A set of van der Waals and coulombic radii of protein atoms for molecular and solvent-accessible surface calculation, packing evaluation, and docking

摘要: We analyze the contact distance distributions between nonbonded atoms in known protein structures. A complete set of van der Waals (VDW) radii for 24 atom types and crystal-bound water is derived from these with a selected group apolar atoms. In addition, Coulombic polar their contacts water. The two sets are systematic self-consistent manner using an iterative procedure. are, on average, 0.18 smaller than VDW radii. radius 1.7 A, which 0.3 larger its radius. show that both needed calculating molecular solvent-accessible surfaces proteins. to generate portions surface portions. fact have apparent sizes implies hydrophobic cavity has be order accommodate same number molecules. Most area calculations used only one each atom. As result, unreal cavities, grooves, or pockets may generated if used. On other hand, used, details regions lost. accuracy proteins can improved allowed change depending nature contacting neighbors. at protein-protein interface differs solution it least kinds probes, representing typical This observation important implications docking, relies complementarity interface.