Figure 1. Proteins are constructed from a common and repetitive polypeptide main chain and an individual sequence of side chains. S_i represents the side chain of the ith residue.

Figure 2. Ramachandran plot, showing the contours of low energy for the conformation of a typical residue in a protein, as a function of two angles of internal rotation (ϕ and ψ) that determine the main chain conformation of a residue. The points correspond to the residues in crambin. Residues are found primarily in the allowed regions α_R and β, except for glycine (marked by G), which has greater conformational freedom.

Figure 3. (a) α Helix. (b) β Sheet. Single circles: carbon atoms; double circles: oxygen atoms; large triple circles: nitrogen atoms; small triple circles: hydrogen atoms; solid lines: primary chemical bonds; broken lines: hydrogen bonds. N and C indicate the N‐terminus and C‐terminus of the chains, showing their direction. (b) β sheet in which all strands are pointing in the same direction (a parallel β sheet); it is also possible to form sheets with strands pointing in opposite directions.

Figure 4. Structure of human hemoglobin represented by threading the backbone atoms with a ribbon (based on Protein Data Bank entry 1bbb). The picture illustrates the different hierarchical levels of a structure: the amino acid sequence (primary structure) (1) governs the folding into secondary structure (here an α helix). (2) The α helices assemble together to form the tertiary structure or fold of the protein (3). The way in which different units (here a tetramer) assemble together determines the quaternary structure (4). The prosthetic group, the heme (shown in line representation in (3) and (4)), is noncovalently bound to hemoglobin.

Figure 5. Extracellular modular proteins from the blood coagulation cascade. These contain different combinations of the same structural modules. EGF, F1, F2, γ and Kr identify the modules: epidermal growth factor, fibronectin type 1 and type 2, gla and kringle respectively. At the top, a representative example of each of these individual structures is illustrated, associated with an icon. Below, the structures of four different molecules in the blood coagulation cascade are shown in terms of their assembly as linear arrays of modules.