[James D]

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, as opposed to a peptide which is a part of a polypeptide.

What I am interested in is to get some intuition as to how might pKr values change when the peptide is a part of a polypeptide. For example, if the peptide in interest is X and its "standard" pKr value is Y, do you expect this pKr value to be higher or lower when X is found in a polypeptide next to some amino acid Z?

I am not looking for exact calculation, but just some thumb rules or intuition.

Thanks,
James