Folding of a polypeptide chain can occur because of the formation of hydrogen bonds between C=O groups in the backbone with N-H groups located four amino acid residues further along the chain. This leads to a helical structure called the alpha helix. (For clarity, no hydrogens are shown in the ball-and-stick models on this page.)

Another type of secondary structure, the beta pleated sheet, results from the polypeptide chain looping back to form hydrogen bonds between C=O and N-H groups in different regions of the polypeptide, or even between two different polypeptides.