Hello,
I use some standard tables of amino acids pKa values, as the one here:
http://www.cem.msu.edu/~cem252/sp97/ch24/ch24aa.html
and I am especially interested in the pKr (i.e. pKa of the side chains).
Correct me if I'm wrong, but pKa values listed in such tables refer to a "free" peptide...