I do love a nice salt bridge…

Salt bridges are a type of electrostatic ( i.e. positive and negative charged components being attracted towards one another) interaction in proteins. In this case, the amino acid on the left is an Arginine (positively charged at pH 7.5, the pH of the crystal) and on the right is a Glutamate (negatively charged). Opposites attract – and these sit ~3 angstroms apart, which is 3 ten-billionths of a metre (0.0000000003 m).

There are many different types of interactions within a protein that combine to determine what the overall fold of the protein will be, and the protein fold determines its function.  The mesh surrounding the atoms is the electron density map, which is a 3D contour map of the probability that electrons will be found in a specific position. Here dark blue is contoured at 1 sigma, light blue at 1.5, and white at 2 sigma. Building and fitting protein sequences into the electron density that is the experimental result of X-ray crystallography allows us to construct accurate, atomic resolution models of proteins.

In the picture above, hydrogens atoms are omitted for clarity (and because hydrogen scatters X-rays very poorly and therefore does not appear in the majority of electron density maps), carbon atoms are shown in yellow, nitrogen in blue and oxygen in red.

The image is a screenshot from the crystallographic model building program COOT.