The pKa, or acid dissociation constant, of an amino acid is
strongly tied to the properties of the surrounding solvent. The
hydrophobic core of a protein is a distinctly different environment
than the water exposed surface of the protein and the pKa in the
core is different than the normal, solvent exposed pKa. This is
related to the dielectric constant, or the ease at which charge is
"felt" over a distance, which is much lower in the hydrophobic core
of the protein. In addition, the now fixed locations of other
possibly charged amino acids nearby will also impact the pKa of the
residue.