Hydrogen bonds: Difference between revisions
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==Donor and Acceptor Atoms== | ==Donor and Acceptor Atoms== | ||
<table align='right' border='0' width='184' cellpadding='10' bgcolor='#d0d0d0' hspace='8'><tr><td rowspan='2'> </td><td bgcolor='#e8e8e8'> | <table align='right' border='0' width='184' cellpadding='10' bgcolor='#d0d0d0' hspace='8'><tr><td rowspan='2'> </td><td bgcolor='#e8e8e8'> | ||
[[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 (dotted white line) 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 (dotted white line) between a <font color='#6565b4'><b>nitrogen donor</b></font> and an <font color='red'><b>oxygen acceptor</b></font>. Distances shown in Å are typical for those found in proteins. In this example, the N-H bond is covalent and fixed in length. The dotted hydrogen bond is non-covalent and variable in length, ~1.5-2.5 Å.</td></tr></table> | ||
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. | [[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. | ||
Carbon atoms lack sufficient electronegativity to serve as energetically significant hydrogen bond donors or acceptors. The C-H bond has insufficient charge separation, and C in amino acids has no lone electron pair. | |||
==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== | ||
===Software=== | |||
''This section needs updating. Jmol can now display hydrogen bonds, as can several other software packages.'' | |||
<Structure size='450' align=right scene='Hydrogen_bonds/Calculate_hbonds_structure/1'/> | |||
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.<ref>The hbonds which are displayed by this command are among the hydrogen bonds identified but not displayed by recalculating the secondary structure using Jmol's implementation of DSSP.</ref> 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. | |||
===Challenges=== | |||
Since many [[PDB file|PDB files]] lack [[Hydrogen in macromolecular models|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.). | |||
<table align='right' border='0' width='184' cellpadding='10' bgcolor='#d0d0d0' hspace='8'><tr><td rowspan='2'> </td><td bgcolor='#e8e8e8'> | |||
<Structure size='450' scene='Help:Copying_FirstGlance_Scenes_into_Proteopedia/Selected_ligand_contacts/4' /></td></tr><tr><td bgcolor='#e8e8e8'><div style='color: white; background-color: black;'> Elements: {{Template:ColorKey_Element_C}}, {{Template:ColorKey_Element_N}}, {{Template:ColorKey_Element_O}}, <font color="magenta">'''Water Oxygen'''</font>. Drug atoms are darker.</div>Selected contacts between an anti-Alzheimer`s drug analog and acetylcholinesterase in [[1gpk]]. Scene generated largely and quite easily in [[FirstGlance in Jmol]] ([[Help:Copying FirstGlance Scenes into Proteopedia|details]]). Atoms shown as balls are within non-covalent bonding distances. Click the '''popup''' button above to see details in this scene!</td></tr></table> | |||
[[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 | ===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]]. | ||
==Content Attribution== | ==Content Attribution== | ||
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==References== | ==References== | ||
<references /> | <references /> | ||
[[Category: BioMolViz]] | |||
[[Category: Alternate Renderings]] | |||