Four Distances between Pairs of Amino Acids Provide a Precise Description of their Interaction Export

@article{citeulike:5436847, abstract = {The three-dimensional structures of proteins are stabilized by the interactions between amino acid residues. Here we report a method where four distances are calculated between any two side chains to provide an exact spatial definition of their bonds. The data were binned into a four-dimensional grid and compared to a random model, from which the preference for specific four-distances was calculated. A clear relation between the quality of the experimental data and the tightness of the distance distribution was observed, with crystal structure data providing far tighter distance distributions than NMR data. Since the four-distance data have higher information content than classical bond descriptions, we were able to identify many unique inter-residue features not found previously in proteins. For example, we found that the side chains of Arg, Glu, Val and Leu are not symmetrical in respect to the interactions of their head groups. The described method may be developed into a function, which computationally models accurately protein structures.}, author = {Cohen, Mati and Potapov, Vladimir and Schreiber, Gideon}, citeulike-article-id = {5436847}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1000470}, day = {14}, doi = {10.1371/journal.pcbi.1000470}, journal = {PLoS Comput Biol}, keywords = {amino\_acids, distances, interactions, pairs, plos, sep09}, month = {August}, number = {8}, pages = {e1000470+}, posted-at = {2009-10-07 14:08:56}, priority = {2}, publisher = {Public Library of Science}, title = {Four Distances between Pairs of Amino Acids Provide a Precise Description of their Interaction}, url = {http://dx.doi.org/10.1371/journal.pcbi.1000470}, volume = {5}, year = {2009} }

TY - JOUR ID - citeulike:5436847 L3 - citeulike-article-id:5436847 N2 - The three-dimensional structures of proteins are stabilized by the interactions between amino acid residues. Here we report a method where four distances are calculated between any two side chains to provide an exact spatial definition of their bonds. The data were binned into a four-dimensional grid and compared to a random model, from which the preference for specific four-distances was calculated. A clear relation between the quality of the experimental data and the tightness of the distance distribution was observed, with crystal structure data providing far tighter distance distributions than NMR data. Since the four-distance data have higher information content than classical bond descriptions, we were able to identify many unique inter-residue features not found previously in proteins. For example, we found that the side chains of Arg, Glu, Val and Leu are not symmetrical in respect to the interactions of their head groups. The described method may be developed into a function, which computationally models accurately protein structures. IS - 8 JF - PLoS Comput Biol TI - Four Distances between Pairs of Amino Acids Provide a Precise Description of their Interaction PB - Public Library of Science VL - 5 SP - e1000470 KW - amino_acids KW - distances KW - interactions KW - pairs KW - plos KW - sep09 AU - Cohen, Mati AU - Potapov, Vladimir AU - Schreiber, Gideon PY - 2009/08/14/ UR - http://dx.doi.org/10.1371/journal.pcbi.1000470 ER -