Ramachandran plot
Encyclopedia
Introduction and early history
A Ramachandran plot (also known as 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 backbone dihedral angleDihedral angle
In geometry, a dihedral or torsion angle is the angle between two planes.The dihedral angle of two planes can be seen by looking at the planes "edge on", i.e., along their line of intersection...
s ψ against φ of amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
residues in protein structure
Protein structure
Proteins are an important class of biological macromolecules present in all organisms. Proteins are polymers of amino acids. Classified by their physical size, proteins are nanoparticles . Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino...
.
The figure at left illustrates the definition of the φ and ψ backbone dihedral angles (called φ and φ' by Ramachandran). The ω angle at the peptide bond is normally 180°, since the partial-double-bond character keeps the peptide
Peptide
Peptides are short polymers of amino acid monomers linked by peptide bonds. They are distinguished from proteins on the basis of size, typically containing less than 50 monomer units. The shortest peptides are dipeptides, consisting of two amino acids joined by a single peptide bond...
planar. The figure at top right shows the allowed φ,ψ backbone conformational regions from the Ramachandran et al. 1963 and 1968 hard-sphere calculations: full radius in solid outline, reduced radius in dashed, and relaxed tau (N-Calpha-C) angle in dotted lines. Because dihedral angle
Dihedral angle
In geometry, a dihedral or torsion angle is the angle between two planes.The dihedral angle of two planes can be seen by looking at the planes "edge on", i.e., along their line of intersection...
values are circular and 0° is the same as 360°, the edges of the Ramachandran plot "wrap" right-to-left and bottom-to-top. For instance, the small strip of allowed values along the lower-left edge of the plot are a continuation of the large, extended-chain region at upper left.
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 theoretically favored regions.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. In practice this does not appear to be the case; only the methylene group at Cβ has a large influence. GlycineGlycine
Glycine is an organic compound with the formula NH2CH2COOH. Having a hydrogen substituent as its 'side chain', glycine is the smallest of the 20 amino acids commonly found in proteins. Its codons are GGU, GGC, GGA, GGG cf. the genetic code.Glycine is a colourless, sweet-tasting crystalline solid...
has only a hydrogen atom for its side chain, with a much smaller van der Waals radius
Van der Waals radius
The van der Waals radius, r, of an atom is the radius of an imaginary hard sphere which can be used to model the atom for many purposes. It is named after Johannes Diderik van der Waals, winner of the 1910 Nobel Prize in Physics, as he was the first to recognise that atoms had a finite size and to...
than the CH3, CH2, or CH group that starts all other amino acids. Hence it is least restricted, and this is apparent in the Ramachandran plot for glycine (see Gly plot at left) for which the allowable area is considerably larger. In contrast, the Ramachandran plot for proline
Proline
Proline is an α-amino acid, one of the twenty DNA-encoded amino acids. Its codons are CCU, CCC, CCA, and CCG. It is not an essential amino acid, which means that the human body can synthesize it. It is unique among the 20 protein-forming amino acids in that the α-amino group is secondary...
, with its 5-membered-ring side chain connecting Cα to backbone N, shows only a very limited number of possible combinations of ψ and φ (see Pro plot at left).
More recent updates
The first Ramachandran plot was calculated just after the first protein structure at atomic resolution was determined (myoglobinMyoglobin
Myoglobin is an iron- and oxygen-binding protein found in the muscle tissue of vertebrates in general and in almost all mammals. It is related to hemoglobin, which is the iron- and oxygen-binding protein in blood, specifically in the red blood cells. The only time myoglobin is found in the...
, 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
Crystallography
Crystallography is the experimental science of the arrangement of atoms in solids. The word "crystallography" derives from the Greek words crystallon = cold drop / frozen drop, with its meaning extending to all solids with some degree of transparency, and grapho = write.Before the development of...
and deposited in the Protein Data Bank (PDB)
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
. Many studies have taken advantage of this data to produce more detailed and accurate φ,ψ plots (e.g., Morris et al. 1992; Kleywegt & Jones 1996; Hooft et al. 1997; Hovmöller et al. 2002; Lovell et al. 2003). The three figures at left show the datapoints from a large set of high-resolution structures and contours for favored and for allowed conformational regions for the general case (all amino acids except Gly, Pro, and pre-Pro), for Gly, and for Pro. The most common regions are labeled: α for α helix
Alpha helix
A common motif in the secondary structure of proteins, the alpha helix is a right-handed coiled or spiral conformation, in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier...
, Lα for lefthanded helix, β for β-sheet
Beta sheet
The β sheet is the second form of regular secondary structure in proteins, only somewhat less common than the alpha helix. Beta sheets consist of beta strands connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet...
, and ppII for polyproline II.
Related conventions
One can also plot the dihedral angles in polysaccharidePolysaccharide
Polysaccharides are long carbohydrate molecules, of repeated monomer units joined together by glycosidic bonds. They range in structure from linear to highly branched. Polysaccharides are often quite heterogeneous, containing slight modifications of the repeating unit. Depending on the structure,...
s (e.g. with CARP; ) and other polymers in this fashion. For the first two protein side-chain dihedral angles a similar plot is the
Janin Plot
Janin Plot
In biochemistry, a Janin plot is like a Ramachandran plot — a way to visualize dihedral angle distributions in protein structures. While a Ramachandran plot relates the two backbone dihedral angles, a Janin plot relates the first side chain dihedral angle χ-1 against χ-2...
.
Software
- Ramachandran plot 2.0
- 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
- STINGSTINGSTING is a free Web-based suite of programs for a comprehensive analysis of the relationship between protein sequence, structure, function, and stability.STING is freely accessible at .-Sting Millennium:...
- PymolPyMOLPyMOL is an open-source, user-sponsored, molecular visualization system created by Warren Lyford DeLano and commercialized by DeLano Scientific LLC, which is a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities...
with the DynoPlot extension - VMDVisual Molecular Dynamics- External links :* * *...
, distributed with dynamic Ramachandran plot plugin - WHAT CHECK, the stand-alone validation routines from the WHAT IF softwareWHAT IF softwareWHAT IF is a computer program used in a wide variety of in silico macromolecular structure research fields such as:* Homology models of protein tertiary structures as well as quaternary structures,...
- UCSF ChimeraUCSF ChimeraUCSF Chimera is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality and can be created...
, found under the Model Panel. - SiriusSirius visualization softwareSirius is a molecular modeling and analysis system developed at San Diego Supercomputer Center. Sirius is designed to support advanced user requirements that go beyond simple display of small molecules and proteins...
- Swiss PDB Viewer
- TALOS
See also PDB for a list of similar software.