Effect of sidechain anisotropy on residue contact determination

The criteria used to determine the residue contact is a fundamental factor in deriving knowledge-based mean force potential energy for protein structures. A commonly used criterion for two residues in contact is to require the sidechain center distance or the C_alpha atom distance to be within a predetermined cutoff distance. However, the anisotropic nature of the sidechains can result in error in the counting of the contact pairs. This study compared three sidechain contact models: the surface-to-surface model based on atom distance criteria (ADC), the isotropic sphere sidechain (ISS) model and the anisotropic ellipsoid sidechain (AES) model. A test using 424 high resolution protein structures from the Protein Data Bank suggests that the ADC model is the most accurate and the AES eliminate about half of the incorrectly counted contact pairs when this model is compared to the ISS model.