FIGURE 2.

Pairwise correlations between the selected physicochemical amino acid properties. The actual correlation coefficients are presented in the upper triangle together with correlation significance symbols: ***p < 0.001, **p < 0.01, *p < 0.05, ’p < 0.1. Lower triangle shows smoothed trend lines together with confidence 1 SD ellipses. The vast majority of the selected properties show low pairwise correlation thus spanning a close-to-orthogonal coordinates frame in the physicochemical property space. As expected, there is a significant correlation between polarity-and transfer of free energy from octanol to water as the latter is to a large degree amino acid polarity-dependent. Similarly, normalized frequency of alpha-helix and normalized frequency of turn, the two secondary structure-related properties show significant pairwise correlation. This partial redundancy is the result of the physicochemical property selection procedure where the initial set of available AAindex descriptors has been narrowed down to only the easy-to-interpret properties. Thus, the selected seven properties are a reasonable trade-off between minimizing the number of dimensions necessary to preserve amino acid discernibility and the ease of interpretation. For a more detailed discussion, see Rudnicki and Komorowski (2004) and Kierczak et al. (2009).