Alpha helices and beta sheets are the two main shapes that a protein’s backbone folds into as it builds its three-dimensional structure. They’re called “secondary structures” because they represent the second level of protein organization: after a chain of amino acids is assembled (primary structure), local sections of that chain twist into coils (alpha helices) or stretch out and align side by side (beta sheets), held together by hydrogen bonds between atoms in the protein backbone. Nearly every protein in your body contains some combination of these two shapes, and their arrangement determines how the protein functions.
How Alpha Helices Form
An alpha helix looks like a coiled spring or spiral staircase. The protein backbone winds tightly around a central axis while the amino acid side chains stick outward, away from the core of the coil. What holds this shape together is a repeating pattern of hydrogen bonds: the oxygen atom on one amino acid forms a hydrogen bond with the nitrogen-hydrogen group on the amino acid four positions ahead in the chain. This “i to i+4” bonding pattern runs the entire length of the helix and gives it remarkable regularity.
The geometry is precise. An alpha helix completes one full turn every 3.6 amino acid residues, rising about 5.4 angstroms (roughly half a nanometer) with each turn. Each residue contributes 1.5 angstroms of vertical rise along the helix axis, and consecutive residues are rotated 100 degrees from each other around the central axis. The helix is almost always right-handed, meaning it spirals clockwise as you look down its length.
Not all amino acids are equally happy in a helix. Alanine, one of the smallest amino acids, has one of the highest tendencies to appear in alpha-helical regions. In protein crystal structures, alanine residues are three times as likely to be found in alpha helices as in beta sheets. By contrast, glycine (the smallest amino acid, with no real side chain) and proline (which has a rigid ring that kinks the backbone) tend to disrupt helices. The side chains of neighboring residues in a helix also interact with each other across turns, and these lateral contacts help tighten and stabilize the coil beyond what hydrogen bonds alone can do.
How Beta Sheets Form
Beta sheets have a very different look. Instead of coiling, sections of the protein chain stretch out into nearly flat strands. Two or more of these strands then line up next to each other, connected by hydrogen bonds that run sideways between the strands rather than along a single strand. The result is a broad, pleated surface, sometimes called a beta pleated sheet. The side chains of each amino acid alternate above and below this sheet, pointing in opposite directions like teeth on a comb.
Beta sheets come in two arrangements depending on which direction the neighboring strands run. In a parallel beta sheet, adjacent strands run in the same direction (both from the starting end to the finishing end of the chain). In an antiparallel beta sheet, neighboring strands run in opposite directions. This distinction matters because it changes the hydrogen bonding geometry. Parallel sheets form a network of evenly spaced 12-atom rings between strands. Antiparallel sheets form an alternating pattern of smaller 10-atom rings and larger 14-atom rings, which creates a mix of tightly bonded pairs and more loosely connected pairs.
Antiparallel sheets tend to be slightly more stable because their hydrogen bonds align more directly between the two strands, while parallel sheets have bonds that sit at a slight angle. In antiparallel sheets, the side chains in the tightly bonded 10-atom rings can also interact more closely with each other, which adds extra stability but also means bulky side chains are more likely to clash in those positions.
What Keeps These Structures Stable
Hydrogen bonds between backbone atoms are the primary glue for both alpha helices and beta sheets, but they’re not the whole story. Side-chain interactions between amino acids play a surprisingly important role. In alpha helices, the side chains of residues that sit on adjacent turns of the coil can attract each other, effectively squeezing the helix into its preferred shape. Simulations have shown that hydrogen bonding alone can stabilize either a standard alpha helix or a slightly different helix type (called a 3₁₀ helix) equally well. It’s the attractive forces between side chains that explain why alpha helices overwhelmingly dominate in real proteins.
For beta sheets, side-chain interactions are even more critical. The lateral contacts between amino acids on neighboring strands help hold the sheet together and influence which amino acids pair up across strands. Computer simulations suggest that without these side-chain forces, isolated beta hairpins (a simple two-strand sheet connected by a turn) essentially never form on their own. Both backbone hydrogen bonds and side-chain contacts are needed, and these structures tend to form early during the protein folding process, serving as scaffolding around which the rest of the protein organizes itself.
Backbone Angles Tell the Story
Every amino acid in a protein chain has two key rotational angles along the backbone, commonly called phi and psi. These angles describe how each amino acid is oriented relative to its neighbors, and they determine which secondary structure a stretch of protein adopts. Scientists visualize these angles on a Ramachandran plot, a map that shows which combinations of phi and psi are physically possible and which ones correspond to known structures.
Alpha helices cluster very tightly on this map, centered around phi = -63 degrees and psi = -43 degrees. This narrow clustering reflects how rigid and uniform the helical shape is. Beta strands, by contrast, are more flexible. Their most common angles fall near phi = -120 degrees and psi = +130 degrees, but they spread across a range of about 80 degrees in each direction. This broader distribution means beta strands can accommodate more variation in their geometry, which is part of why beta sheets can form such diverse shapes in different proteins.
Where You Find Them in Real Proteins
Most proteins contain a mix of alpha helices and beta sheets, but some lean heavily toward one or the other. Proteins that bind DNA and RNA often rely on alpha-helical structures. The Pumilio homology domain, found in proteins that regulate gene expression by binding RNA, is built almost entirely from two layers of alpha helices that curve to fit the shape of a nucleic acid strand.
Beta-sheet-rich proteins are common in the immune system and in structural roles. The leucine-rich repeat domain, found in immune receptors that recognize pathogens and in proteins involved in cell adhesion, features an inner layer of beta sheets backed by an outer layer of alpha helices. This arrangement forms a curved, basket-like shape with an inner diameter of up to 30 angstroms, perfectly sized to cradle a binding partner.
Structural proteins outside the cell also showcase these shapes. Keratin, the protein in hair and nails, is built from coiled alpha helices wound around each other. Silk fibroin, the protein in spider silk, consists of stacked beta sheets that give the material its combination of strength and flexibility. The shape a protein adopts at this secondary level directly influences its mechanical properties, binding ability, and biological role.