Here we report data describing some principles of the interaction between small GTP-binding proteins and large Clostridial cytotoxins (LCTs). Our investigation was based on the differential glucosylation of Rac1 versus RhoA by LCTs TcsL-1522, TcdB-1470 and TcdB-8864. Chimeric RhoA/Rac1 proteins and GTPases mutated at defined regions or single amino acids were used as substrates. Starting with chimeric Rac/Rho proteins we demonstrated that proteins containing the N-terminal 73 amino acids of Rac1 (but not those of RhoA) were efficiently glucosylated. Within this stretch, three regions differ significantly in Rac1 and RhoA. Regions containing amino acids 41-45 and 50-54 had no effect on toxin induced glucosylation, whereas amino acids 22-27 had a drastic impact on the potential of all three toxins to covalently modify the GTPases. Point mutations K25T of RhoA (numbering according to Rac1) and K27A of Cdc42 significantly increased glucosylation by the cytotoxins; introduction of lysines at the equivalent positions of Rac1 hindered modification. Our experiments demonstrate the influence of this charged residue on GTPase-LCT interactions. Amino acids 22-27 are part of the transition between the alpha1-helix to the switch I region of small GTP-binding proteins; both are known structures for specificity determination of the interactions with physiologic partners. Comparing these structures with data from our investigation we suggest that TcsL-1522, TcdB-1470 and TcdB-8864 mimic aspects of the physiologic interactions of small GTP-binding proteins.