Figure 4. Structural features encoding distinct protein geometries.

A. Sequence patterns of the hydrophobic cores in three designed models for the Rossman fold, aligned by corresponding secondary structure elements (top). Hydrophobic residues are shown as letters in rainbow colors ordered by position in the primary protein sequence and scaled by side chain size. Grey underlines indicate positions of surface exposed polar residues. The residues in the boxes are the knob residues shown in (C). B. Atomic packing of hydrophobic cores in the three experimentally determined structures for the Rossman fold (Fig. 2). The hydrophobic side chains in the designed cores are shown as spheres. C. Knob-socket packing motifs found in the designs. Three residues on a helix (grey sticks and surfaces) form a socket accommodating a knob residue shown as colored spheres. D. Examples of tertiary motifs matching the designed LHL structures. The designed structures are shown in grey and the matched motifs are shown in magenta. Sidechains of the best matched tertiary motifs and design models are shown as sticks. Insets indicate location of the tertiary motif in the structure in the same orientation as in B.