Every amino acid can form hydrogen bonds through its backbone, but 11 amino acids also form hydrogen bonds through their side chains. These fall into two groups: polar uncharged amino acids (serine, threonine, asparagine, glutamine, tyrosine, cysteine, and tryptophan) and charged amino acids (aspartic acid, glutamic acid, lysine, arginine, and histidine). The remaining amino acids have nonpolar side chains that lack the right atoms to participate in hydrogen bonding.
How Hydrogen Bonds Work in Amino Acids
A hydrogen bond forms when a hydrogen atom attached to an electronegative atom (usually oxygen or nitrogen) is attracted to another electronegative atom nearby. This requires two things: a donor group that provides the hydrogen and an acceptor group that attracts it. In proteins, the optimal distance between donor and acceptor atoms is about 2.9 angstroms, with a bond angle around 155 degrees.
Every amino acid shares the same backbone structure, which contains both a nitrogen-hydrogen group (donor) and a carbonyl oxygen (acceptor). These backbone atoms are responsible for the hydrogen bonds that create alpha helices and beta sheets, the two most common structural patterns in proteins. In an alpha helix, each backbone carbonyl oxygen bonds to the nitrogen-hydrogen group four residues ahead, coiling the chain into a tight spiral. In beta sheets, two stretches of the chain lie side by side and are stitched together by hydrogen bonds running between them.
Side chain hydrogen bonds are a separate matter. Only amino acids whose side chains contain oxygen, nitrogen, or (in some cases) sulfur atoms can participate. These side chain interactions help fine-tune protein shape, stabilize enzyme active sites, and mediate interactions between proteins and other molecules.
Polar Uncharged Amino Acids
Six amino acids have polar but uncharged side chains, and all six form hydrogen bonds.
- Serine and threonine each carry a hydroxyl group (an oxygen bonded to a hydrogen). This group acts as both a donor and an acceptor, making these two amino acids versatile hydrogen bonding partners. Their side chains are small and flexible, so they frequently appear on protein surfaces where they interact with water.
- Asparagine and glutamine carry an amide group, which combines a nitrogen-hydrogen donor with a carbonyl oxygen acceptor. Glutamine’s side chain is one carbon longer than asparagine’s, giving it slightly more reach. Both are common at positions where proteins need to form specific, directional contacts.
- Tyrosine has a hydroxyl group attached to a six-membered aromatic ring. This ring makes the hydroxyl slightly more acidic than in serine or threonine, but it still functions as both donor and acceptor. Tyrosine is particularly important in structural motifs like the “tyrosine corner,” where its hydrogen bond helps anchor turns in the protein chain.
- Cysteine carries a sulfhydryl group, a sulfur atom bonded to hydrogen. Sulfur is less electronegative than oxygen, so cysteine’s hydrogen bonds are weaker. Interestingly, cysteine acts as a hydrogen donor far more often than as an acceptor, at a ratio of roughly 2:1 to 5:1. When donating, its usual partner is a backbone oxygen. This imbalance may partly result from the sulfur atom participating in other types of interactions that compete with its acceptor role.
Charged Amino Acids
Five amino acids carry a net electrical charge at physiological pH, and all five form hydrogen bonds. Their charged status actually makes their hydrogen bonds stronger than those of uncharged polar residues, because the full charge creates a more powerful electrostatic attraction.
- Aspartic acid and glutamic acid (the acidic pair) carry negatively charged carboxylate groups at neutral pH. Each carboxylate has two oxygen atoms that serve as hydrogen bond acceptors. These residues are critical in enzyme active sites, where their ability to shuttle protons and form precise hydrogen bond networks drives chemical reactions.
- Lysine has a long, flexible side chain ending in a positively charged amino group with three hydrogens available for donation.
- Arginine carries a guanidinium group with five potential hydrogen bond donors spread across three nitrogen atoms. This makes arginine one of the most prolific hydrogen bonding amino acids and explains why it frequently appears at protein-protein interfaces and in DNA-binding regions.
- Histidine has an imidazole ring containing two nitrogen atoms. One acts as a donor, the other as an acceptor. Histidine is unique because its side chain has a pKa near 6.5, meaning small shifts in pH around the physiological range can flip it between charged and uncharged states. This switching ability makes histidine essential in enzyme catalysis, where it often shuttles protons between other residues.
Tryptophan: The Overlooked Contributor
Tryptophan is often grouped with the nonpolar amino acids because its large, double-ringed side chain is mostly hydrophobic. But it contains a nitrogen-hydrogen group on its indole ring that acts as a hydrogen bond donor. Studies of buried, conserved residues in proteins show that tryptophan has a high tendency to form hydrogen bonds to backbone atoms, particularly in beta strands and tight helical turns. It cannot accept hydrogen bonds through this group, however, so its role is more limited than that of tyrosine or serine.
Methionine: A Weak Acceptor
Methionine is another amino acid usually classified as nonpolar, but its sulfur atom can act as a weak hydrogen bond acceptor. The sulfur is buried within a thioether linkage (bonded to two carbon atoms with no hydrogen of its own to donate), so it can only accept, never donate. These interactions are weaker than typical oxygen- or nitrogen-based hydrogen bonds and are relatively rare in protein structures, but they do occur.
How pH Changes the Picture
The hydrogen bonding capacity of charged amino acids depends on their protonation state, which shifts with pH. At neutral pH (around 7), aspartic acid and glutamic acid are deprotonated and carry negative charges, acting as acceptors. Drop the pH below about 4, and they pick up a proton, gaining donor capability but losing their charge.
Histidine is the most pH-sensitive of all. With a pKa around 6.5, it transitions from mostly protonated (positively charged, strong donor) at slightly acidic pH to mostly neutral at pH 7 and above. In its neutral state, one ring nitrogen donates while the other accepts. In its charged state, both nitrogens can donate. This dual personality is why histidine appears so frequently in enzyme active sites. In the serine protease family, for example, a histidine residue sits between a serine and an aspartate, forming a hydrogen bond relay that enables the enzyme to cut protein chains.
Lysine and arginine, with pKa values above 10, remain positively charged and fully capable of hydrogen bond donation across virtually the entire physiological pH range.
Which Amino Acids Cannot Form Side Chain Hydrogen Bonds
The remaining amino acids have side chains made entirely of carbon and hydrogen atoms, which lack the electronegativity needed for hydrogen bonding. These are glycine (which has no side chain beyond a single hydrogen), alanine, valine, leucine, isoleucine, proline, and phenylalanine. Their role in protein structure centers on hydrophobic packing in the protein interior rather than directional hydrogen bonding. Proline is a special case: its side chain loops back and bonds to its own backbone nitrogen, which eliminates that nitrogen’s ability to donate a backbone hydrogen bond as well.