Automatic Determination of Hydrophobic Cores

Mark B Swindells

Protein Engineering Research Institute


An algorithm is described for automatically detecting hydrophobic cores in proteins of known structure. Three pieces of information are considered in order to achieve this goal. These are; secondary structure, side chain accessibility and side chain-side chain contacts. Residues are considered to contribute to a core when they adopt a regular secondary structural conformation and have buried side chains which form mainly non-polar contacts with other buried contacts. The efficacy of this method has been assessed by comparing the predictions for interleukin-1 and Erythrina trypsin inhibitor structures, with those proposed by different authors on the basis of visual inspection. In these cases the automated procedure shows good agreement with the author definitions despite using only simple descriptives for residue interactions. This method will be useful to all those involved in protein structure analysis by providing an ability to reliably distinguish between buried residues which contribute to a hydrophobic core and those which are only locally buried.