A peptide diagram may contain many dashed lines labelled hydrogen bonds. These lines describe proposed interactions between particular groups; they are not additional peptide bonds. Understanding the participants and geometry makes the diagram more informative than simply counting its contacts.
Identify the donor, hydrogen and acceptor
A conventional hydrogen-bond sketch uses X–H···Y. X–H is the donor group and Y is the acceptor site. IUPAC's 2011 recommendations emphasise evidence for the interaction and its directional preferences, rather than defining every sufficiently short contact as a hydrogen bond.IUPAC — Definition of the hydrogen bond (opens in a new tab)
In peptide backbones, a carbonyl oxygen can act as an acceptor and an available backbone N–H can act as a donor. Their repeated arrangement contributes to the familiar hydrogen-bond pattern of an alpha helix.EMBL-EBI — Alpha helix (opens in a new tab)
The word available prevents a common counting error. An internal proline does not carry the usual backbone N–H donor. Likewise, chemical modification or protonation can change the groups present at a proposed interaction site. Start from the actual structure, not just the number of N and O atoms.
Within-chain and between-chain contacts differ
| Contact | What is being connected by the interaction |
|---|---|
| Intramolecular | Two groups belonging to the same molecule |
| Intermolecular | Groups on different molecules |
| Solvent contact | A peptide group and a surrounding solvent molecule |
For an original illustration, take one carbonyl oxygen in a folded peptide drawing. A nearby N–H on that same chain could be its depicted partner. In a different conformation, a group on another chain or in the solvent might occupy a relevant position instead. The sequence alone does not decide which arrangement is populated.
This is why a proposed internal hydrogen bond should not be evaluated as though the unconnected groups had no interactions beforehand. The comparison includes the surrounding chemical environment and the alternative arrangements being displaced.
A dashed line is a claim to inspect
IUPAC notes that hydrogen-bond geometry has directional preferences and cautions against using a simple donor–acceptor distance criterion as an infallible identifier. Structural and spectroscopic evidence can contribute to the assignment.IUPAC — Definition of the hydrogen bond (opens in a new tab)
A figure may show hydrogens explicitly, add them computationally or omit them. It may also draw contacts automatically using a software cutoff. Those conventions should be distinguished from a direct experimental observation of every displayed hydrogen position.
Look for the figure legend, the structure method and the rule used to display interactions. If several structures are compared, check that the same rule was applied. Otherwise, a difference in the number of dashed lines may come from the display settings rather than the molecules.
More drawn bonds does not automatically mean more stability
Suppose model A shows four internal hydrogen bonds and model B shows six. That count alone does not compare their free energies: the geometries, solvent contacts, conformational restrictions and other interactions have not been accounted for.
Nor does a donor added by a sequence substitution guarantee a new bond. The proposed partner must be chemically suitable and spatially accessible in the relevant conformation. A plausible drawing is a useful hypothesis that a structural study can test.
- Name the donor and acceptor groups.
- Record whether the contact is within a molecule, between molecules or with solvent.
- Check how the contact was assigned and drawn.
- Keep the number of displayed bonds separate from a measured stability result.
Sources and further detail
- IUPAC — Definition of the hydrogen bond (opens in a new tab)
Recommendations 2011, DOI 10.1351/PAC-REC-10-01-02. Emphasises evidence and directional preferences rather than a universal distance-only rule.
- EMBL-EBI — Alpha helix (opens in a new tab)
Backbone carbonyl/N–H hydrogen-bond pattern in a helix.
Sources checked 19 September 2026. Worked examples are illustrative unless a supplied report is explicitly identified. This article has not undergone independent scientific peer review.