Protein Secondary Structure


Proteins are molecular chains, composed of amino acids joined together by peptide bonds. Two of the most easily achievable folding patterns of a protein chain correspond to the most common forms of protein secondary structure, the α-helix and the β-pleated sheet. Let's get a quick overview of each struture using examples from the chlorophyll A protein.

View α-helix
View β-sheet

The fact that these are the most common shapes that a protein chain adopts is important--it indicates that these specific shapes are somehow stabilized efficiently in many different chains of amino acids.

While the α-helix is the most common form of helix in proteins, there are other kinds of helices too. They are rare, however, and we will not consider them here. β-sheets exist in two varieties: parallel and anti-parallel. Different kinds of turns in the chain are also classified as secondary structures. A fourth and final type of secondary structure, known as random coil, refers to folds of the protein that do not fit into a classification. About 50% of all protein structure comes under this category.

Peptide Bonds

Peptide bonds are formed as a protein is synthesized, between the carboxylic acid group of one amino acid and the amimo group of the next. Peptide bonds are rigid, planar bonds due to a degree of resonance that gives them a partial double bond character. There is no rotation around a peptide bond, so it confers some limitations to the folding of a protein chain.


The α-helix is formed when the amino acid backbone curls around at 3.6 amino acids per turn.

An α-helix is a "right-handed" helix: point the thumb of your right hand along the axis of the helix as it grows in the animation, and then curl your fingers. They will curl in the same direction as the helix's spiral. If you do the same with your left hand, your fingers will curl in the opposite direction from the folding of the helix. (This is a convention that makes it easy to talk about the folding direction of helices, whether they are in proteins or in any other context.)

Hydrogen Bonding

Secondary structure is stabilized by hydrogen bonds between backbone carbonyl oxygens and the amide hydrogens. This occurs very regularly due to the characteristic twist of the α-helix backbone, which places these atoms in a good position for hydrogen bonding with a partner atom four residues further along trhe chain.

Sidechain Conformation

The sidechains point outward, away from the helix, where they are available for interaction with solvent, with other parts of the protein, or with other macromolecules.


β sheets are compact and stable structures. They are formed when two or more lengths of a protein chain lie next to each other so as to form hydrogen bonds between their respective backbones. In order for the backbones to be close enough for hydrogen bonds to form, the sidechains must not come between the backbones. Each length that participates in a β sheet is called a β strand.

There are two ways the strands can orient themselves to form &beta sheets: parallel and anti-parallel.

Anti-parallel β Sheets

Protein chains are synthesized starting at the amino terminus and ending at the carboxyl terminus. Thus a protein chain has a directionality. In an anti-parallel β sheet, the beta strands are aligned next to each other, running in opposite directions.

Hydrogen bonding

The backbone hydrogen bonding partners are the carbonyl oxygens and amide hydrogens. They are lined up nearly directly across from each other when the strands of a sheet are anti-parallel. They form fairly straight hydrogen bonds.

Sidechain conformation

The sidechains project out of the plane of the sheet, each consecutive sidechain emerging from the opposite side of the sheet.

Parallel β sheets

When β strands are in the parallel orientation, i.e., they run alongside each other in the same direction, the carbonyl oxygen and the amide protons are staggered, and the hydrogen bonds are on an angle across to the opposite strand.

As with the α-helix, the sidechains of the β sheet are free to interact with the environment, and the tertiary structure of the protein will be influenced by the sidechains projecting out of the β-sheet.

Secondary structure and the Jmol Menu

The secondary structure of a protein can be quickly seen using menu commands. First click View Animation to reset the display.

The α-helices are magenta, β sheets are yellow, and random coil is white.


The following interactive question(s) require you to interact with the structure to arrive at the correct answer. You may use any of the visualization controls or the dropdown menus to help you to answer the questions - direct manipulation of the structure may be required.

Question 1- Load structure

The α heilix and β sheets we've been looking at are parts of the ribosomal protein L9. It is composed of two globular domains with a very long α-helix between them. Given this image of L9 in spacefill, colored by element, use the Jmol menu to change the display to so that you can clearly see both (1) the pattern of the protein chain and (2) the default colors for secondary structure.

View Answer

Question 2 - Load structure
Explore the Jmol menu to find commands relating to hydrogen bonds. Given this display of the backbone of ribosomal L9, display the hydrogen bonds that stabilize secondary structres.
View Answer

Back to Introduction to Jmol page

For additional information or help with Jmol, see Structure Tutorial Help.

Science Technologies