The interactions between redox proteins are transient in nature. Therefore, very few crystal structures are available for the complexes formed between these proteins. Computational docking simulations thus provide a useful alternative method for studying the interactions between electron transfer proteins. In this paper, we have studied the interactions between the aa3-type cytochrome c oxidase of the cyanobacterium Phormidium laminosum and its redox partners plastocyanin and cytochrome c6 using a combination of comparative modelling techniques and docking simulations. Rigid-body docking orientations were scored with a combined energy function that accounts for electrostatics and desolvation. These simulations have identified two plausible docking sites, one of which appears to be unique to the binding of plastocyanin to the oxidase. This unique binding site may be due to the presence of a long loop region in the subunit II of cyanobacterial oxidases. Control simulations were performed with the ba3-type cytochrome c oxidase and its redox partner cytochrome c552 from Thermus thermophilus. The docking between cytochrome c oxidase and its redox partners plastocyanin and cytochrome c6 is dominated by hydrophobic residues, a feature already observed from kinetic and structural studies in other complexes of P. laminosum (e.g. plastocyanin or cytochrome c6 with cytochrome f and photosystem I).