Figure 4
Definition of effective atomic interactions. (A) To determine if the interaction between DNA atom X and protein atom Y is effective, all other atoms inside the X interacting sphere (Zi atoms) are evaluated by comparing each ωi angle (i.e. the angle between atoms X, Zi and Y) with a defined shielding angle value Ω. If all the ωi angles observed are smaller than Ω, then the interaction between X and Y is defined as effective. (B) Three-dimensional view of three example interacting spheres of X, which only differ in the value of Ω. Red balls represent those protein atoms interacting effectively with DNA atom X. Pink balls represent protein atoms not interacting effectively with X, since they are shielded by other atoms inside the interacting sphere of X, according to the Ω value defined and used. A definition of Ω = 90° commonly captures the first interacting atom shell, while using Ω = 180° all the interactions observed inside the contacting sphere are considered as effective. To build this database a value of 90° for Ω was adopted.