Falcipain-1 versus falcipain-2 S2, S3 and S4 specificity site analysis. To highlight differences that affect the S2, S3 and S4 specificity sites, the sites were analyzed with respect to sequence differences between the two plasmodial proteases (see Methods). Residues that gained hydrogen bonding functionality relative to the other sequence are marked with blue dashes, residues that gained charge functionality are marked by a red ball within a blue ball. The table of residue changes highlights the sequence that gained functionality with a boldfaced font. The figure was generated with WEBMOL (20) and a sequence to structure alignment and family analysis JAVA™ package (M.P. Joachimiak, in preparation).