Stability of NS3/4A protease structure (native and mutant) contributes significantly towards the discovery of new drug molecules. In the present study, we have investigated the role of non canonical interactions (CH/Π, NH/Π, C-H..O) on the structural stability of NS3/4A protease structure by means of analyzing the existence of these interactions in the native and mutant form of the structures. The study initiated by analyzing effect of the mutation in the binding of the drug molecule by molecular docking analysis. Subsequently the results were validated by means of PEARLS program and Flexibility analysis. Finally, the prevalence of non canonical interaction in the native type structure examined by using HBAT algorithms and compared with ASP168ALA structure. The obtained results certainly indicate that the non canonical interactions contribute significantly to the overall stability of protein structure.