
What is the angle of a Ramachandran plot?
When was the Ramachandran plot first calculated?
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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).
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.
Why is proline Ramachandran plot different?
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.
How do you make a Ramachandran plot in Pymol?
1:1321:55How to generate a Ramachandran plot using PyMol (extension ...YouTubeStart of suggested clipEnd of suggested clipYou'll have to click on fetch. And it asks you pymol will now download executable code from theMoreYou'll have to click on fetch. And it asks you pymol will now download executable code from the internet. Proceed you say yes. And in the next window it shows in which directory.
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 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.
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.
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.
Where is proline found in Ramachandran plot?
Proline has restrictions in phi-psi space that arise from the 5-membered ring. Phi is restricted to approxamatly -60 by the ring and psi angles fall into two groupings near -45 and +135 in the helical and sheet regions of the Ramachandran plot.
What are psi and phi angles?
The alpha carbon (Cα) in the center of each amino acid is held in the main chain by two rotatable bonds. The dihedral (torsion) angles of these bonds are called3 Phi and Psi (in Greek letters, φ and ψ).
What are outliers in Ramachandran?
Ramachandran outliers are those amino acids with non-favorable dihedral angles, and the Ramachandran plot is a powerful tool for making those evident. Most of the time, Ramachandran outliers are a consequence of mistakes during the data processing.
Torsion Angles and the Ramachnadran Plot in Protein Structures
Definition Two torsion angles in the polypeptide chain, also called Ramachandran angles (after the Indian physicist who worked on modeling the interactions in polypeptide chains, Ramachandran, GN, et al., J Mol Biol, 7:95-99) describe the rotations of the polypeptide backbone around the bonds between N-Cα (called Phi, φ) and Cα-C (called Psi, ψ, see image for the graphics view of the angles).
The Ramachandran plots of glycine and pre-proline | BMC Structural ...
The Ramachandran plot is a fundamental tool in the analysis of protein structures. Of the 4 basic types of Ramachandran plots, the interactions that determine the generic and proline Ramachandran plots are well understood. The interactions of the glycine and pre-proline Ramachandran plots are not. In glycine, the ψ angle is typically clustered at ψ = 180° and ψ = 0°.
Ramachandran Plot - an overview | ScienceDirect Topics
The Verify3D also uses the knowledge of the structural database of proteins and it predicts the compatibility of a 3D structure with the 1D amino acid sequence based on its structure assignments, such as loops, sheets, alpha-helix, and others (Eisenberg, Lüthy, & Bowie, 1997).It compares the quality of modeled protein with high-resolution protein structures from the database.
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 ...
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.
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In evaluating the model there are many different aspects to consider; the residue placement, the interaction of neighbouring residues and the atoms within the residues.
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In silico drug design plays a vital role in target identification and designing novel drugs in the field of biotechnology. They mainly used to inspect the expression of genes, sequence analysis, molecular modeling, and their 3D structure ( Wadood et al., 2013 ).
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This first stage generates an initial set of loop conformations via a dihedral angle search. Residues are added sequentially from both loop stems, and the process terminates at the middle (closure) residue. Thousands of loop halves are generated, and if two meet at the closure residue, these two comprise a loop candidate.
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 ...
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.
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