Fluorescent organic chemosensors for the detection of divalent copper with high selectivity and sensitivity are the subject of intense research in the recent years. Structurally, ionophore and fluorophore are two essential parts determining the resultant performance of the chemosensor. While much work has been focused on designing highly selective ligands, little attention has been paid to the possible influence of ionophore-fluorophore interaction on their properties in metal ion binding. We studied here fluorescent chemosensors based on the Gly-His peptidyl motif and found that the functionality of the chemosensors was greatly influenced by the spatial alignment of the fluorophore in the molecules. In Gly-His-Lys(Dns) (1), the dansyl group is on a side branch and does not interact with copper, while in Dpr(Dns)-His-Lys (2), the dansyl group is also on a side branch but the close placement allows it to directly participate in the binding with copper ions. Therefore, although dansyl can signal the binding event in both molecules, the mechanisms involved are quite different, and this difference resulted in different sensing performance, e.g., the selectivity. Even more strikingly, the dansyl group in Dns-Gly-His-Gly (3) exhibited a profound effect on the molecular complexation. The binding constant decreased, and binding mode was affected since only 1:1 binding was observed while in side-branch-labeled ligands, a 2:1 binding may also be involved. In contrast to those side-chain-labeled ligands, molecule 3 is extremely simple in structure and possesses superior detecting qualities such as selectivity, molecular sensitivity, and applicability in a wide range of pH.