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Dihedral angles in a protein chain. There are two degrees of freedom of rotation, identified by two angles ? and ?. The peptide bonds are in yellow and R1 and R2 indicate the side chains of two consecutive amino acids The main chain contains three covalent bonds per amino acid. The peptide bond is a bond plane, there are two single bonds around which rotation is possible. We can therefore determine the backbone conformation of an amino acid from two dihedral angles, ? and ?.

• The dihedral angle ? is defined by four successive atoms skeletal CO-NH-C?-CO, the first being the carbonyl of the preceding residue.
• The dihedral angle ? is defined by four successive backbone atoms NH-C?-CO-NH, the second being that of the amide residue following.

Ramachandran plot of a protein. The energetically favorable areas are represented by colored contours. Each amino acid is represented by a red dot. The crosses correspond to the amino acid glycine, which does not contain side chains. All values of angles ? and ? are not possible because some lead to too close contacts between atoms that are energetically unfavorable. A systematic study of combinations of allowable angles ? and ? has been made by the Indian physicist and biologist Gopalasamudram Narayana Ramachandran in 1963 [2]. He devised a graphical representation of the space (?, ?) that bears the name of Ramachandran diagram. This diagram shows three main areas energetically favorable. When analyzing a protein structure, we observe that most of the amino acids have combinations of angles (?, ?) that fall within these areas. The two main regions correspond to regular secondary structures are mainly observed in proteins: the ? helix region and the ? sheets. The third area is smaller, corresponding to a left-handed helix conformation (?> 0). There are two specific amino acids that are exceptions to this rule diagram Ramachandran: glycine and proline. Glycine has no side chain (R = H) and, thus, is much less constrained in terms of steric hindrance. It can adopt values (?, ?) much more diverse in regions outside the normally preferred. In contrast, proline is more constrained: it contains a pyrrole cycle that prevents the rotation corresponding to the angle ?.