Helices E and F form a V-shaped pocket lined with hydrophobic amino acid side chains, into which the heme group (right) is fitted like a silver dollar in a cupped hand. Iron normally prefers octahedral coordination, that is, to have six ligands, or coordinating atoms, arranged around it at the corners of an octahedron. In the heme group four of these six coordinating groups are provided by nitrogen atoms of the porphyrin ring, but the positions above and below the plane of the ring are unoccupied. In myoglobin the fifth position is filled by the nitrogen atom of a histidine side chain, on the F helix, as seen at the left of the heme in the molecular drawing. The sixth octahedral position is open, and it is here that the 0₂ molecule binds when myoglobin stores oxygen. The oxygen-binding position is marked by the light blue lines in the myoglobin drawings. Another five-membered ring of a histidine side chain extends out from position E7 of the E helix, close enough to interact with the bound 0₂ molecule, but not close enough to become a ligand directly to the heme iron.

One of the remarkable aspects of the myoglobin molecule is the way that the properties of the side chains along each a helix help the helices to fold together properly to build the molecule. The inner surfaces of the a helices, where they are to pack against one another, are covered with hydrophobic side chains such as valine, leucine, and phenylalanine. In contrast, the sides of the helices that are to be exposed to the aqueous surroundings in the completely folded molecule have polar side chains, either charged as in lysine and aspartic acid, or merely polar as in asparagine and serine.

If we look at the amino acid sequence of myoglobin, we see that hydrophobic side chains tend to recur every three or four positions along the main chain. Since the a helix has 3.6 residues per turn, this means that these hydrophobic side chains occur on the same side of the a helix. This is one example of how the linear amino acid sequence of a protein can contain the instructions for folding in three dimensions.