Measurement of hydrophobicity distribution in proteins – non-redundant Protein Data Bank

The cluster analysis is applied to the analysis of the data describing the status of protein structure in respect to hydrophobic core characteristics. The analysis revealed presence of two clusters distinguishing the proteins accordant with the “fuzzy oil drop” model and those which appear as discordant in respect to this model. The analysis was performed separately for chains treated as structural unit and for units defined according to IV-order (taking the functional protein complex). The characteristics of these two classification system appeared to differ in respect to number of proteins belonging to each of two clusters as well as relation between them.