A protein contact map represents the distances between all possible aminoacid resid pairs in the
form of a matrix. Usually contact maps are defined in a binary manner: two residues are in contact
if their distances is below a certain threshold, and not in contact otherwise.
In ProteinTools we plot the raw distances to allow the user to get all the data.
The distance contact map of the protein TOP7
as rendered in ProteinTools.
Contact maps provide a 2 dimensional representation of a protein structures with the advantage that are
invariant to rotations and translations. Given their
similarity with images, they have been exploited by machine learning
methods [1]. They are also incredible powerful, as it is possible to reconstruct the 3D
coordinates of a protein using a contact map [2].
References
[1] Gobel, U.; et al. (1994). "Correlated mutations and residue contacts in proteins". Proteins. 18 (4): 309–317. doi:10.1002/prot.340180402. PMID 8208723. S2CID 14978727.
[2] Pietal, MJ. Bujnicki, JM. Kozlowski, LP. (Jun 2015). "GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function". Bioinformatics. 31 (21): 3499–505. doi:10.1093/bioinformatics/btv390. PMID 26130575.
