The free energy of transfer measures the change in solvation energy, taking a side-chain from the hydrated environment of the unfolded state to the hydrophobic core of a folded protein. A conserved structural water molecule is found in the core of many V k domains, adjacent to amino acid 21. It makes very good hydrogen bonds to donors and acceptors from three strands iof the protein. From inspection, one would expect a significant stabilizing effect from the presence or absence of this water molecule. The frequency is given as the percentage of occurence of the respective amino acid in poistion 21 in the Kabat Database of immunoglobulin sequences.
Stability is measured experimentally from unfolding transition curves by denaturation in urea.
The change from the folded to the unfolded state is monitored with the fluorescence of the domain's single tryptophan. As can be seen from the table, the consideration of amino acid properties in three variants does not even predict qualitatively the observed stability of the respective proteins. Only the frequency of observation of the amino acids in the Kabat database of sequences of proteins of the immune system follows the experimentally observed stabilities. This raises the question of whether this connection between frequency and stability had any significance. Of course, the relationship between the observed frequency of a system's state and the energy associated with this state is the realm of statistical thermodynamics.