What does a Ramachandran plot illustrate?

A Ramachandran plot is a graphical representation used to visualize the backbone dihedral angles (phi and psi) of amino acids in protein structure. It illustrates the conformational angles that are favorable or allowed, showcasing the steric hindrance that arises from the spatial arrangement of atoms in proteins. The plot essentially identifies regions where certain combinations of the phi (φ) and psi (ψ) angles are physically possible based on steric interactions, indicating which conformations lead to stable structures in proteins.

The plot highlights clusters that correspond to common secondary structural elements in proteins, such as alpha helices and beta sheets, demonstrating where these favorable angles reside. By analyzing this plot, scientists can gain insights into allowable conformations that a peptide or protein can adopt, which is crucial for understanding protein folding and stability.

The other options address concepts that are distinct from the focus of a Ramachandran plot. Protein-protein interaction sites involve the regions where proteins bind to one another, which is not represented in the angle plot. The sequence of amino acids in a peptide pertains to the primary structure, while thermodynamic stability refers to the favorability of a protein's overall stability, which is evaluated through different methods rather than directly through the Ramachandran plot.