Anchor prediction
Hierarchical clustering (Kozakov, Clodfelter, Vajda & Camacho, 2005) determined the most stable conformation of dipeptides between A1 and L5. Clustering is based on the Root Mean Square Deviation (RMSD) between MDS snapshots less than 1 Å for A1R2, R2S3, S3R4, and R4L5. We also determined the contacts of side chains as a proxy for ability to bind the receptor, i.e., if side chains are interacting with each other, their interaction with the receptor is hindered. Atomic contacts are defined as atoms from the peptide that are less than 3.8 Å of Cβ-alanine, [Nε, NH2]-arginine, Cβ-serine, [Cδ1, Cδ2]-leucine from dipeptides. The prediction is that the stable motif accessible to solvent is critical for molecular recognition, i.e., the anchor of the protein-protein interaction (Rajamani, Thiel, Vajda & Camacho, 2004).