Hydrogen bonds

Hydrogen bonds are electrostatic interactions resulting from the interaction of partial charges or 'dipoles'. They are essential for the stabilization of secondary structures.

Practical work

View this structure (crambin, 1crn) using PyMOL. Describe its tertiary structure. Now let's look at the hydrogen bonds.

• Show the molecule as Cartoons
  
• Now, under Actions select find->polar contacts->just intra-main chain
  
• You should now see the hydrogen bonds displayed as dotted lines.
  
• Identify an alpha-helix and observe the hydrogen bonding.
  
• Identify the two-strand beta-sheet and observe the hydrogen bonding.
  

Hydrogen bonds are also formed between side chain and main chain or between two side chains. To see these

• under Actions select find->polar contacts->involving side chains
  

You should now see a less regular pattern of hydrogen bonding, involving individual side chains.