Hydrogen bonds: Difference between revisions
Jump to navigation
Jump to search
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) |
||
| Line 9: | Line 9: | ||
==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.'' | |||
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 further assessment of hydrogen bonding to the user. | 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 further assessment of hydrogen bonding to the user. | ||
===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: | 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: | ||
| Line 21: | Line 25: | ||
* 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.). | ||
===HBonds in FirstGlance in Jmol=== | |||
<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'> | ||
<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> | <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> | ||