The three-dimensional spatial arrangement of a peptide backbone is determined by the relative orientation of the atoms connected by three repeating bonds in the peptide backbone. The relative orientation of the atoms in the peptide backbone, and therefore the conformation of a polyupeptide, can be described by dihedral (or torsion) angles.

For the three repeating bonds in a peptide backbone the dihedral angles are defined as:

ϕ - to describe rotation about the N-C(α) bond and involves the C(O)-N-C(α)-C(O) bonds

ψ- to describe rotation about the C(α)-C(O) bond and involves the N-C(α)-C(O)-N bonds

ω - to describe rotation about the C(O)-N bond and involves the C(α)-C(O)-N-C(α) bonds

We can visualize the ϕ and ψ dihedral angles using a model polypeptide.

(1). into the JMol window (left). Using the mouse you can interact with the molecule. Familiarize your self with the polypeptide chain.

(2). Concentrate on the third amino acid, move the molecule around, and try to visualize the ϕ and ψ angles for this residue.

(3). It may help to Visualizing the ϕ dihedral angle.

(4). Concentrate only on the



NOTE: Atom label CA designates the C(α) atom, and label C designates the carbonyl carbon atom. The number represents the amino acid to which these atoms belong.

(5). Now rotate the molecule so that you are looking down the bond undergoing rotation. For ϕ torsion angles the bond undergoing rotation is the N-C(α) bond. Rotate the molecule so that you are looking at the N with the C(α) directly behind, and the C(O) group closest to the N-terminus towards the top of the screen, positioned vertically.

(6). It may help to


(7). Now estimate the angle that separates the first and fourth atoms (i.e. the first and second C(O) groups with the first being closest to the N-terminus). This is the ϕ torsion angle.
NOTE: The ϕ torsion angle is the angle that the first C(O) gorup needs to be rotated to eclipse the second C(O) group. Clockwise rotations are positive and counter clockwise rotations are negative.

(8). Now lets concentrate on the





(9). Rotate the molecule so that you are looking down the bond undergoing rotation. For ψ torsion angles the bond undergoing rotation is the C(α)-C(O) bond. This time rotate the molecule so that you are looking at the C(α) with the C(O) directly behind, and the N closest to the N-terminus towards the top of the screen, positioned vertically.

(9). Estimate the angle that separates the first and fourth atoms (i.e the first and second N atoms). This is the ψ torsion angle.
NOTE: The ψ torsion angle is the angle that the first N atom needs to be rotated to eclipse the second N atom. Clockwise rotations are positive and counter clockwise rotations are negative.

Let's check your estimates:

The ϕ torsion angle for the third residue in this peptide -

The ψ torsion angle for the third residue in this peptide -