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Donor and Acceptor Atoms
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 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 Hbonds
This section needs updating. Jmol can now display hydrogen bonds, as can several other software packages.
Before the availability of Jmol ver. 12, free molecular visualization programs displayed potential donor-acceptor pairs, deeming them "putatively" hbonded because determining the positions of hbonds with high confidence required expert and detailed examination of the donor-acceptor chemistry and geometry. Protein Explorer and FirstGlance in Jmol (see applet below) 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. One of the new features of Jmol 12.0 is a command, calculate hbonds structure, which determines and displays the hbonds in helices, sheets and turns. Click on the Jmol frank, in the main menu which opens click on Console, in the bottom box enter the commands: select protein; calculate hbonds structure; and then click Run. Try using the above method to display the hbonds in the helices, sheets and turns in the protein shown on the right.
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 (hydroxyl vs. ketone, amine vs. imine, etc.).
Elements: C, N, O, Water Oxygen. Drug atoms are darker.Selected contacts between an anti-Alzheimer`s drug analog and acetylcholinesterase in 1gpk. Scene generated largely and quite easily in FirstGlance in Jmol (details). Atoms shown as balls are within non-covalent bonding distances. Click the popup button above to see details in this scene!
HBonds in FirstGlance in Jmol
There is a link to FirstGlance in Jmol beneath the molecule (rotatable scene in Jmol) on every Proteopedia page title with a PDB identification code. 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" oxygens and nitrogens (shown as balls) as those within 3.5 Å of other oxygens or nitrogens.
Any molecular scene obtained in FirstGlance in Jmol can be ported into a Proteopedia green link. See Help:Copying FirstGlance Scenes into Proteopedia.