FIGURE 2.

Procedure to characterize C-C interactions between Ag and Ab. (A) The example of interacting carbon pair from PDB ID: 4CMH shows that the distances between CE1 atom from Tyr92 (paratope) and CB and CG atoms from His79 (epitope) are within the threshold (5 Å), but not between CE1 and CD2. (B) Evaluation of the potential shielding between CE1 and CG. The first dot product between ${\vec{V}}_{\mathit{CE1-CG}}$ and ${\vec{V}}_{\mathit{CE1-ND1}}$ exceeds the threshold (0.85) and indicates that the ND1 atom from His79 is either between the C atoms, or behind CG. The second dot product between ${\vec{V}}_{\mathit{CE1-CG}}$ and ${\vec{V}}_{CG-ND1}$ confirms the shielding as its value is below the threshold (−0.2). (C) Evaluation of the potential shielding between CE1 and CB. The first dot product value between ${\vec{V}}_{CG-CE2}$ and ${\vec{V}}_{CG-ND1}$ below the threshold (0.85) already proves that CE1-CB interaction is cleared. In all figures, carbon atoms accepted for the hydrophobic cluster are shown in brown, while rejected C atoms are in yellow and nitrogen in blue.