David W. Deerfield II, Pittsburgh Supercomputing Center

The following animation is from an educational video produced by the PSC Biomed group describing protein helices. This example is helix seven and eight from lysozyme and represents a helix-turn-helix motif, where the residues defining the turn are colored purple.

Here we see an example of helix-helix packing where the backbone atoms are shown in red and blue. The green sidechains of the blue helix define a ridge, which will fit into the groove defined by the yellow sidechains of the red helix. The green and yellow sidechains produce the principal interaction defining the helix-helix packing; these residues are referred to as the core. In addition, there are two cyan sidechains on the blue helix and an orange sidechain on the red helix that are also involved in the helix-helix contact. These latter residues are often referred to as the outer core. The remaining sidechains are not involved in the helix-helix packing and are colored white.