Hydrogen bonds: Difference between revisions
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* 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.). | ||
< | <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_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.</td></tr></table> | |||
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! | |||
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. | ||