Hydrogen Bond Interactions
- When atoms have large partial charges, electrostatic interactions are possible. In the case of hydrogen bonds a hydrogen atom with a large positive partial charge interacts with an atom with a large negative partial charge. The opposite charges attract each other and the hydrogen atom which is covalently bound to the "hydrogen bond" donor atom comes very close to the "hydrogen bond" acceptor atom with its lone pairs. In general the two partial charges are part of dipoles leading to the positive hydrogen to be positioned between two negative atoms.
The energy of a hydrogen bond lies in between the energies of covalent bonds and Vander Waals interactions, and is of the order of 2-10 kcal mol-1.
The strength of the hydrogen bond is dependent on the distance between the donor and acceptor atoms, which in turn is dependent on their electronegativities. The standard hydrogen bond between the donor and acceptor atoms is of the order of 2.6Å - 3.5Å, with the optimum at 2.8Å. Distances may be less accurate at low resolution.
The highest bonding energy for the hydrogen bond is obtained, when the two negative charges are approximately in line with the positive charge inbetween (O...H-O in water, O...H-N in the oxygen amide hydrogen bond). Deviations from linearity will reduce the bonding energy rapidly. It follows that the "best" hydrogen bond is "close" to linear.Here the angle between the D-H bond and the H...A hydrogen bond should be close to 180° for a strong hydrogen bond. However, usually the structural restraints in proteins will enforce minor deviations from linearity. Most main chain-main chain hydrogen bonds in high resolution protein structures have D-H...A angles between 150° and 180°.
Donor-Acceptor distance cut-off (oxygen and nitrogen) = 4.50Å
Donor-Acceptor distance cut-off (sulphur) = 4.50ÅREFERENCES :
[1] http://pps00.cryst.bbk.ac.uk/course/section9/index.shtml
[2] J. Overington, et al. Proc. Roy. Soc. Biol Sci. 1990, pg.132Â145