(A) The model of the secreted form of truncated protein C, PC410, in the presence of water molecules. The full set of protein C protease domain coordinates was subjected to energy optimization in a sphere of 76Å diameter packed with 5,738 water molecules to obtain the best structural deletion models. The activated protein C was shown by tube model (red) and the water molecules were shown by blue. (B) The model of the secreted form, PC410. The average main chain coordinates during 45 and 60 ps obtained from MD calculation was shown by the tube model structure. The active site triad was shown by the CPK shells (blue), and the carboxyl-terminal three-rounds alpha-helix from Tyr399 to Lys410 was shown by yellow. The side chains of Arg408, Asp409, and Lys 410 were shown by the ball and stick model by red, green, and blue, respectively. (C) Hydrophobic interaction of the carboxyl-terminal alpha-helix with the surrounding residues. The carboxyl-terminal structure of PC410 was enlarged and the residues involved in the hydrophobic interaction with the carboxyl-terminal alpha-helix from Tyr399 to Lys410 were shown by the ball and stick model in yellow. This figure was taken from the backside of Fig 5B.