A protein primary sequence is linear, but forms a three dimensional shape in order to form the functional protein. The most basic layer of this structure formation is the protein secondary structure.

Figure 1: Examples of protein secondary structures represented as cartoon form using PyMol, depicting (A) α-Helix, (B) β-Sheet and (C) Loop structures found in Mouse Dihydrofolate Reductase (DHFR) (PDB ID: 3D80). Also shown is a part of the DHFR sequence with protein secondary structures shown against each residue. As protein secondary structure is local, it can be represented in this way as a linear string alongside the protein primary sequence.

The protein secondary structure is a description of the local interactions between nearby amino acids, and what sort of shape that small region of the protein adopts. These take place between amino acids that are near each other (at most five or six amino acids) in the primary sequence. These local interactions form 4 types of structure (Figure 1), these are:

Alpha helix - These are spiral structures where the amino acids form a helical structure, resembling a spiral, or old fashioned telephone coil. This is a very common type of structure, and is found in a lot of different types of protein. One particularly notable example is collagen, which is a structural protein found in hair and muscle tissue.

Beta sheet - These are zigzagging chains. Several of them together also frequently interact with each other to form sheets, where the zigzagging protein chains layer upon one another, hence the name, beta sheet. These are found less frequently than alpha helices, but a notable protein that contains them is silk. They form quite strong structures.

Turn - Turns are sharp kinks in the protein chain where the protein changes direction. They take up a smaller number of amino acids than other forms of secondary structure, and so in terms of proportion of amino acids in proteins they occur less frequently than other secondary structures, however they are important for forming the correct protein structure. They are frequently formed by proline amino acids, which are rigid and force the protein chain into the turn structure.

Loops - Loops are the least structured of the protein secondary structures. As the name suggests, the protein chain forms an long loop, like a lasso. These types of structure occur quite frequently in proteins, and usually link together other forms of protein secondary structure, and their flexibility in which shapes they form is an important part of how they form higher level protein structures.

Protein secondary structures can be represented linearly, as each amino acid will form one of these structures. So this information can be considered like an additional sequence, providing additional information on top of the protein primary sequence.

There are algorithms for predicting protein secondary structures based on the composition of the protein primary sequence. A commonly used one is the Williams method, which is able to predict helices, sheets, turns and loops from protein primary sequence. A method specific for helices is AGADIR, which predicts the likelihood that a sequence will form an alpha helix, and provides more sophisticated predictions specifically for this type of sequence, but is less useful for general secondary structure predictions.

A protein secondary structure formed by local interactions is the structure that allows the protein's gross macro-structure to form, or the protein tertiary structure.