Research Paper Volume 12, Issue 4 pp 3516—3557

Adaptive selection in the evolution of programmed cell death-1 and its ligands in vertebrates

Figure 6. (A) Proteins analysis showing the results of the binding site, solvent accessibility and protein disorder predictions in the human PD1, PD-L1 and PD-L2 sequences. (B) Hydrophobic cluster analysis (HCA) plots of the human PD proteins. HCA plots were constructed with the HCA 1.0.2 program. HCA uses the standard one-letter amino acid abbreviations except for four amino acids, as shown in the key. Hydrophobic residues are outlined. Clusters of hydrophobic residues are usually associated with regular secondary structures (α helices or β sheets). Zigzagging vertical lines of hydrophobic residues indicate alternating hydrophobic and non-hydrophobic residues, typical of exposed β sheets (for example, β2, β3, β5, and β6). Continuous hydrophobic clusters are more common in internal β sheets.