(excerpted from Help, Index & Glossary for Protein Explorer[1] by Eric Martz)
Hydrogen bonds occur when a “donor” atom donates its covalently bonded hydrogen atom to an electronegative “acceptor” atom. The oxygen in -OH (e.g. Ser, Thr, Tyr), HOH, and the nitrogen in -NH3+ (as in Lys, Arg) or -NH- (as in the main chain peptide bond, Trp, His, Arg, nucleotide bases) are typical donors. The lone electron pairs on these same donors can serve as H bond acceptor sites. So can those on carbonyl oxygens =O (as in the main chain) or nitrogens with three covalent bonds =N- (as in His, Trp, or nucleotide bases). Lacking hydrogens, these latter cannot serve as donors.
Jeffrey[2] categorizes H bonds with donor-acceptor distances of 2.2-2.5 Å as “strong, mostly covalent”, 2.5-3.2 Å as “moderate, mostly electrostatic”, 3.2-4.0 Å as “weak, electrostatic” (page 12). Energies are given as 40-14, 15-4, and <4 kcal/mol respectively. Most H bonds in proteins are in the moderate category, strong H bonds requiring moieties or conditions that are rare within proteins. The hydrogen atoms in moderate H bonds often do not lie on the straight line connecting the donor to acceptor, so donor-acceptor distance slightly underestimates the length of the H bond (Jeffrey, p. 14). The mean donor-acceptor distances in protein secondary structure elements are close to 3.0 Å, as are those between bases in Watson-Crick pairing (Jeffrey, pp. 191, 200). Since many pdb files lack hydrogen atoms, the presence of an energetically significant hydrogen bond can be inferred when a probable donor and acceptor are within 3.5 Å of each other.