Abstract
For glycoside hydrolysis families, there are two known catalytic residues in the active site are important to the catalytic function. We assume the two catalytic residues should be superimposed together after alignment and we want to observe the chemical properties and geometric features around the two catalytic residues in same functional group. Protein structure alignment can superimpose and comparison of variance components, the common or specific features of protein could be identified. But traditional structure alignment may not superimpose the catalytic residues in same coordinates, so we design a position constraint structure alignment that superimpose the catalytic residues first and align the remaining residues. We select the 42 proteins in EC3.2.1.4 as experimental material. EC3.2.1.4 includes two mechanisms, inverting and retaining, 5 catalytic domain folds, many SCOP domains and glycoside hydrolysis families. Final, observe what residues can be the common features in the hierarchical classification.