HCAtk and pyHCA: A Toolkit and Python API for the Hydrophobic Cluster Analysis of Protein Sequences

Tristan Bitard-Feildel; Isabelle Callebaut

169 Figures S7 and S8 show two examples of HCA plots for sequences extracted from the PDB. Figure S7 170 corresponds to the HCA plot of the Archeoglobus fulgidus VapC ribonuclease (Uniprot O28590, amino 171 acids 1 to 156) whose 3D structure has been solved X-ray crystallography (PDB entry 1W8I). This The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/249995 doi: bioRxiv preprint Figure S8 is another example of a globular protein HCA plot, i.e. with a high HCA score. The figure shows the HCA plot of the mature mouse interferon beta (Uniprot P01575, amino acids 22 to 181, PDB 179 entry 1WU3 [26] ). The protein is made of one domain (Pfam amino acids 27 to 179 (PF00143)), including 180 5 long α-helices with 42% of hydrophobic residues. As for Fig. S7 , the protein contains large hydrophobic 181 clusters, typical of regular secondary structures, separated by loops. Examples of PDB sequences with low HCA scores. (Uniprot protein P59595, PDB entry 2OFZ [16] ). This nucleoprotein has RNA binding activity, packaging 186 the positive strand of the human SARS coronavirus RNA genome into a helical ribonucleocapsid [27] .