Is it a good idea to compare the b factor of a particular loop of different proteins from same family? I have seen that these proteins are having similar orientation of loops.
No, you can't compare B-factors between different structures directly.
You can do is compare the B-factors within a structure and draw conclusions as to the relative disorder of the loop in that structure.
Dear Mathew thanks for the answer. When l superimposed all the structures from the same family , I observed the loops are highly ordered. This loop is connecting two beta strands. What l have done is l have just calculated the average b factor for the beta strand 1, loop and beta strand 2 and plotted each other to see the correlations. There is a reasonable correlation with r2 value 0.89.
This depends very much on the question you want to answer. You see a correlation, but what are you trying to infer?
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