We compare the conductance of 1,4-bis(methylthio)benzene with that of 2,3,6,7-tetrahydrobenzo[1,2-b:4,5-b']dithiophene and the conductance of 1,4-bis(methylseleno)benzene with that of 2,3,6,7-tetrahydrobenzo[1,2-b:4,5-b']diselenophene and show explicitly that the orientation of an Au-S or Au-Se bond relative to the aromatic pi system controls electron transport through conjugated molecules. Specifically, we have found that the conduction pathway connects the Au electrodes to the aromatic pi-system via the chalcogen p lone pairs, and greater overlaps among these components lead to higher conductivity through the molecular junction.