  Residue-wise contact order (RWCO) is a new kind of one-dimensional protein
structures which represents the extent of long-range contacts. We have recently
shown that a set of three types of one-dimensional structures (secondary
structure, contact number, and RWCO) contains sufficient information for
reconstructing the three-dimensional structure of proteins. Currently, there
exist prediction methods for secondary structure and contact number from amino
acid sequence, but none exists for RWCO. Also, the properties of amino acids
that affect RWCO is not clearly understood. Here, we present a linear
regression-based method to predict RWCO from amino acid sequence, and analyze
the regression parameters to identify the properties that correlates with the
RWCO. The present method achieves the significant correlation of 0.59 between
the native and predicted RWCOs on average. An unusual feature of the RWCO
prediction is the remarkably large optimal half window size of 26 residues. The
regression parameters for the central and near-central residues of the local
sequence segment highly correlate with those of the contact number prediction,
and hence with hydrophobicity.
