Choose any three regions in the Ramachandran plot and discuss the likelihood of observing that combination of \(\phi\) and \(\psi\) in a peptide or protein. Defend your answer using suitable molecular models of a peptide.

The Ramachandran plot is a graphical representation of the possible conformations of a polypeptide chain based on the dihedral angles phi (φ, the angle between the nitrogen and the α-carbon) and psi (ψ, the angle between the α-carbon and the carbonyl carbon). The plot represents an array of φ and ψ values, giving us energetically favorable regions that correspond to secondary structures in proteins (α-helix, β-sheet, and left-handed helix)

Let's choose three regions: (1) the bottom left quadrant, corresponding to the beta (β-sheet) region, (2) the top left quadrant, corresponding to the alpha helix (α-helix) region, and (3) the small blob in the bottom right quadrant corresponding to the left-handed alpha helix (αL-helix) region. The β-sheet region is characterized by extended conformations (ψ near 180°, φ near -180°), making it likely to occur in proteins, as they can form hydrogen bonds with each other and provide good structural stability. α-helix regions also provide stable structures (ψ near -60°, φ near -60°). The αL-helix area (-60°<ψ<-30°, 30°<φ<60°) is much less populated because, although it's theoretically possible, such conformations are rarely seen due to steric hindrance.

The α-helix conformation allows for internal hydrogen bonding, creating a stable, helical structure. The β-sheet conformation also permits hydrogen bonding, but between different strands, allowing for extended, planar structures. The left-handed helix, the least common conformation, suffers from structural issues because of steric clashes between the side chains leading to higher energy states, hence it's rarely seen in nature.