Pat Fleming - Surface Analysis of Macromolecules

Calculation of Atomic Packing in Proteins

• Dependence on atom radii

• Analytical Calculation [VDW vol]/[Molecular Surface vol] ~= 0.80
  Connolly, M.L. (1985) J. Am. Chem. Soc. 107, 1118

• Voronoi Good for buried atoms [VDW vol]/[Voronoi vol] = 0.70 - 0.78
  Richards, F.M. (1974) J. Mol. Biol. 82,1
  
  • Protein Core Packing = Peptide Crystal Packing

• Cavities: Void space >= Probe Size
  Lee, B. and Richards, F.M. (1971) J. Mol. Biol. 55,379
  Hubbard, S.J., Gross, K-H. and Argos, P. (1994) Protein Eng. 7,613
  
  
  • Vacuum
  • Water Filled