HYPOTHESIS: A variety of nanostructures with different chiral features can be self-assembled from short peptides with highly similar sequences. We hypothesize that these supramolecular nanostructures are ruled by the constituent amino acid residues which adopt their conformations under the influence of intra-/inter-molecular interactions during peptide self-assembly. APPROACH: Through reviewing recent advances in the self-assembly of short peptides and focusing on the relationship between amino acid conformations, peptide secondary structures and intra-/inter-molecular interactions within the supramolecular architectures, we aim to rationalize the complex interactive processes involved in the self-assembly of short, designed peptides. RESULTS: Given the highly complexing interactive processes, the adoption of amino acid conformations and their control over peptide self-assembly consist of 4 main steps: (1) Each amino acid residue adopts its unique conformation in a specific sequence; (2) The sequence exhibits its own main chain geometry and determines the propensity of the intermolecular alignment within the building block; (3) The structural propensity of the building block and the packing mode between them determine the self-assembled structural features such as twisting, growth and chirality; (4) In addition to intra-/inter-molecular interactions, inter-sheet and inter-building block interactions could also affect the residue conformations and nanostructures, causing structural readjustment.