The side chain atoms of amino acids are named in the Greek alphabet according to this scheme.
The side chain torsion angles are named c1(chi1), c2(chi2), c3 (chi3), etc., as shown below for lysine.
The c1 angle is subject to certain restrictions which arise from steric hindrance between the g side chain atom(s) and the main chain. The different conformations of the side chain as a function of c1 are referred to as gauche(+), trans and gauche(-). These are indicated in the diagrams below in which the amino acid is viewed along the Cb-Ca bond.
The most abundant conformation is gauche(+) in which the g side chain atom is opposite to the residue's main chain carbonyl group when viewed along the Cb-Ca bond.
The second most abundant conformation is trans in which the side chain g atom is opposite the main chain nitrogen.
The least abundant conformation is gauche(-) which occurs when the side chain is opposite the hydrogen substituent on the Ca atom. This conformation is unstable because the g atom is in close contact with the main chain CO and NH groups. The gauche(-) conformation is occasionally adopted by serine or threonine residues in a helix where the steric hindrance is offset by a hydrogen bond between the g oxygen atom and the main chain.
With most amino acids the gauche(+) and trans conformations are adopted with similar abundances although the gauche(+) conformation tends to dominate.
Aliphatic amino acids which are bifurcated at Cb, ie valine and isoleucine, do not adopt the trans conformation very often as this involves one of the Cg atoms being in the unfavourable gauche(-) 'position'.
In general, side chains tend to adopt the same three torsion angles (+/-60 and 180 degrees) about c2 since these correspond to staggered conformations. However, for residues with an sp2 hydridised g atom such as phenylalanine, tyrosine, etc., c2 rarely equals 180 degrees because this would involve an eclipsed conformation. For these side chains the c2 angle is usually close to +/-90 degrees as this minimises close contacts. For residues such as aspartate and asparagine the c2 angles are strongly influenced by the hydrogen bonding capacity of the side chain and its environment. Consequently, these residues adopt a wide range of c2 angles.
Here are some conformations that can be adopted by Arginines:
Last modification: Please note that these pages have not been updated since 1999 and are provided on a "as is basis". We are currently working on an updated version of this course.