Hydrogen bonds: Difference between revisions
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==Donor and Acceptor Atoms== | |||
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[[Image:Hbond.gif]]</td></tr><tr><td bgcolor='#e8e8e8'><div style='color: white; background-color: black;'> Elements {{Template:ColorKey_Element_C}}, {{Template:ColorKey_Element_H}}, {{Template:ColorKey_Element_N}}, {{Template:ColorKey_Element_O}}.</div>A hydrogen bond between a <font color='#6565b4'><b>nitrogen donor</b></font> and an <font color='red'><b>oxygen acceptor</b></font>. Distances shown are typical for those found in proteins.</td></tr></table> | [[Image:Hbond.gif]]</td></tr><tr><td bgcolor='#e8e8e8'><div style='color: white; background-color: black;'> Elements {{Template:ColorKey_Element_C}}, {{Template:ColorKey_Element_H}}, {{Template:ColorKey_Element_N}}, {{Template:ColorKey_Element_O}}.</div>A hydrogen bond between a <font color='#6565b4'><b>nitrogen donor</b></font> and an <font color='red'><b>oxygen acceptor</b></font>. Distances shown are typical for those found in proteins.</td></tr></table> | ||
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Hydrogen bonds ("hbonds") 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. | Hydrogen bonds ("hbonds") 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. | ||
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 requiring 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). 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. PE's DISPLAY Contacts defines "likely noncovalently bonded" oxygens and nitrogens (shown as balls) as those within 3.5 Å of other oxygens and nitrogens. | ==Distances and Energies== | ||
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 requiring 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). | |||
==Finding and Visualizing Hbonds== | |||
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. PE's DISPLAY Contacts defines "likely noncovalently bonded" oxygens and nitrogens (shown as balls) as those within 3.5 Å of other oxygens and nitrogens. | |||
==Content Attribution== | ==Content Attribution== | ||
Revision as of 19:06, 18 October 2008
Donor and Acceptor AtomsDonor and Acceptor Atoms
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Elements C, H, N, O. A hydrogen bond between a nitrogen donor and an oxygen acceptor. Distances shown are typical for those found in proteins. |
Hydrogen bonds ("hbonds") 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
Jeffrey[1] (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 requiring 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[1], 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[1], pp. 191, 200).
Finding and Visualizing HbondsFinding and Visualizing Hbonds
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. PE's DISPLAY Contacts defines "likely noncovalently bonded" oxygens and nitrogens (shown as balls) as those within 3.5 Å of other oxygens and nitrogens.
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.