Schematic of the representation of Gag binding in the model.

<p><b>(a)</b> Gags are modeled as circular particles with a position and orientation, but in terms of orientation of interaction, they can be thought of as interacting triangles. When two Gags come within a distance r_b of each other, a bond can form if 1) The angles of approach (θ_a) are 60° or 180° or 300° and 2) if the angle between their orientation vectors (θ_b) is 60° or 180°. <b>(b)</b> Bonding between Gag molecules in Bonding Scheme 1. All three faces are equivalent and any face (black) of two Gag molecules can interact. <b>(c)</b> Bonding between Gag molecules in Bonding Scheme 2. Two of the three interfaces (black) are equivalent and can interact with each other, and a second dimer interface (red) can only interact with other dimer interfaces. <b>(d)</b> Bonding between Gag molecules in Bonding Scheme 3. All three potential bonds are not equivalent. In this scheme, a red interface can only interact with a red interface, and a green interface can only interact with a blue interface. <b>(e)</b> Bonding between Gag molecules in Bonding Scheme 4. The available interfaces for Gag-Gag binding is the same as in Bonding Scheme 3, but the orientation of the inter-hexamer bond has shifted relative to Bonding Scheme 3. The bond distances and orientations were taken from the crystal structure 4USN using the center of mass of CA as a reference [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0196133#pone.0196133.ref016" target="_blank">16</a>].