A peptide is a chain of amino acids linked together by peptide bonds. Polypeptides usually refer to long peptides whereas oligopeptides are short peptides (< 10 amino acids). Proteins are made up of one or more polypeptides with more than 50 amino acids.
The primary structure of a protein refers to its amino acid sequence. The amino acid in a peptide is also called a residue.
A peptide bond is the linkage between two amino acids, formed by the condensation reaction, as shown below:
Due to the specific electronic structure of the peptide bond, the atoms on its two ends cannot rotate around the bond. Hence, the atoms of the group, O=C-N-H, are fixed on the same plane, known as the peptide plane. The whole plane may rotate around the N-Cα bond (φ angle) or C-Cα bond (ψ angle). Cα is the carbon atom connected to the R group.
Mathematically, phi (φ) and psi (ψ) are the dihedral angle (also known as torsional angle) which is defined as the angle between the point (e.g., Cα) at the end of a 4-point sequence and the plane (e.g., peptide plane) occupied by the other three points. In a peptide, phi-psi angles are restricted to certain ranges. A plot of their distribution is called the Ramachandran plot.