The side-chain effects of metalated and protonated dipeptides, including GGH(+)M(+), GAH(+)M(+), AGH(+)M(+), AAH(+)M(+), GWH(+)M(+), GSH(+)M(+), GTH(+)M(+), GFH(+)M(+), GYH(+)M(+), and GVH(+)M(+) (G = glycine, A = alanine, W = tryptophan, S = serine, T = threonine, F = phenylalanine, and V = valine; M = Li, Na, and K), are theoretically explored in this paper on their positive binding energies (PBEs), which are derived from interactions of M+ with the carboxyl oxygen(s). The B3LYP/6-311++G**// B3LYP/6-31G* calculations suggest that the PBEs of dipeptides with side chain(s) are much smaller than those with no side chain (GGH(+)M(+)). Generally, larger side chains and smaller M+ radii would lead to fewer PBEs for the M+ involved systems. On the basis of the direct dependence of PBE on the electrostatic repulsion between two kinds of cations (H+ and M+) in these dipeptide models, it could be reasonably expected that the side-chain effect on the electrostatic repulsion and consequently on the PBEs could offer one good insight, on a chemical-physical basis, into the origin of regular ordering of the amino acids when they form a filter in the K+ channel protein (MacKinnon, et al. Science 1998, 280, 106).