This is tool is not online, but you can download HEX and carry out protein protein docking, its pretty good.

http://hex.loria.fr/

Hi Brian,

The best dock-dock server is HADDOCK (http://haddock.science.uu.nl/). This program was specially created for protein-protein docking, although you can perform protein-ligand docking. Hope this help!

I hope that it will be useful. but i suggest you  check swissdock .

http://curie.utmb.edu/prosurf.html

http://www.hsls.pitt.edu/obrc/index.php?page=protein_protein_interactions

You can try SwarmDock and ClusPro as well.

Here's a good review that summarise all the docking tools available . 

Rodrigues, João PGLM, and Alexandre MJJ Bonvin. "Integrative computational modeling of protein interactions." FEBS Journal 281.8 (2014): 1988-2003

at first you can use:

http://galaxy.seoklab.org/cgi-bin/submit.cgi?type=PEPDOCK

and secound you can use:

http://www.swissdock.ch/docking#

Hope it will be useful!

http://hdock.phys.hust.edu.cn