Predicting absolute contact numbers of native protein structure from amino acid sequence.
The contact number of an amino acid residue in a protein structure is defined by the number of C(beta) atoms around the C(beta) atom of the given residue, a quantity similar to, but different from, solvent accessible surface area. We present a method to predict the contact numbers of a protein from its amino acid sequence. The method is based on a simple linear regression scheme and predicts the absolute values of contact numbers. When single sequences are used for both parameter estimation and cross-validation, the present method predicts the contact numbers with a correlation coefficient of 0.555 on average. When multiple sequence alignments are used, the correlation increases to 0.627, which is a significant improvement over previous methods. In terms of discrete states prediction, the accuracies for 2-, 3-, and 10-state predictions are, respectively, 71.4%, 54.1%, and 18.9% with residue type-dependent unbiased thresholds, and 76.3%, 59.2%, and 21.8% with residue type-independent unbiased thresholds. The difference between accessible surface area and contact number from a prediction viewpoint and the application of contact number prediction to three-dimensional structure prediction are discussed.
Kinjo
Akira R
AR
Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Japan. akinjo@genes.nig.ac.jp <akinjo@genes.nig.ac.jp>
Horimoto
Katsuhisa
K
Nishikawa
Ken
K
D000595:Amino Acid Sequence / Q000235:genetics; D003198:Computer Simulation; D008958:Models, Molecular; D011237:Predictive Value of Tests; D017434:Protein Structure, Tertiary / Q000235:genetics; D011506:Proteins / Q000737:chemistry* / Q000235:genetics
D011506:Proteins