Elements of Protein Structure
The hydrogen bond (H-bond) is a SPECIAL CASE of polar interaction. While it is called a "hydrogen bond", it is NOT a covalent bond. Like any other polar interaction it is between two separate molecules. Recall from the previous page that a polar interaction was ANY interaction between two polar molecules. The H-bond, while it also requires favorable interaction between two polar molecules also includes specific rules about:
Depicted are the sidechains of a threonine and a serine. Note the orientation of the "O-H" bond of the serine relative to the "O" atom of th threonine.
- Orientation of the dipole
Orientation must be favorable and highly specific. You must be able to draw a "straight line" between the three atoms
involved. Note that in the picture below that the covalent the O-H bond is pointing directly toward a lone pair of electrons on
the "O" atom of the neighboring molecule. We can draw a straight line through all three of these atoms.
- Distance between the molecules
Distance must be short. The distance between the two "O" atoms in the picture below is very short. In fact the distance is
actually shorter than that calculated for two "O" atoms and one "H" atom. Since both "O" atoms are somewhat negatively charged,
this short distance can occur IF and ONLY IF there is a somewhat positively charged hydrogen atom in the middle.
The hydrogen bond involves neither a group whose proton can dissociate nor is it covalent
Note: in the two examples presented on this page neither involve a group that is readily ionized at physiological pH.
Nomeclature of H-bond
Two Peptide bonds are represted. Note how the "N-H" bond of the "bottom" group is pointing right at the Oxygen atom of another peptide bond.In this picture which is the H-bond donor and which is the H-bond acceptor?
Represetnted here are two peptide bonds. The blue nitrogen of the "lower" amide very close to the red oxygen of the "upper" amide. It is easy to see the N-H bond points directly at the "O" of the neighboring amide.
- H-bond DONOR --- The molecule whose Hydrogen is covalently attached to O, S or N and thus is presenting it "+" end
- H-bond ACCEPTOR --- The molecule that is presenting is "-" end toward a hydrogen atom in a noncovalent interaction
Recall that the amide bond (peptide bond) is also polar! H-bonds between peptide bonds are very common (See helices and sheets)