Hydrogen bonds: Difference between revisions
Jump to navigation
Jump to search
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) |
||
| Line 21: | Line 21: | ||
* 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.). | * 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.). | ||
<applet load='1gpk' size=' | <applet load='1gpk' size='400' frame='true' align='right' caption="Selected contacts between an anti-Alzheimer`s drug analog and acetylcholinesterase in [[1gpk]]. Scene generated largely and quite easily in [[FirstGlance in Jmol]]. Atoms shown as balls are within non-covalent bonding distances. Use '''popup''' to see details in this scene!" | ||
scene='Help:Copying_FirstGlance_Scenes_into_Proteopedia/Selected_ligand_contacts/4' /> | scene='Help:Copying_FirstGlance_Scenes_into_Proteopedia/Selected_ligand_contacts/4' /> | ||
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. | 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. | ||
==Content Attribution== | ==Content Attribution== | ||