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In course of evolution similar sequences may diverge to change topology of the structure but active sites that are essential to protein function have a possibility to be maintained. Moreover, protein molecules of overall different structures could converge to similar functions by evolutionary development of similar active sites. In such cases, mere sequence based structure comparisons are likely to be inadequate in describing or identifying protein functions and evolutionary relationships among them. In this paper we show the importance of studying the surface roughness of protein to get the holistic information about protein structural similarity profile. Using an invariant coordinate system designed and referred by us as molecular coordinate system we have introduced a new parameter surface roughness index (SRI) to study the protein surface. The possible utility of SRI to explore protein structure is discussed.