3 Side Chain Conformation.


The side chain atoms of amino acids are sequentially named according to the Greek alphabet. This naming scheme is commonly translated to latin characters. For example, a lysine side chain is comprised of a β carbon (CB), a γ carbon (CG), a δ carbon (CD), an ε carbon (CE) and a Ζ nitrogen (NZ). Ambiguities, for example in phenylalanine, are resolved with numbers.

Atom naming in amino acid side chains
Atom naming in amino acid side chains Left: Lysine, Right: Phenylalanine

We suggest to consult the protein data bank as a naming reference, e.g. https://www.rcsb.org/ligand/LYS. Due to almost constant bond lengths and bond angles, amino acid side chains can approximately be described with a set of up to 4 dihedral angles (sequentially numbered chi angles, i.e. Χ1-4). The side chain conformations, so called rotamers, cluster around energetically preferred conformations.

Naming convention in protein side chains
Side chain dihedrals Chi (Χ) angles defining side chain conformations in a lysine-tyrosine di-peptide

The Χ1 angle is subject to restrictions due to steric hindrance between the γ side chain atom(s) and the main chain. The favoured conformations of the side chain torsion angles are referred to as gauche(+), trans and gauche(-). These are indicated in the diagrams below in which the amino acid is viewed along the Cβ-Cα bond (Χ1).

Overview of different chi-angle conformations
Side chain conformations. Left: Χ12 plot for Lysine. The color gradient indicates the frequency of conformations found in experimentally determined protein structures. Right: Schematic view into the Cβ (top)-Cα (hidden below) bond. Here the Χ1 angle can be seen as the angle between the Nitrogen and Cγ atom.

The most frequent Χ1 conformation is gauche(+) in which the γ side chain atom is opposite to the residue main chain carbonyl group when viewed along the Cβ-Cα bond.

The second most frequent Χ1 conformation is trans in which the side chain γ atom is opposite the main chain nitrogen.

The least frequent Χ1 conformation is gauche(-) which occurs when the side chain is opposite the hydrogen substituent on the Cα atom. This conformation is unstable because the γ 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 γ oxygen atom and the main chain.

Aliphatic amino acids which are bifurcated at Cβ, i.e. valine and isoleucine, do not adopt the trans conformation for Χ1 very often as this involves one of the Cγ atoms being in the unfavourable gauche(-) 'position'.

In general, side chains tend to adopt the same three torsion angles (+/-60 and 180 degrees) about Χ2 since these correspond to staggered conformations. However, for residues with an sp2 hybridised γ atom such as phenylalanine, tyrosine, etc., Χ2 rarely equals 180 degrees because this would involve an eclipsed conformation. For these side chains the Χ2 angle is usually close to +/-90 degrees as this minimises close contacts. For residues such as aspartate and asparagine the Χ2 angles are strongly influenced by the hydrogen bonding capacity of the side chain and its environment. Consequently, these residues adopt a wide range of Χ2 angles.