Background The Ramachandran plot
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…
What does a Ramachandran plot look like?
Figure: Ramachandran Plot showing two core regions (blue) and three allowed regions (green). The core regions (blue in the Figure) contain the most favorable combinations of φ and ψ and contain the greatest number of points. Plots of some proteins contain a small third core region in the upper right quadrant.
How to plot backbone dihedral angles on Ramachandran plot?
You can upload a PDB-formatted file to the server and the backbone dihedral angles will be plotted on our accurate Ramachandran Plot Instructions: Select a protein structure file in PDB format from your hard disk. Select Amino Acid type to show.
What is the Ramachandran plot for proline?
In contrast, the Ramachandran plot for proline, with its 5-membered-ring side chain connecting Cα to backbone N, shows a limited number of possible combinations of ψ and φ (see Pro plot in gallery ). The residue preceding proline ("pre-proline") also has limited combinations compared to the general case.
What stabilizes the ζ region of the Ramachandran plot?
In pre-proline, we analyse the origin of the ζ region of the Ramachandran plot, a region unique to pre-proline. We show that it is stabilized by a CO i-1 ···C δ H δi+1 weak hydrogen bond. This is analogous to the CO i-1 ···NH i+1 hydrogen bond that stabilizes the γ region in the generic 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 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 are torsion angles in proteins?
A torsion angle, also known as a dihedral angle, is formed by three consecutive bonds in a molecule and defined by the angle created between the two outer bonds. The backbone of a protein has three different torsion angles.
What is the Ramachandran plot and how are the bond angles used to understand protein structure?
All Answers (30) Ramachandran plot is when on x-axis You put value of phi torsion angle, and on y-axis psi angle is. Both from one residue of protein. By comparing position of your residue on that plot, with a model plot where allowed and favourite areas are marked You can evaluate structure of Your protein.
What is phi and psi angles in Ramachandran plot?
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.
What are torsion angles in molecular Modelling?
The torsion angle, also known as the dihedral angle, is the relative position, or angle, between the A-X bonds and the B-Y bonds when considering four atoms connected in the order A-X-Y-B. It can also be considered as the angle between two planes defined as A-X-Y and X-Y-B.
How do you read a torsion angle?
8:3313:08Torsional angle (dihedral angle) - YouTubeYouTubeStart of suggested clipEnd of suggested clipYou will find that four points and in each of the side this is a four point this is another fourMoreYou will find that four points and in each of the side this is a four point this is another four point so from that what you will find there will be two planes creating angles in this bond.
How do you find the torsional angle?
Torsion angle φ = Tor(p1, p2, p3, p4). The angle is measured in the plane perpendicular to b = p3 − p2. of the atoms. Let a = p2 − p1 (1) b = p3 − p2 c = p4 − p3.
Is torsional angle and dihedral angle same?
Dihedral angle and torsional angle are the same. Dihedral angle and torsional angle are the same.
How do you calculate psi and Phi angles?
As with any peptide the conformation of the backbone is determined by the values of two torsional angles. In sequence order, phi (φ) is the C(i-1),N(i),Ca(i),C(i) torsion angle and psi (ψ) is the N(i),Ca(i),C(i),N(i+1) torsion angle.
What are the torsional angles of amino acid residues in proteins?
All the amino acids have negative phi and psi angles, typical values being -60 degrees and -50 degrees, respectively.
What is dihedral angle of protein?
A dihedral angle of a protein is the internal angle of polypeptide backbone at which two adjacent planes meet. The conformation of the backbone can be described by two dihedral angles per residue, because the backbone residing between two juxtaposing Cα atoms are all in a single plane.
Drug Discovery Technologies
R.A. Laskowski, G.J. Swaminathan, in Comprehensive Medicinal Chemistry II, 2007
Polymers in Biology and Medicine
M. Wetzer, ... A.E. Barron, in Polymer Science: A Comprehensive Reference, 2012
Algorithms for Structure Comparison and Analysis: Homology Modelling of Proteins
Marco Wiltgen, in Encyclopedia of Bioinformatics and Computational Biology, 2019
Homology modeling: Developing 3D structures of target proteins missing in databases
Om Silakari, Pankaj Kumar Singh, in Concepts and Experimental Protocols of Modelling and Informatics in Drug Design, 2021
Applied Mycology and Biotechnology
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.
Biotechnology-based therapeutics
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 ).
G Protein Coupled Receptors
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 Ramachandran plot?
The Ramachandran plot. A special way for plotting protein torsion angles was introduced by Ramachandran and co-authors and since then is called the Ramachandran plot. The Ramachandran plot provides a way to view the distribution of torsion angles in a protein structure and shows that the torsion angles corresponding to the two major secondary ...
What is the third possible torsion angle?
The third possible torsion angle within the protein backbone (called omega, ω) describes the rotation at the peptide bond and is mostly flat and fixed to around 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 α-carbons and C, O, ...
How to read Ramachandran plot?
How to read Ramachandran plot? A Ramachandran plot is a way to visualize backbone dihedral angles ψ against φ of amino acid residues in protein structure. 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. A second is to show the empirical distribution of data points observed in a single structure .
Who is G N Ramachandran?
