The integrase protein from the bacteriophage ~C31 is a member of the large serine recombinase family. Purified ~C31 integrase has been shown to only catalyse site-specific recombination between the DNA sites attB and attP in vitro. Mutagenesis of the protein enabled the identification of mutants defective in recombination and some which were 'hyperactive'. Hyperactivity was defined as the ability of a mutant integrase to recombine the products of integration (attL x attR) and reform attB and attP. The primary block on this type of recombination has been shown previously to be an inability to form a stable synapse between ~C31 integrase and attL x attR. This block was noticeably absent for the hyperactive mutant E449K and synaptic complexes were detected between attL and attR. Hyperactive mutations all localised to an area of the extended C-terminus that was predicted to form a canonical coiled-coil structure. Investigation of this coiled-~oil region as a two-helix fusion protein strongly suggested that it was capable of protein-protein interactions. Defective mutations within the N-terminal domain of ~C31 integrase were positioned close to mutations known to be important in resolvase and invertase recombination. Characterisation of the mutation V129A revealed that it was destabilising synapsis and thus inferred that the N-terminus of integrase was capable of influencing synapsis. This study has therefore identified two distinct regions of integrase that playa role in the synapsis of ~C31 integrase during recombination.