194. Amide bonds between two amino acids (as shown below) are generally in trans-conformation.
The atoms are labeled as A1 through A6. The angle measured for defining the trans-conformation
of the amide bond is the angle between:
A. the atoms A2, A3 and A4.
B. the planes formed by A1, A3, A4 and A3, A4, A6.
C. the planes formed by A2, A3, A4 and A6, A4, A5.
D. the planes formed by A2, A3, A4 and A3, A4, A6

Explanation:

Amide bonds in proteins, formed between the carboxyl group of one amino acid and the amino group of another, typically adopt a trans-conformation to minimize steric hindrance. This geometric preference is due to the partial double bond character of the amide linkage, which restricts rotation and creates planar peptide bonds.

🔬 What defines the trans-conformation?

• The trans-conformation is defined by the dihedral angle (omega, ω).

• It involves the planarity around the peptide bond, specifically between:

  • The plane before the carbonyl carbon (C=O) — defined by atoms like Cα–C–N.

  • And the plane after the amide nitrogen — defined by C–N–Cα.

In the context of labeled atoms:

• A2–A3–A4 defines part of the amide plane.

• A3–A4–A6 defines the adjacent part.

So the trans angle is best measured between these two planes, i.e.:

Plane 1: A2–A3–A4
Plane 2: A3–A4–A6

Correct Answer: D. the planes formed by A2, A3, A4 and A3, A4, A6