This is unrelated to PyMol, but I just wanted to spam the community to see what they think about different protein parameters. Let me know if this sort of question is inappropriate for the forum. 

I have thousands of randomly generated 7 amino acid peptide sequences that are within a virus. As we subject this virus to reproduction selective pressure in cell lines, we get back functional viruses with certain 7 amino acid sequences, while most random sequences are null mutations. So I am now testing the the positive sequences to see what they have in common, or what is most important.

I am doing this with a likely structural sequence and a likely surface sequence.

So far I have these params from http://web.expasy.org/protparam/ and ConSurf

1) Isoelectric Point
2) Molecular Weight (may mean bulkiness)
3) GRAVY: grand average of hydropathicity
4) Conservation of AAs at given locations

Do any of you protein experts know of other parameters that I could be testing? Maybe something like Phi-value analysis?