Table 3.

Peptide-substrate interactions in the DnaK binding site. DnaK site, numbered relative to site 0, the hydrophobic pocket into which Leu⁴ is buried; φ and ψ, the torsion angles of the peptide residue; <B>, average main-chain temperature factors of the peptide residue; S, fraction of the peptide residue accessible to solvent; φ_O, the total number of hydrophobic atoms (carbon and sulfur) in DnaK making van der Waals contacts with the peptide side chains (first number) and the number of these from DnaK side-chain atoms (second number). φ_i, the total number of hydrophilic atoms (nitrogen and oxygen) of DnaK in contact with the peptide side chain (first number) and the number of these from DnaK side-chain atoms (second number); hydrogen bond, residue number and atom of DnaK contributing to the bond is cited first followed by peptide residue number and atom; residues in contact, each residue making van der Waals contact with the peptide side chains is listed. The designation of van der Waals contacts was done as described in (54), except that the upper limit was set at r_min + 2(r_min − r_O) where r_min is the radius at potential energy minimum and r_O is the crossing radius for zero energy.

DnaK site	Peptide residue	φ, ψ (°)	<B> (Å2)	S	van der Waals contacts		Hydrogen bonds	Residues in van der Waals contacts
					φo	φi
−3	Asn1	–, 109	41.0	0.84	–	–	–	–
−2	Arg2	119, 133	30.8	0.30	6,6	3,0	427N:20	Thr403, Phe426, Thr409, Val407
−1	Leu3	106, 155	23.2	0.07	17,10	6,0	404N:3O	Met404, Ala429, Ser427
0	Leu4	122, 153	25.2	0.00	17,16	2,0	429N:40 433Nε2:40 4270:4N	Phe426, Val436, Ile401, Thr403, Ile438
1	Leu5	−96, 182	29.7	0.42	3,3	0,0	437N:50	Met404, Ala429
2	Thr6	105, 177	44.3	0.42	7,5	0,0	–	Gln433, Ala435
3	Gly7	106, –	52.2	0.72	–	–	4370γ:7N