Solvent-accessible surface

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  • the CCP4 program surface writes a list of accessible are per atom per residue
  • the CCP4 program areaimol in its latest versions has an option of showing the fraction of accessible area per residue (relative to its accessible surface in the Gly-X-Gly peptide) both in the log file and in the B-factor column of the pdb file it produces.
  • RasMol 2.7.5 and later:
load ../data/pdb1w0k.ent
restrict not hoh
map generate LRsurf dots
map select atom within 1.8
show selected
  • Diffusion accessibility server - slightly different from "surface accessibility" : "Diffusion accessibility gives a measure of surface accessibility that is longer range in nature than ordinary solvent accessibility. The idea of diffusion accessibility was introduced several years ago (Yeates, TO (1995) Algorithms for Evaluating the Long-range Accessibility of Protein Surfaces. J Mol Biol 249(4): 804-15). Diffusion accessibility is a measure of how easily or frequently a specific point on a surface would capture a hypothetical diffusing (or randomly-walking) probe that is captured upon its first encounter with any part of a surface. Naturally, parts of a surface that are solvent-exposed in the traditional sense but lie in a deep surface depression will capture the probe only rarely, since the probe will more often encounter another part of the surface first. The results of a diffusion accessibility calculation can be useful in quantitatively evaluating potential binding regions of a protein surface, and are particularly useful in visualization."