Bench Primer

Primer 07 of 09 · Structure

Reading a line drawing

Skeletal formulas leave out the carbons and the hydrogens on purpose. Five rules are enough to read any of them, with glycine, leucine and isoleucine drawn out.

4 min read · Updated 21 Oct 2026

A skeletal formula is a compression scheme. It leaves out the atoms that are everywhere, carbon and the hydrogens attached to carbon, so that what is unusual about a molecule stands out. Five rules are enough to read one.

Rule 1 — every corner and every line end is a carbon

Bonds are drawn as lines. Where two lines meet, or where a line simply stops, there is a carbon atom that is not written. A zigzag of four segments is a chain of five carbons.

Rule 2 — hydrogens on carbon are implied

Carbon makes four bonds. Count the lines reaching a corner; whatever is missing from four is hydrogen. A corner with two lines is a CH2, a line end is a CH3.

Rule 3 — anything that is not carbon is written

Nitrogen, oxygen and sulfur appear as their symbols, usually with their own hydrogens attached: OH, NH2, SH. A double bond is two parallel lines.

Glycine, skeletal formula: H2N–CH2–COOHH2NOOH
Glycine. One corner (a CH2), one line end that is a carbon carrying a double-bonded O and an OH, and an NH2. Count it up: C2H5NO2. Source structure: CHEBI:15428.

Rule 4 — wedges show depth

A flat drawing cannot show that a carbon with four different neighbours is a three-dimensional centre. A filled wedge means the bond comes toward you; a hashed wedge means it goes away. Where it matters, the configuration is also named in the text: (S) or (R) for each such centre, L or D for amino acids and sugars.

L-leucine, skeletal formula with the amino group on a filled wedgeNH2OOH
L-Leucine, (2S). One stereocentre, the carbon carrying NH2. CHEBI:15603
L-isoleucine, skeletal formula with the amino group on a filled wedge and the branch methyl on a hashed wedgeNH2OOH
L-Isoleucine, (2S,3S). Two stereocentres: the NH2 carbon and the branching carbon beside it. CHEBI:17191

Rule 5 — charges are written, and a drawing is one form

An amino acid in water exists mostly as a zwitterion: NH3+ at one end, COO− at the other. Drawings usually show the neutral form because it is simpler and the mass is identical. If a charge matters, it is written as a superscript beside the atom that carries it.

In short

  1. 01Corners and line ends are carbons; missing bonds to four are hydrogens.
  2. 02Everything else is written: N, O, S and their hydrogens, double bonds, charges.
  3. 03Wedges are the only depth information. Without them a drawing cannot distinguish mirror-image forms.

Figures on this page are computed at render time from one set of constants (the IUPAC abridged standard atomic weights and the exact masses of the most abundant isotopes), the same set the tables and the calculators use. Structures and identifiers after ChEBI, CC BY 4.0.