We report the results of a theoretical study intended to elucidate the molecular basis of the effect of hydrophobicity on the pK(a)＇s of ionizable groups in polypeptides and proteins. In particular, we have focused on a polypentapeptide of a family associated with the process of free energy transduction. Our theoretical calculations, carried out by using a conformational search method in combination with a fast multigrid boundary element method to solve the Poisson equation, led to results that are in good agreement with the experimental observations.