The analysis of grain boundary structure in high resolution electron microscopy is often hindered by contrast variation within the grain boundary region which is not explained by simple models of the grain boundary structure. Recent work suggests that structural disorder along the beam direction and the presence of vacancies contribute significantly to this effect. One might expect a significant reduction in contrast in a Z-contrast image of a grain boundary would imply that vacancies present must result from the absence of heavier elements. Using a (210) S5 grain boundary in SrTiO3 as a test case and first principles structure relaxation to calculate stable defect structures, we show that the reduction in the intensity from fully occupied Sr columns due to the structural distortion resulting from a nearby O vacancy can be as great as that due to introducing a Sr vacancy in the column itself. The effect on energy dispersive X-ray spectroscopy signals is also considered, but found to be smaller than that on Z-contrast images.