Summary of the charged and polar groups of amino acid residues in the melittin binding sites that interact with polar head groups of truncated PC. Hypothetical binding sites in melittin that bind to the charged and polar groups of PC polar head were determined by AutoDock modeling. Designation of N+(CH3)3, PO4−, COδ−C and C=Oδ− in PC polar head is shown in Figure 3A.

Table 2: Summary of the charged and polar groups of amino acid residues in the melittin binding sites that interact with polar head groups of truncated PC. Hypothetical binding sites in melittin that bind to the charged and polar groups of PC polar head were determined by AutoDock modeling. Designation of N+(CH3)3, PO4−, COδ−C and C=Oδ− in PC polar head is shown in Figure 3A.

Binding site # and

affinity energy values

PC polar head

groups

Melittin a. a. residues’

charged & polargroups

Bond type

Binding site 1

Affinity: -3.50 kcal/mol

PO₄^–

CO^δ⁻C

C=O^δ⁻

R22 (C=N⁺H₂)

R22 (C–NH₂^δ⁺)

ionic

ion-polar

hydrogen

Binding site 2

Affinity: -3.50 kcal/mol

PO₄^–

CO^δ⁻C

C=O^δ⁻

R22 (C=N⁺H₂)

S18 (C–OH^δ⁺)

R22 (C=N⁺H₂)

S18 (C–OH^δ⁺)

R22 (C–NH₂^δ⁺)

ionic

ion-polar

hydrogen

Binding site 3

Affinity: -3.40 kcal/mol

C=O^δ⁻

T10 (C–OH^δ⁺)

hydrogen

Binding site 4

Affinity: -3.30 kcal/mol

PO₄^–

CO^δ−C

C=O^δ⁻

Q25 (C–NH₂^δ⁺)

Q26 (C–NH₂^δ⁺)

ion-polar

hydrogen

Binding site 5

Affinity: -3.30 kcal/mol

PO₄^–

R22 (C=N⁺H₂)

R22 (C–NH₂^δ⁺)

ionic

ion-polar

Binding site 6

Affinity: -3.20 kcal/mol

C=O^δ⁻

T10 (C–OH^δ⁺)

hydrogen

Binding site 7

Affinity: -3.20 kcal/mol

PO₄^–

CO^δ⁻C

C=O^δ⁻

R22 (C–NH₂^δ⁺)

R22 (C=N⁺H₂)

ion-polar

Binding site 8

Affinity: -3.20 kcal/mol

CO^δ⁻C

T10 (C–OH^δ⁺)

hydrogen

Binding site 9

Affinity: -3.20 kcal/mol

C=O^δ⁻

R22 (C–NH₂^δ⁺)

hydrogen