Protein contact map
Encyclopedia
A protein contact map represents the distance between all possible residue pairs of a three-dimensional protein structure
using a binary two-dimensional matrix. For two residues
and 
, the 
element of the matrix is 1 if the two residues are closer than a predetermined threshold, and 0 otherwise. Various contact definitions have been proposed: The distance between the Cα-Cα atom with threshold 6-12 Å
; distance between Cβ-Cβ atoms with threshold 6-12 Å (Cα is used for Glycine
); distance between the side-chain centers of mass
; distance between the Van der Waals radius
of selected atoms; or consideration of any atom and lower threshold 4.5-6 Å.
Contact maps provide a more reduced representation of a protein structure than its full 3D atomic coordinates. The advantage is that contact maps are invariant to rotations and translations. They are more easily predicted by machine learning
methods. It has also been shown that under certain circumstances it is possible to reconstruct the 3D coordinates of a protein using its contact map.
Contact maps are also used for protein superimposition
and to describe similarity between protein structures.. They are either predicted from protein sequence or calculated from a given structure.
Contact maps have been used in the prediction of membrane proteins where helix-helix interactions are targeted.
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...
using a binary two-dimensional matrix. For two residues
and , the element of the matrix is 1 if the two residues are closer than a predetermined threshold, and 0 otherwise. Various contact definitions have been proposed: The distance between the Cα-Cα atom with threshold 6-12 ÅÅngström
The angstrom or ångström, is a unit of length equal to 1/10,000,000,000 of a meter . Its symbol is the Swedish letter Å....
; distance between Cβ-Cβ atoms with threshold 6-12 Å (Cα is used for Glycine
Glycine
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...
); distance between the side-chain centers of mass
Center of mass
In physics, the center of mass or barycenter of a system is the average location of all of its mass. In the case of a rigid body, the position of the center of mass is fixed in relation to the body...
; distance between the 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...
of selected atoms; or consideration of any atom and lower threshold 4.5-6 Å.
Contact maps provide a more reduced representation of a protein structure than its full 3D atomic coordinates. The advantage is that contact maps are invariant to rotations and translations. They are more easily predicted by machine learning
Machine learning
Machine learning, a branch of artificial intelligence, is a scientific discipline concerned with the design and development of algorithms that allow computers to evolve behaviors based on empirical data, such as from sensor data or databases...
methods. It has also been shown that under certain circumstances it is possible to reconstruct the 3D coordinates of a protein using its contact map.
Contact maps are also used for protein superimposition
Superimposition
In graphics, superimposition is the placement of an image or video on top of an already-existing image or video, usually to add to the overall image effect, but also sometimes to conceal something .This technique is used in cartography to produce photomaps by superimposing grid lines, contour lines...
and to describe similarity between protein structures.. They are either predicted from protein sequence or calculated from a given structure.
Contact maps have been used in the prediction of membrane proteins where helix-helix interactions are targeted.
See also
- Ramachandran plotRamachandran plot-Introduction and early history:A Ramachandran plot , originally developed in 1963 by G. N. Ramachandran C. Ramakrishnan and V...
- Structural classification of proteinsStructural Classification of ProteinsThe Structural Classification of Proteins database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences. A motivation for this classification is to determine the evolutionary relationship between proteins...
- CATHCATHThe CATH Protein Structure Classification is a semi-automatic, hierarchical classification of protein domains published in 1997 by Christine Orengo, Janet Thornton and their colleagues....
- HB plotHB plotKnowledge of the relationship between a protein's structure and its dynamic behavior is essential for understanding protein function. The description of a protein three dimensional structure as a network of hydrogen bonding interactions was introduced as a tool for exploring protein structure and...
- Dot plot (bioinformatics)Dot plot (bioinformatics)A dot plot is a graphical method that allows the comparison of two biological sequences and identify regions of close similarity between them. It is a kind of recurrence plot.-Introduction:...
External links
- GPCPRED — a web based contact prediction server
- DISTILL — prediction of protein structural features (including protein residue contact maps)
- Structural Proteomics Tools — includes amino acid contact maps
- ProfCon — prediction of inter-residue contacts
- TMHcon — prediction of helix-helix contacts specifically within the transmembrane parts of membrane proteins
- TMhit — A new transmembrane helix-helix interaction prediction method based on residue contacts
- CMAPpro — A protein contact map prediction server