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Stellar active regions, including spots and faculae, can create radial velocity (RV) signals that interfere with the detection and mass measurements of low mass exoplanets. In doing so, these active regions affect each spectral line differently, but the origin of these differences is not fully understood. Here we explore how spectral line variability correlated with S-index (Ca H & K emission) is related to the atomic properties of each spectral line. Next we develop a simple analytic stellar atmosphere model that can account for the largest sources of line variability with S-index. Then we apply this model to HARPS spectra of α Cen B to explain Fe I line depth changes in terms of a disk-averaged temperature difference between active and quiet regions on the visible hemisphere of the star. This work helps establish a physical basis for understanding how stellar activity manifests differently in each spectral line, and may help future work mitigating the impact of stellar activity on exoplanet RV surveys.