The helix-coil transition of poly(L-lysine) in water and in methanol solutions of a 1:1 salt is studied as a function of pH. The relative electrostatic free energy between the ionized microstates of poly(L-lysine) is evaluated as the sum of the potentials of mean force (PMF) between pairs of charged lysine residues. The PMFs in the alpha-helical and the statistical-coil conformations in water and in methanol-water solutions were calculated with a continuum electrostatic model based on a numerical solution of the nonlinear Poisson-Boltzmann equation. It was found that the PMFs in a polar solution of a 1:1 salt are strongly dependent on the ionization microstate of the poly(L-lysine). A 24-residue peptide served as a model for the helix to coil transition. An ensemble of 1200 statistical-coil conformations was generated for neutral poly(L-lysine) with the ECEPP/3 program. A representative ensemble of the statistical-coil conformation was then built by constraining the average end-to-end distance of the polymer to fit the experimental value of the characteristic ratio.