A systematic study of the potentials of mean force (PMF) of hydrogen-bonded amino acid side chains in water is reported. Hydrogen-bonding (HB) partners are classified according to the hybridization state of their donor and acceptor atoms, as well as the net charge of the interacting pairs. This classification leads to a total of 42 classes of representative HB interactions. Constrained molecular dynamics simulations are carried out to calculate the intermolecular mean force (MF) of the solute molecules in an explicit solvent composed of nonpolarizable TIP3P water. Long-range forces are calculated using particle mesh Ewald (PME) summation in a cubic lattice with periodic boundary conditions. The intermolecular PMF are obtained by integrating the MF along a specified reaction path. MF autocorrelation functions and correlation times are calculated for each HB class. Statistical errors in the MF and PMF are estimated and reported. The results are compared with those reported in the literature for simpler systems in the liquid phase. The implications of the results for the description of effective HB interactions in continuum approximations of solvent effects in mesoscopic systems are discussed.