Hydrogen bonds: Difference between revisions
No edit summary |
Eric Martz (talk | contribs) |
||
| Line 9: | Line 9: | ||
==Distances and Energies== | ==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<ref name='jeffrey' />, pp. 191, 200). Jeffrey<ref name='jeffrey'>Jeffrey, George A., An introduction to hydrogen bonding, Oxford University Press, 1997.</ref> (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<ref name='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<ref name='jeffrey' />, pp. 191, 200). Jeffrey<ref name='jeffrey'>Jeffrey, George A., An introduction to hydrogen bonding, Oxford University Press, 1997.</ref> (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<ref name='jeffrey' />, p. 14). | ||
A common cutoff donor-to-acceptor distance for energetically significant hydrogen bonds in proteins is 3.5 Å (see legend to Table 6 in Kajander ''et al.''<ref name="kajander">PMID:11080642</ref>). | |||
==Finding and Visualizing Hbonds== | ==Finding and Visualizing Hbonds== | ||