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Lastly, the 3D coordinates were normalized using the same method as the sequence analysis. The catalytic serine was set as (0,0,0) and the other residues were mapped relative to the catalytic serine. The resulting 3D plots were created, mapping the residues within an 8A radius of the serine.
Trypsin 3D Analysis
From the three dimensional analysis of the nearby residues in the trypsin family, there exist evident trends. For example, there is an abundance of GLY and CYS residues in the active site. Furthermore, it appears that the ASP residues tend to cluster on the exterior of the active site. Then, polar amino acids tend to localize in the 6-8A range of the active site, while charged residues tend to be towards the outside. Overall, this suggests a tight, coordinated environment close to the catalytic site with increased flexibility as you get distant from the catalytic serine with the chemical properties of the residues changing as well.
Substilin 3D Analysis
In the Substilin family, there are also interesting trends. In the complete amino acid distribution, you can see clustering of "rare" amino acids like PRO, and GLY. There's also a cluster of MET residues extremely close to the active site. Furthermore, you can also see how amino acids with similar structures (VAL, THR) tend to cluster together. This shows how conserved the enzyme active site is, even across different proteins within the mechanism. Furthermore, this also displays hydrophobic residues far from the active site, and polar residues near the active site.
Prolyl Oligopeptidase 3D Analysis
Prolyl Oligopeptidase also has interesting 3D active site. The overall distribution of the residues tends to be less spherical, and more skewed towards the +Y and +Z axis. Furthermore, we can see the TRP distributed on the exterior of the active sites. Also, the PRO residues tend to cluster together, along with the TYR residues. This family also appears to have a lot of "other" residues near the active site (GLY and PRO), showing the active site's rigid structural requirements. This contrasts from the other families where hydrophobic residues dominate the active site.
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