Proteins of the regulator of G protein signaling (RGS) family accelerate GTP hydrolysis by the ␣ subunits (G␣) of G proteins, leading to rapid recovery of signaling cascades. Many different RGS proteins can accelerate GTP hydrolysis by an individual G ␣, and GTP hydrolysis rates of different G ␣s can be enhanced by the same RGS protein. Consequently, the mechanisms for specificity in RGS regulation and the residues involved remain unclear. Using the evolutionary trace (ET) method, we have identified a cluster of residues in the RGS domain that includes the RGS-G ␣ binding interface and extends to include additional functionally important residues on the surface. One of these is within helix ␣3, two are in ␣5, and three are in the loop connecting ␣5 and ␣6. A cluster of surface residues on G␣ previously identified by ET, and composed predominantly of residues from the switch III region and helix ␣3, is spatially contiguous with the ET-identified residues in the RGS domain. This cluster includes residues proposed to interact with the ␥ subunit of Gt␣'s effector, cGMP phosphodiesterase (PDE␥). The proximity of these clusters suggests that they form part of an interface between the effector and the RGS-G ␣ complex. Sequence variations in these residues correlate with PDE␥ effects on GTPase acceleration. Because ET identifies residues important for all members of a protein family, these residues likely form a general site for regulation of G protein-coupled signaling cascades, possibly by means of effector interactions.H eterotrimeric G proteins (G ␣␥ ) mediate a ubiquitous eukaryotic pathway that converts extracellular signals received by transmembrane serpentine receptors into changes in the concentrations of intracellular ions and small molecule second messengers, thereby controlling vision, cardiac function, and many aspects of neuroendocrine signaling. Upon activation, a receptor catalyzes the exchange of GDP for GTP in the ␣ subunit of a specific G protein (G ␣ ), and either G ␣-GTP or its G ␥ partner can interact with a membrane-bound downstream effector protein, leading to amplification of the initial signal. Essential to G protein signaling is the intrinsic temporal regulation of the cascade imposed by G ␣ 's ability to switch back to its inactive form through hydrolysis of GTP. The regulator of G protein signaling (RGS) family of proteins plays a critical role in this process by increasing the intrinsic GTP hydrolysis rate of G ␣ (1-4) and accelerating recovery of the system. Nearly 50 different RGS family members have been identified in eukaryotes thus far, ranging from yeast to humans; and in mammals, individual RGS proteins display distinct expression patterns. However, in general, different types of RGS proteins coexist with a variety of G proteins, leading to the question of how RGS-G ␣ specificity is maintained (5). The crystal structure of the RGS4-G i␣1 complex (6) reveals that the contact residues between the RGS domain and G ␣ are highly conserved in both proteins, implying that in situ RGS-G pr...