Hydrophobicity primary amino adds

At the primary interaction site, M84Reco defines the amino adds that contact the substrate-like 80 s loop. A hydrophobic P4 interaction occurs between Trp-215, Tyr-99 and Phe-174 of the protease with Val-84 of eco. Gln-192 primarily mediates the P3 interaction. Previous structures of factor Xa bound to small molecule inhibitors also implicated these amino adds [29, 30]. The unusual preference at the P2 substrate position for Gly and Tyr-Trp-Phe is clarified in this structure. Tyr-99 rotates over 120° from the previous position, opening up the P2 pocket to the eco residue Thr-83, and closing down the S4 pocket. This conformational change at Tyr-99 explains the factor Xa preference for large hydrophobic P2 amino acids that was so puzzling in the initial structures. 

A phenylalanine amino add on a protein strand undergoes hydrophobic interactions with another phenylalanine amino acid that is 26 amino acid units away. The resulting fold in the protein is an example of which kind of structure (primary, secondary, tertiary, or quaternary)... 

This class of peptides typically contains 18 or 19 amino acid residues and share a common 13 amino acid sequence, which is Cys -Cys-Glu-Leu-Cys-Cys °-Asn-Pro-Ala-Cys-Ala -Gly-Cys (full peptide position) and Cys -Cys-Glu-Leu-Cys-Cys -Asn-Pro-Ala-Cys-Ala -Gly-Cys (toxic domain). Since the domain is conserved in several enterotoxins, one expects this 13 residue domain to be the primary reason for the toxicity. The six Cys residues form three disulphide bridges, and provide stability to the structure of the protein. lETN has a simple structure it has got three beta ((3) turns. In addition, the crystal structure contains five intramolecular hydrogen bonds that also add to the stability of the protein. Another interesting aspect of this protein is the presence of 13 water molecules in the crystal structure (Sato et al., 1986). Overall, this protein has a hydrophobic character, as the side chains of all residues are oriented to the outside of the molecule (Balasubramanian et al., 2003). 

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