A protein's primary structure is the covalent sequence of amino-acid residues in each polypeptide chain. Because the chain has N-to-C directionality, sequence is ordered information: changing the position of a residue can change the molecule even when the overall amino-acid composition stays the same.

For example,

$$\mathrm{Ala-Gly-Ser}$$

and

$$\mathrm{Ala-Ser-Gly}$$

have the same three kinds of residues but different primary structures.

Primary structure determines which side chains occur at each position and constrains every higher level of protein organization.

Secondary structure

The polypeptide backbone contains repeated carbonyl groups, C=O, and N-H groups capable of hydrogen bonding. Regular patterns of backbone hydrogen bonds can stabilize recurring local conformations called secondary structures.

Two especially common motifs are the α helix and β sheet.

α helix

In an α helix, the backbone coils into a right-handed helix in ordinary proteins. Hydrogen bonds form between backbone C=O and N-H groups separated along the same chain. The side chains project outward from the helical backbone, where they can interact with solvent or other parts of the protein.

β sheet

A β sheet is built from extended β strands lying alongside one another. Hydrogen bonds form between backbone groups on neighboring strands. The strands can run in the same N-to-C direction (parallel) or in opposite directions (antiparallel).

The side chains alternate roughly above and below the sheet.

Secondary structure is a backbone pattern

The defining hydrogen-bond pattern of α helices and β sheets belongs mainly to the backbone. Side chains influence which local conformations are favorable through their size, charge, polarity and steric interactions, but they are not what defines a helix or sheet.

Other local conformations, including turns and loops, connect these regular motifs and can be equally important for protein function.

Secondary structure therefore describes local backbone organization. The complete three-dimensional arrangement of an entire polypeptide is a separate level of structure.