Anyway, all the salt bridges and the hydrogen bonds remains the same and there was no change in the distances too. I was excepting some change even minor ones as only the surface residue was replaced and of course one should not except much change in the internal structure. But even one internal residue when exchanged made no difference. Now this time I was expecting much. Phe was replaced by Asp and then by Ala. Literature did show change in the stability by this alteration and I want to inspect it by change in the hydrophobic interaction and salt bridges.
Refining makes things more difficult.
The other important studies that I want to carry out is the effect of sugar binding to the structure as well as binding of the small molucules like phosphate, cyanate etc. I used Web lab Viewer Pro version to paste and connect the small mol. to my protein. When the cleaned structure is then refined by the 'refi' command of whatif, it removes bad contacts but many residues were still in the disallowed region of the Ramachandaran plot. When the structure was left as such without cleaning and without refining, then there is no change in the structure. The Ramachandaran plot is OK but the structure is exactly the same.