Q.41 The crystal structure of a peptide has an ordered structural repeat of amino acids with a distance
of ∼ 𝟔. 𝟓Å between the alternate 𝐂𝜶 atoms. Which one of the following pair of dihedral angles ( 𝚽 and
𝚿 ) accurately represents the peptide structure?
(A) Φ ≈ −60∘,Ψ ≈ −50∘
(B) Φ ≈ −120∘, Ψ ≈ −50∘
(C) Φ ≈ −60∘, Ψ ≈ +120∘
(D) Φ ≈ −120∘, Ψ ≈ +120∘
Peptide crystal structures reveal secondary motifs through characteristic repeats like the 6.5Å distance between alternate Cα atoms. This spacing points to a specific conformation defined by φ and ψ dihedral angles.
Correct Answer
Option (A) Φ ≈ −60°, Ψ ≈ −50° accurately represents the structure. This combination defines the right-handed α-helix, where the pitch yields ∼6.5Å between every second Cα atom along the helical axis. In α-helices, 3.6 residues turn per coil, with 1.5Å rise per residue, confirming the axial repeat calculation.
α-Helix Details
The α-helix features tight hydrogen bonding between carbonyl oxygen of residue i and amide hydrogen of i+4. Standard dihedral values cluster around Φ = -57°, Ψ = -47°, closely matching option (A). Ramachandran plots show this region as highly favored for non-glycine residues due to steric allowance.
Option Analysis
Each option corresponds to distinct secondary structures, evaluated against the 6.5Å repeat:
| Option | Φ (degrees) | Ψ (degrees) | Structure | Cα Repeat (Å) | Matches? |
|---|---|---|---|---|---|
| (A) | -60 | -50 | α-helix | ∼6.5 | Yes |
| (B) | -120 | -50 | Distorted helix/2.2₇ ribbon | ∼4-5 | No |
| (C) | -60 | +120 | Collagen helix | ∼10 (triple helix) | No |
| (D) | -120 | +120 | β-sheet (parallel/antiparallel) | ∼7 (strand), 4.5-5 (sheet) | No |
β-sheets (D) show ∼3.5Å between adjacent strands but larger repeats across sheets; collagen (C) extends per turn.
Ramachandran Insights
Ramachandran plots map allowed φ-ψ regions: α-helix at (-60,-50), β-sheet at (-120,+120). The 6.5Å repeat excludes β regions, as alternate Cα distance in extended β strands approximates 7Å per residue pair, not matching precisely.
