The Ramachandran Plot

Question 1

What is the ramachandran plot based on?

Answer 1

Based on van der waals repulsions

Question 2

What is a ramachandran plot?

Answer 2

Shows which values of psi and phi are allowed
Visualise energetically allowed regions for dihedral angles
Shows what’s allowed for alanine dipeptide
Plot is like energy surface in 3D

Question 3

What is alanine dipeptide

Answer 3

Central to 3D structure of proteins

Question 4

What is the actual plot of?

Answer 4

Plot of van der waals repulsive energy as a function of psi and phi
3D energy surface

Question 5

What is an exception regarding conformation?

Answer 5

Proline

Can be cis or trans and is a helix breaker

Question 6

Describe the ramachandran plot of glycine

Answer 6

Plot untypical and symmetric as it has no side chain
Also an exception
Confers special folding possibilities- right turns

Question 7

Describe the ramachandran plot of of the other 18 amino acids with CB atoms

Answer 7

Extra steric clashes involving CB

This eliminates considerable region and means only 2 regions are allowed - correspond to aR and B

Question 8

How do you read a ramachandran plot?

Answer 8

White with tick is allowed
Grey hatched area is forbidden- labels show clashes
Labels show pairwise steric clashes between main chain atoms
Dotted lines- ok