Hydrogen bonds

Donor and Acceptor AtomsDonor and Acceptor Atoms

	Elements: C, H, N, O. A hydrogen bond (dotted white line) between a nitrogen donor and an oxygen acceptor. Distances shown in Å are typical for those found in proteins.

Hydrogen bonds ("hbonds") are non-covalent bonds that occur when a donor atom donates its covalently bonded hydrogen atom to an electronegative acceptor atom. Typical donor atoms are the oxygens in -OH (e.g. the sidechains of Ser, Thr, Tyr), HOH, and the nitrogen in -NH3+ (as in the sidechains of Lys, Arg) or -NH- (as in the main chain peptide bond, and the sidechains of Trp, His, Arg, and nucleotide bases). The lone electron pairs on these same donors can serve as hbond acceptor sites. So can those on carbonyl oxygens =O (as in the protein main chain) or nitrogens with three covalent bonds =N- (as in the sidechains of His, Trp, or in nucleotide bases). Lacking hydrogens, these latter cannot serve as donors.

Distances and EnergiesDistances and Energies

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). Jeffrey (page 12) categorizes hbonds with donor-acceptor distances of 2.2-2.5 Å as "strong, mostly covalent", 2.5-3.2 Å as "moderate, mostly electrostatic", and 3.2-4.0 Å as "weak, electrostatic". Energies are given as 40-14, 15-4, and <4 kcal/mol respectively. Most hbonds in proteins are in the moderate category. Strong hbonds require moieties or conditions that are rare within proteins. The hydrogen atoms in moderate hbonds often do not lie on the straight line connecting the donor to acceptor, so donor-acceptor distance slightly underestimates the length of the hbond (Jeffrey, p. 14).

Finding and Visualizing HbondsFinding and Visualizing Hbonds

Few, if any, free molecular visualization programs show hbonds as rods or sticks between atoms. This is because determining the positions of hbonds with high confidence requires expert and detailed examination of the donor-acceptor chemistry and geometry. Instead, some molecular visualization programs display potential donor-acceptor pairs, deeming them "putatively" hbonded. Protein Explorer and FirstGlance in Jmol have Contacts dialogs that show putatively hbonded donors and acceptors based simply on the chemical elements and interatomic distances. PyMOL likewise displays "polar contacts" using dashed bonds between the involved atoms, leaving further assessment of hydrogen bonding to the user.

Since many PDB files lack hydrogen atoms, the possibility of an energetically significant hydrogen bond exists when donor and acceptor atoms are within about 3.5 Å of each other. However, before rigorously concluding that a hydrogen bond is present in a macromolecular crystal structure, viewers should first:

• Consider the overall coordinate error implied by the resolution of the structure.
• Survey local temperature factor values to see if the involved model coordinates are well-determined.
• Factor in corroborating evidence such as involvement in surrounding elements of secondary structure.
• Inspect the electron density, if available, to confirm that the model coordinates are actually in density.
• Assess whether or not nearby side chain conformations make sense (ASN, GLN, and HIS must often be flipped).
• Evaluate the local electrostatic potential to confirm that it is consistent with the assumed ionization states.
• If the putative hydrogen bond involves a small-molecule ligand, check that the ligand donors and acceptors have been correctly assigned (hydroxy vs. ketone, amine vs. imine, etc.).

FirstGlance in Jmol has a Contacts dialog, where you can select any moiety by clicking on it. (The moiety can be a chain, a segment of a chain, a single residue or ligand, or a single atom.) All the likely non-covalent bonds to the designated target moiety are then shown automatically. The putatively non-covalently bonded atoms can be hidden or shown in any combination of seven subsets: hydrogen bonds not involving water, hydrogen bonds involving water, water bridges, hydrophobic interactions, salt bridges, cation-pi orbital interactions, metal and miscellaneous interactions. This display defines "likely hydrogen bonded bonded" oxygens and nitrogens (shown as balls) as those within 3.5 Å of other oxygens or nitrogens.

An interactive example in Jmol is needed here.

Content AttributionContent Attribution

The text initially provided on this page was adapted by Eric Martz from the hydrogen bonds entry that he wrote several years earlier for the glossary in ProteinExplorer.Org.