An efficient waste management and recycling system provides new materials and energy for sustained functioning of a city. Similarly, under starvation conditions, eukaryotic cells maintain homeostasis through a process termed “autophagy”. During this process, aggregated, redundant and misfolded proteins are degraded and recycled into amino acids. It is a complex cellular pathway orchestrated by more than 30 autophagy related proteins and dysfunction in autophagy leads to various types of cancer and neurodegenerative disorders. Mammalian autophagy is initiated by the ULK1 complex, comprised of number of autophagy related proteins, and requires the LC3 and GABARAP proteins as scaffolds. The interactions of LC3 and GABARAP with autophagy related proteins are highly specific through a motif called the “LC3 interacting region”, although the mechanisms of interaction are not entirely clear. We have probed these interaction using X-ray crystallography. Our crystal structures and molecular dynamics simulations demonstrate that residue Arg70 in LC3A and Arg67 in GABARAP contribute to binding through a “lock and key” type mechanism. This was further confirmed with SPR analysis which demostrated a lower binding affinity for LC3A R70L and GABARAP R67L mutants. Our results demonstrate for the first time that Arg70 in LC3A and Arg67 in GABARAP are required for recruiting substrates and inturn proper autophagosome formation.