Hydrogen bonds: Difference between revisions
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* Assess whether or not nearby side chain conformations make sense (ASN, GLN, and HIS must often be flipped). | * 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. | * 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 ( | * 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.). | ||
[[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. | [[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. | ||
