Protein contact map

Protein contact map

A protein contact map represents the distance between every two residues of a three-dimensional protein structure using a binary two-dimensional matrix. For two residues i and j, the ij 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 Angstrom; distance between or Cβ-Cβ atoms with threshold 6-12 Angstrom (Cα is used for Glycine) or consideration of any atom and lower threshold 4.5-6 Angstrom.

Such matrices 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 [Marco Vassura, Luciano Margara, Pietro Di Lena, Filippo Medri, Piero Fariselli and Rita Casadio, Reconstruction of 3D Structures from Protein Contact Maps, IEEE TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, (Accepted)] .

Contact maps are also used for protein superimposition and to describe similarity between protein structures [Holm, L. & Sander, C. Mapping the protein universe. Science, 1996, 273, 595-603] . They are either predicted from protein sequence or calculated from a given structure.

Recently contact maps are predicted for membrane proteins where helix-helix interactions are targeted.

ee also

*Ramachandran plot
*Structural classification of proteins, CATH
*HB plot

External links

* [http://www.sbc.su.se/~maccallr/contactmaps/ GPCPRED]
* [http://distill.ucd.ie/distill/ DISTILL]
* [http://www.igb.uci.edu/?page=tools&subPage=psss Structural Proteomics Tools]
* [http://rostlab.org/services/profcon/index.php ProfCon]
* [http://webclu.bio.wzw.tum.de/tmhcon/ TMHcon]


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