The primary structure is the number and sequence of amino acids held together by peptide bonds in a polypeptide chain. The primary structure of a protein only describes the order of amino acids in the chain but tells.us nothing of the shape of the chain. While folding, kinking, or even pleating of the protein chain by the interactions between the bonded amino acids of the primary structure constitute the secondary structure of the protein molecule. Ionic bonds, van der Waals interactions, and hydrogen bonding are largely responsible. for these changes in the configuration of the protein chain.