Peptide Secondary Structure: Helices, Sheets and Turns

By What Peptides Editorial Team · Updated 2026-09-14 · Part of What Peptides Are: Structure, Bonds and How Chains Are Built

Secondary structure is the local, repeating arrangement of the peptide backbone, held in place by hydrogen bonds between backbone carbonyl and amide groups. It does not describe how side chains are arranged or how the whole chain folds up, only how short stretches of backbone pack against themselves. Three motifs account for almost everything observed: the alpha helix, the beta sheet, and the turns and loops that connect them.

Secondary structure is possible because of what the peptide bond cannot do. With the amide group locked planar by resonance and only phi and psi free to rotate, the backbone has so few degrees of freedom that a handful of regular arrangements satisfy its hydrogen bonding capacity without steric clashes. This page gives the patterns, the geometry and the angles. The chemical background is in our peptide chemistry and structure reference.

What Secondary Structure Means

The definition has three parts: local, repeating, and stabilised by backbone hydrogen bonds. Local means it involves residues near each other in the sequence, not the long-range contacts that define tertiary structure. Repeating means the same phi and psi values recur residue after residue. Backbone hydrogen bonding means the amide hydrogen and carbonyl oxygen of the chain itself are the partners, which is why secondary structure can form in almost any sequence and why side chains mostly modulate rather than determine it.

The alpha helix is the most familiar motif. The carbonyl oxygen of residue i hydrogen bonds to the amide hydrogen of residue i plus four, giving an i to i+4 pattern that runs the length of the helix. There are 3.6 residues per turn, the rise along the helix axis is 1.5 angstroms per residue, and the pitch is therefore 5.4 angstroms. All carbonyls point one way along the axis and all amide hydrogens the other, which gives the helix a net dipole with a partial positive charge at the N-terminal end.

Beta sheets are built differently. Instead of a single chain coiling, two or more extended strands lie side by side and hydrogen bond between them. Strands are nearly fully extended at about 3.5 angstroms per residue, which produces the pleated appearance of the sheet. Side chains project alternately above and below the sheet plane. When neighbouring strands run in the same direction the sheet is parallel and the hydrogen bonds are slanted; when they run in opposite directions it is antiparallel and the bonds are close to perpendicular, which makes antiparallel sheets slightly more stable.

Turns, Loops and the Residues That Break Motifs

A chain cannot run in a straight line and fold back on itself without a reversal, and that reversal is the turn. A beta turn involves four residues and is often stabilised by a hydrogen bond from residue i to residue i plus three. Glycine and proline appear in turns far more often than their overall frequency would predict: glycine because its single-hydrogen side chain allows angles no other residue can reach, and proline because its ring already imposes a bend and because it is comfortable in the cis configuration the tightest turns require.

Proline is also the classic helix breaker, and for a simple structural reason. Its nitrogen is part of a five-membered ring, so it has no amide hydrogen to donate to an i to i+4 hydrogen bond, and its fixed phi angle does not match the helical value. A proline in the middle of a predicted helix therefore usually introduces a kink of roughly 20 to 30 degrees and terminates the helix. Loops, by contrast, are longer irregular regions that lack a repeating pattern; they are frequently the parts of a structure that move and that carry functional residues.

Two less common backbone arrangements are worth knowing. The 3-10 helix uses an i to i+3 hydrogen bond with three residues per turn, and appears as a short segment at the ends of alpha helices. The polyproline II helix is an extended left-handed arrangement with three residues per turn and a rise of about 3.1 angstroms, stabilised without any backbone hydrogen bonds because proline has none to donate, and it is a common motif in collagen and in unfolded chains.

Which Backbone Angles Allow Which Motif

Plotting phi against psi for each residue gives a map in which observed conformations cluster into a few permitted regions, because most combinations produce steric clashes between backbone and side chain atoms. The right-handed alpha helix occupies a region near minus 57 and minus 47 degrees. Beta strands sit in the upper left of that map, near minus 120 and plus 120, in a broad region rather than at one point. Left-handed helices, with positive phi values, are essentially restricted to glycine.

The table collects the geometric parameters of the common motifs. Residues per turn and rise per residue are the two numbers worth committing to memory, because they let you convert a helix length into a residue count and back. backbone geometry and chain direction explains where those angles come from, and what holds a folded chain together covers the level above. How these motifs respond to drying is discussed in how lyophilisation is carried out.

This page is part of the What Peptides Are: Structure, Bonds and How Chains Are Built guide.