Figure 5

Several examples of hydrophobic clusters. Top panel: Example of two hydrophobic clusters, found in ferredoxin reductase (pdb 1f3p) and mainly associated with helices (P-code 153) and strands (P-code 45), respectively. These hydrophobic clusters are colored on the corresponding 3D representation, in which side chains of hydrophobic residues, constituting the internal face of regular secondary structures, are shown in atomic details. Note that the alpha-helix is larger than the corresponding hydrophobic cluster, alanine residues present upstream and downstream from the cluster contributing to the extension of the alpha helix outside the cluster limits. Bottom panel: Example of two hydrophobic clusters within a same protein sequence, which belong to the same species (P-code 89) but are associated with two different regular secondary structures (glycerol dehydrogenase, pdb 1r8w). The chemical nature of residues in the vicinity of hydrophobic clusters can orientate the secondary structure prediction. For instance, five alanine residues in the vicinity of the first hydrophobic cluster are indicative of a helical structure, whereas the cysteine embedded within the second hydrophobic cluster reinforces the probability of a β-strand. In addition to these examples of simple clusters, two "multiple" hydrophobic clusters are shown. These are associated with more than one regular secondary structure (P-codes 345167 and 199). The secondary structure assignments, as deduced from DSSP [31], are shown above the plots.