Bonding

Hydrogen Bonding:

Hydrogen bonding is a special kind of dipole-dipole interaction that occurs between a hydrogen molecule which is bound to a weakly acidic donor molecule and a lone pair of a weakly basic acceptor molecule. The bond can be represented as follows, where "D-H" represents the weak acid  and "A" represents the weakly-acidic acceptor molecule:

DHd+ . . . . Ad -

In biological systems, the donor molecule is typically either an -OH or an -NH group, while the acceptor is either a lone pair on an O or N atom. Water is one such biologically significant molecule which contains hydrogen bonds. The characteristics of water in its various physical states make water unique. In the liquid stage of water, molecules are loosely bonded together via hydrogen bonds (in fact, liquid water has 15% fewer hydrogen bonds than ice).  In the solid stage, water molecules form four hydrogen bonds with surrounding molecules, forming a crystal structure.  Due to the multiple bonds formed by the molecules, water actually expands upon freezing. For more information regarding the biological significance of water, consult page 40 of the text.

When looking for candidate hydrogen bonding interactions in the visual rendering of pdb files, look for bond distances between the acidic "H" and basic donor atom on the order of 1.5 - 2.0 Angstrom units. Remember that "D" and "A" will be N, O, or F.