Hydrogen bonds: Difference between revisions

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==Finding 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.

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 assessment of hydrogen bonding to the user.

Since many [[PDB file|PDB files]] lack [[Hydrogen in macromolecular models|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.

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 atom 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.

[[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.

Hydrogen bonds: Difference between revisions

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@@ Line 9: / Line 9: @@
 ==Finding 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.
+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 assessment of hydrogen bonding to the user.
-Since many [[PDB file|PDB files]] lack [[Hydrogen in macromolecular models|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.
+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 atom 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.
 [[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.