Secondary Structure, a Missing Component of Sequence-Based Minimotif Definitions
A. Surface plot of the Grb2-SH2 domain bound to a tyrosine-phosphorylated Shc1 peptide (1JYR). The SYVN Shc1 peptide is colored: S (red), Y (blue), V (green), N (yellow); these are the only four residues that make contact with the SH2 domain (gold). The C-terminal V residue in the SYVNV peptide is colored purple and does not contact the SH2 domain. Three different cut-away planes are shown in A1–A3. B. Alignment of structures of peptides when bound to the Grb2 SH2 domain—Grb2-SH2 domain binds to a conserved 3D structural β-turn motif. Peptides are 1BMB (black), 1FYR (blue), 1JYR (orange), 1TZE (purple), 1BM2 (red), 2H5K (cyan), 3N7Y (violet), 3N8M (green), and 3N84 (pink), 1ZFP (salmon), 2B3O (pale yellow), 2SHP (teal), 1QG1 (olive), and 3KFJ (brown). Backbone RMSD for 14 peptides = 0.4 Å average, with a maximum of 1.1 Å. The conserved Asn and pTyr side chains are shown. Numbering of residues is relative to P-Tyr in the +1 position.