Gopalasamudram Narayana Ramachandran (8 October 1922 – 7 April 2001) is an Indian biophysicist and crystallographer who, along with Gopinath Kartha, worked out the triple helical structure of collagen. G N Ramachandran is an Indian biophysicist who was known for his work that led to his creation of the Ramachandran plot for understanding peptide ...
When was the torsional angle plot developed?
The 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, as for the image at left. Plotting the torsional angles in this way graphically shows which combination of angles is possible. What Is Peptide Linkage?
How to get Ramachandran in JSmol?
Right-click on an empty space of the JSmol panel showing the 3D structure on the page, or click on the JSmol logo (or frank) in the bottom right corner. When the menu comes up, select Console. Click in the lower text panel of the console that comes up and type the command Ramachandran, followed by the return key.
When was the torsional angle plot developed?
The plot was developed in 1963 by G. N. Ramachandran, et. al. by plotting the φ values on the x-axis and the ψ values on the y-axis, as for the image at left. 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 ...
Introductions about Ramachandran Plot Tutorial
According to the minimum contact distance between non-bonded atoms in the protein, Ramachandran plot determines which pair of dihedral angles (Φ, Ψ) stipulate the conformation of two adjacent peptide units are allowed and which are not allowed, and use Φ as the abscissa and Ψ as the ordinate, mark on the coordinate diagram, which is called Ramachandran plot, which can be used to identify whether the protein conformation is reasonable.
Tutorials
For protein simulation trajectories, gmx rama can be conveniently used to calculate the dihedral angles φ and ψ of peptide bonds, which are used to draw Ramachandran diagrams. This diagram is often used to characterize the secondary structure of the protein, and sometimes it is also used to evaluate whether the protein structure is reasonable.
Why rotate phi and psi?
Rotate Phi and Psi to find angle combinations where there are no clashes. In the early 1960’s, G. N. Ramachandran (University of Madras, India) and coworkers computationally determined the phi and psi angles that avoid steric collisions, initially treating the atoms simply as rigid spheres 5, 6 .
Why are Psi angles impossible?
In fact, most Phi and Psi angle combinations are impossible because two atoms cannot occupy the same space. Check Show Clashes to see where non-bonded atoms are overlapping, and thus in physically impossible positions. (This model simulation allows two atoms to overlap, unlike real atoms.) Check White to make clashes easier to see.
What is a Ramachandran plot?
The Ramachandran plot [ 1] is the 2d plot of the φ-ψ torsion angles of the protein backbone. It provides a simple view of the conformation of a protein. The φ-ψ angles cluster into distinct regions in the Ramachandran plot where each region corresponds to a particular secondary structure. There are four basic types of Ramachandran plots, depending on the stereo-chemistry of the amino acid: generic (which refers to the 18 non-glycine non-proline amino acids), glycine, proline, and pre-proline (which refers to residues preceding a proline [ 2 ]). The generic and proline Ramachandran plots are now well understood [ 3] but the glycine and pre-proline Ramachandran plots are not.
How many types of Ramachandran plots are there?
There are four basic types of Ramachandran plots, depending on the stereo-chemistry of the amino acid: generic (which refers to the 18 non-glycine non-proline amino acids), glycine, proline, and pre-proline (which refers to residues preceding a proline [ 2 ]).
Who Is G N Ramachandran?
Ramachandran Plot and Peptide Torsion Angles
- The figure below shows the three main chain torsion angles of a polypeptide. These are phi (ψ), psi (φ), and omega (w).
Secondary Structure Plot Regions
- 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 confirmation of the residues and, ultimately, repetitive values of ψ and φ. The different secondary structures can be distinguished by their range of ψ and φ values with the values of different secondary structures mapping to dif…
Plot Regions Limited by Steric Hindrance
- Most combinations of ψ and φ are sterically forbidden, as illustrated in the tripeptide, Glu-Ser-Ala. With Ser having values of ψ = -116o and φ = 55othe Ser side chain is in contact with Ala, colored blue. In plots of native peptides, the data points will form clusters in the several areas in which steric hindrance does not occur. 1. Mechanism of Eukaryotic DNA Replication 2. DNA Replicatio…
Ramachandran Plot Explanation
- (Smart Notes Description) How to read Ramachandran plot? A Ramachandran plot is a way to visualize backbone dihedral angles ψ against φ of amino acid residues in protein structure. 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 prot…
Final Words
- The nature of the covalent bonds in the polypeptide chain places constraints on the structure. The peptide bond exhibits partial double bond character that keeps the entire peptide group in a rigid planar configuration. The N-Cα and Cα-C bonds can rotate with bond angles Φ and Ψ, respectively. Secondary structure can be defined completely if the Φ and Ψ angles are known fo…
Secondary Structure Plot Regions
Plot Regions Limited by Steric Hindrance
- Since the 1990's, great expansion in the number and quality of macromolecular crystal structures and advances in methodology have greatly improved understanding of the energetically favored, allowed, and truly disallowed conformations of proteins and nucleic acids. The lower figure plots Ramachandran values for over a million general-case residues with resolution <2.0Å and backbo…
Plots of Proteins
- Myoglobin View of structure: Secondary structure consists of α-helix, loops and ordered, nonrepetitive structures. Ramachandran plot: Red data points outside of the area expected for α-helix most likely involve residues at the end of the α-helix because often these have angle values that are not typical for α-helix. White points are those for loops...