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Ramachandran plot
 
 
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A Ramachandran plot (also known as a Ramachandran map or a Ramachandran diagram), developed by Gopalasamudram Narayana Ramachandran, is a way to visualize dihedral angle
Dihedral angle

In geometry, the angle between two Plane s is called their dihedral or torsion angle.The dihedral angle of two planes can be seen by looking at the planes "edge on", i.e., along their line of intersection....
s φ against ψ of amino acid
Amino acid

In chemistry, an amino acid is a molecule containing both amine and carboxyl functional groups. These molecules are particularly important in biochemistry, where this term refers to alpha-amino acids with the general formula H2NCHRCOOH, where R is an organic substituent....
 residues in protein structure
Protein structure

Proteins are an important class of biological macromolecules present in all biological organisms, made up of such chemical element as carbon,hydrogen, nitrogen, oxygen, and sulphur....
. It shows the possible conformations of φ and ψ angles for a polypeptide.

Mathematically, the Ramachandran plot is the visualization of a function
Function (mathematics)

The mathematical concept of a function expresses dependence between two quantities, one of which is known and the other which is produced. A function associates a single output to each input element drawn from a fixed Set , such as the real numbers , although different inputs may have the same output....
 . The domain
Domain (mathematics)

In mathematics, the domain of a given function is the set of "input" values for which the function is defined. For instance, the domain of cosine would be all real numbers, while the domain of the square root would be only numbers greater than or equal to 0 ....
 of this function is the torus
Torus

In geometry, a torus is a surface of revolution generated by revolving a circle in three dimensional space about an axis coplanar with the circle, which does not touch the circle....
.






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A Ramachandran plot (also known as a Ramachandran map or a Ramachandran diagram), developed by Gopalasamudram Narayana Ramachandran, is a way to visualize dihedral angle
Dihedral angle

In geometry, the angle between two Plane s is called their dihedral or torsion angle.The dihedral angle of two planes can be seen by looking at the planes "edge on", i.e., along their line of intersection....
s φ against ψ of amino acid
Amino acid

In chemistry, an amino acid is a molecule containing both amine and carboxyl functional groups. These molecules are particularly important in biochemistry, where this term refers to alpha-amino acids with the general formula H2NCHRCOOH, where R is an organic substituent....
 residues in protein structure
Protein structure

Proteins are an important class of biological macromolecules present in all biological organisms, made up of such chemical element as carbon,hydrogen, nitrogen, oxygen, and sulphur....
. It shows the possible conformations of φ and ψ angles for a polypeptide.

Mathematically, the Ramachandran plot is the visualization of a function
Function (mathematics)

The mathematical concept of a function expresses dependence between two quantities, one of which is known and the other which is produced. A function associates a single output to each input element drawn from a fixed Set , such as the real numbers , although different inputs may have the same output....
 . The domain
Domain (mathematics)

In mathematics, the domain of a given function is the set of "input" values for which the function is defined. For instance, the domain of cosine would be all real numbers, while the domain of the square root would be only numbers greater than or equal to 0 ....
 of this function is the torus
Torus

In geometry, a torus is a surface of revolution generated by revolving a circle in three dimensional space about an axis coplanar with the circle, which does not touch the circle....
. Hence, the conventional Ramachandran plot is a projection of the torus on the plane, resulting in a distorted view and the presence of discontinuities.

One would 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 the β position has an influence. Glycine
Glycine

Glycine is the organic compound with the chemical formula NH2CH2COOH. It is the smallest of the 20 amino acids commonly found in proteins, coded by codons GGU, GGC, GGA and GGG....
 has a hydrogen atom, with a 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 demonstrate the physical consequences of...
, instead of a methyl group at the β position. Hence it is least restricted and this is apparent in the Ramachandran plot for Glycine for which the allowable area is considerably larger.

In contrast, the Ramachandran plot for proline
Proline

Proline is an a-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 humans can synthesize it....
 shows only a very limited number of possible combinations of ψ and φ.

The Ramachandran plot was calculated just before the first protein structures at atomic resolution were determined. Forty years later there were tens of thousands of high-resolution protein structures determined by X-ray crystallography 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. . The data, typically obtained by X-ray crystallography or Protein NMR and submitted by biologists and biochemistry from around the world, are released into the public domain, and can be accessed at no charge...
. From one thousand different protein chains, Ramachandran plots of over 200 000 amino acids were plotted, showing some significant differences, especially for glycine (Hovmöller et al 2002). The upper left region was found to be split into two; one to the left containing amino acids in beta sheets and one to the right containing the amino acids in random coil of this conformation.

One can also plot the dihedral angles in polysaccharide
Polysaccharide

Polysaccharides are relatively complex carbohydrates. They are polymers made up of many monosaccharides joined together by glycosidic bonds. They are therefore very large, often branched, macromolecules....
s and other polymers in this fashion. For the first two protein side-chain dihedral angles a similar plot is the Janin Plot
Janin Plot

A Janin plot is like the Ramachandran plot - a way to visualize dihedral angle distributions in the protein structures. While Ramachandran plot relates the two backbone dihedral angles, Janin plot relates the first side chain dihedral angle ?-1 against ?-2....
.

Software

  • STING
    Sting

    Gordon Matthew Thomas Sumner, Order of the British Empire , almost universally known by his stage name Sting, is an England musician from Wallsend in North Tyneside....
  • Pymol
    PyMOL

    PyMOL 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
  • VMD
    Visual Molecular Dynamics

    Visual molecular dynamics is a molecular modelling and visualization computer program. VMD is primarily developed as a tool for viewing and analyzing the results of molecular dynamics simulations, but it also includes tools for working with volumetric data, sequence data, and arbitrary graphics objects....
    , distributed with dynamic Ramachandran plot plugin
  • Sirius
    Sirius visualization software

    Sirius 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....
See also 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. . The data, typically obtained by X-ray crystallography or Protein NMR and submitted by biologists and biochemistry from around the world, are released into the public domain, and can be accessed at no charge...
 for a list of similar software.

External links