Figure 2

The Contact Map. Contact Maps without (left) and with (right) hub nodes. Molecules are represented as larger nodes (light gray) while domains and domain states (yellow, orange and purple) are represented as smaller sub-nodes in the molecules. State nodes (green and dark gray) are adjacent to the domain sites to which they apply. Reaction rules are mapped to edges (rules that indicate the creation or destruction of a bond between these two domains) and state nodes (rules that indicate state changes). Selecting a state-node (red boundary on the left) lists all rules that indicate that state change. Similarly, selecting an edge (not shown) lists all rules that create or destroy bonds between the linked domains. Selecting one rule from such a list marks the reaction context in blue and the reaction center in pink. Hub nodes are associated with rules that define molecular level interactions without domains involved, such as the degradation of proteins. Selecting a hub node lists all rules involving the linked molecules as shown on the right.