Chapter 6, Problem 1P

Interpretation Introduction

Interpretation:

The helix with respect to handedness from the Ramachandran plot needs to be described.

Concept introduction:

Ramachandran plot was developed in the year 1963. The amino acid residues in present in the protein structure are represented by the plot using the dihedral angles psi and phi. In this plot, the lower left and upper right quadrant represent residues in helical conformation.

Explanation of Solution

As per the figure, there is left handed alpha helix on the upper right and the right-handed helix on the lower left quadrant. The φ has C − N − C_a − C bonds while Ψ has N − C_a − C − N bonds. In φ, the rotation takes place at N − C_a and in Ψ, the rotation occurs at C_a − C bond.

The Ramachandran plot is as below:

  

The alpha helix observed is likely to be explained by the dihedral angle φ which is -80° and Ψ is +150°, this represents many glycine residues. Therefore, the common observation here in the given plot is that the alpha helix is left handed.

  

The residues number is 3.6 and for every residue, the translation distance is 0.150.

Thus, the alpha helix is left handed.