There is a noted lack of understood, controllable interactions for directing the organization of collagen triple helices. While the field has had success using charge-pair interactions and cation-pi interactions in helix design, these alone are not adequate for achieving the degree of specificity desirable for these supramolecular structures. Furthermore, because of the reliance on electrostatic interactions, designed heterotrimeric systems have been heavily charged, a property undesirable in some applications. Amide-pi interactions are a comparatively understudied class of charge-free interactions, which could potentially be harnessed for triple-helix design. Herein, we propose, validate, and utilize pairwise amino acid amide-pi interactions in collagen triple-helix design. Glutamine-phenylalanine pairs, when arranged in an axial geometry, are found to exhibit a moderately stabilizing effect, while in the lateral geometry, this pair is destabilizing. Together this allows glutamine-phenylalanine pairs to effectively set the register of triple helices. In contrast, interactions between asparagine and phenylalanine appear to have little effect on triple-helical stability. After deconvoluting the contributions of these amino acids to triple-helix stability, we demonstrate these new glutamine-phenylalanine interactions in the successful design of a heterotrimeric triple helix. The results of all of these analyses are used to update our collagen triple-helix thermal stability prediction algorithm, Scoring function for Collagen Emulating Peptides' Temperature of Transition (SCEPTTr).