We present the spectroscopy and photofragmentation dynamics of two isomeric protonated dipeptides, H+AlaTyr and H+TyrAla, in a cold ion trap. By a combination of infrared-ultraviolet double resonance experiments and density functional theory calculations, we establish the conformations present at low temperature. Interaction of the charge at the N-terminus with the carbonyl group and the tyrosine pi-cloud seems to be critical in stabilizing the low-energy conformations. H+AlaTyr has the flexibility to allow a stronger interaction between the charge and the aromatic ring than in H+TyrAla, and this interaction may be responsible for many of the differences we observe in the former: a significant redshift in the ultraviolet spectrum, a much larger photofragmentation yield, fewer stable conformations, and the absence of fragmentation in excited electronic states.