Figure 26

Complementary codes vs amino acid co-locations (modified from [95]). The propensities for the 400 possible amino acid pairs were monitored in 81 different protein structures with the SeqX tool. The tool detected co-locations when two amino acids were within 6 A of each other (neighbors on the same strand were excluded). The total number of co-locations was 34,630. Eight different complementary codes were constructed for the codons (2 optimal and 6 suboptimal). In the two optimal codes, all three codon residues (123) were complementary (C) or reverse complementary (RC) to each other. In the suboptimal codes, only two of three codon residues were C or RC to each other (12, 13, 23), while the third was not necessarily complementary (X). (For example, Complementary Code RC_1X3 means that the first and third codon letters are always complementary, but the not the second, and the possible codons are read in reverse orientation. The 400 co-locations were divided into 20 subgroups corresponding to 20 amino acids (one of the co-locating pairs), each group containing the 20 amino acids (corresponding to the other amino acid in the co-locating pair). If the codons of the amino acid pairs followed the predefined complementary code the co-location was regarded as positive (P); if not, the co-location was regarded as negative (N). Each symbol represents the mean frequency of P or N co-locations corresponding to the indicated amino acid. Paired Student's t-test, n = 20.