ABSTRACT
This chapter compares high-performance liquid chromatography (HPLC) parameters with hydrophobicity parameters. It presents new results of an improved version of a computer program, SurfacePlot, using the HPLC parameters to predict surface regions in proteins. Generally, the largest variation between parameters was observed for the residues cysteine, lysine, and arginine. In most of the other scales, the value of cystine rather than cysteine is reported. Only the value of cysteine is reported for the HPLC parameters because of anomalous results obtained when disulfide-bridged peptides were investigated. Qualitatively, however, most parameters describe the same general features of hydrophilic and hydrophobic patterns with the HPLC parameters generally scoring the highest in predicting surface regions of proteins. It is noteworthy that the Acrophilicity and Welling parameters showed very good agreement with the HPLC parameters in predicting surface regions in proteins but were still not as effective as SurfacePlot.
