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 Cβ atoms around the Cβ 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. Proteins 2005. © 2004 Wiley‐Liss, Inc.

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