Hydrogen bonding

The rotamer preferences can be explained in term of hydrogen bonding. The backbone nitrogene of N-cap, N1, N2, N3 are not involved in the helical (i, i+4) backbone hydrogen bond, so specific bond with the side chain occurs. (For example, the Capping box [Presta & Rose, 1988]). Here we found specific hydrogen bonds in which the side chain of Ni bonds to the nitrogen backbone of Ni (i.e. MiSi) or Ni+1 (i.e. Mi+iSi).
Amino acids present different ability to make this bonds, Glu, Asp, Gln and Asn making the best bonds. Following are the M2S2 and M3S2 hydrogen bonds in N2 which explain the prefrences for g^-g⁺, g⁺g^- and g^- rotamers.

Glu in g- g+ conformation. The g- g+ conformation is due to the M2S2 hydrogen bond, where the side chain oxygen of Glu in N2 bonds to its backbone nitrogen. PDB Models Animated picture

M2S2 with Glu in g- g+ .

Glu in g+ g- conformation. The g+ g- conformation is due to the M2S2 hydrogen bond, where the side chain oxygen of Glu in N2 bonds to its backbone nitrogen. PDB Models Animated picture

M2S2 with Glu in g+ g- .

Asp in g- conformation. The g- conformation is due to the M2S2 and M3S2 hydrogen bonds, where the side chain oxygen of Asp in N2 bonds to backbone nitrogens of N2 and N3. PDB Models Animated picture

M2S2/M3S2 with Asp in g-.