Bioc12fall2012 lecture week 5: protein structures and analysis (chapter 6) Motif/supersecondary structure: a common grouping of secondary structural elements. Structural motifs usually consist of just a few elements. Most motifs contain only a few conserved amino acids. Motif: combination of alpha helix, 2 beta strands and connecting loops an alpha helix is connecting 2 consecutive parallel beta strands. Hair pin motif: antiparallel -strands with tight reverse turns figure b shows 2 hairpins. Motif: antiparallel helices are packed together the side chains contact with each other. Greek key motif: -hairpin is folded over to form a 4 stranded anti-parallel sheet topology: in protein structural biology, the topology represents the way secondary structures are connected. Helix bundle: often occurs in membrane proteins forms transmembrane fragments. Sandwich: strands or sheets stack on top of each other = 2 layers of sheets usually no h bonds between the 2 layers. Overall conformation of a polypeptide chain 3d structure.