Proton conducting polymer electrolyte membranes (PEM) for fuel cell applications often contain a sulfonated perfluorinated side chain, which is attached to a polymeric backbone. Proton conductance in such membranes is a complicated process, which depends on both material properties and operational parameters of the fuel cell. Experimentally, it is well established that proton conductivity in such membranes is strongly dependent on water content, approaching that of bulk water at high water content. The goal of the present study is to analyze the relationship between pore structure on the molecular level and proton transfer dynamics as a function of water content and side chain density. A molecular model of the side chain has been developed and is used to simulate proton transport in a simple slab pore. The polymer backbone is represented as a simple excluded volume, described by a Lennard-Jones interaction potential.