## 3 Results
### Ligand Binding Site and Protein-Protein Interface Determination in Ferredoxin I and II
Numerical output of this experiment is given for FdI in Table 4 and in Table 5 for FdII, while visualization for both molecules is presented in Figure 9, although limited to results for level 2 classes for clarity. A local docking algorithm would primarily search for the optimal conformation around its starting position. To simulate this, we gathered all residues within 3.9 A from given \(D\) and \(B\) class members and performed a single-linkage agglomerative clustering on the resulting atoms with a cut-off distance of also 3.9 A. In addition, we employed a constraint where any two atoms from the same residue were always placed in the same cluster regardless of their distance, although it made no difference here with cut-off of this length. This allowed us however to split the FOD class neighborhood into separate clusters--the individual putative complex interface and ligand cavity search areas. Finally, we left in the output only those residues which were confirmed to be located at most 3.9 A away from vertexes of the solvent-accessible surface of the proteins to simulate a sensible behavior of a docking algorithm which would not enforce contacts from atoms that are buried away from the surface (again, this had no consequence here). \begin{table}
\begin{tabular}{c c c c} \hline \hline \multirow{2}{*}{**Class**} & \multirow{2}{*}{**Cluster**} & **Native P-P Contacts** & **Native P-L Contacts** \\ \cline{3-4}  & & 23, 38, 40, 41, 42, 43, 46 & 6, 11, 12, 13, 14, 15, 17, 54, 56, 58, 59 \\ \hline \multirow{3}{*}{\(D_{2}\)} & 10, 54, 55, **56**, 57, 58 & \(\emptyset\) & (11), 54, 56, 58, (59) \\  & 21, 22, **23**, 24, 25, 37, 38, 39, 40, **41**, 42 & 23, 38, 40, 41, 42, (43) & \(\emptyset\) \\  & 10, 11, **12**, 13, **14**, 15, 16, 54, 55, **56**, 57, 58 & \(\emptyset\) & 11, 12, 13, 14, 15, (17), 54, 56, 58, (59) \\  & 21, 22, **23**, 24, 25, 37, 38, 39, 40, **41**, **42**, 43, 46 & 23, 38, 40, 41, 42, 43, 46 & \(\emptyset\) \\ \multirow{3}{*}{\(B_{2}+B_{1}\)} & 2 3, **4**, 5**, 6, 7, 8, 9, 10, 11, 20, 21, 33, 35, 36, 39, 42, 43, 46 & 6, 11, (12), (54), (59) \\  & 42, 43, 44 45, **46**, **48**, **49**, 50 51, 52, 53, 60, 61 & \(\emptyset\) & (38), (40), (41), 42, 43, 46 & 6, 11, (12), (54), (59) \\ \hline \hline \end{tabular} Note: cells in Native columns present residue numbers from the native P-P and P-L contacts that are matched by residues from Cluster column in the same row (clustered nearest neighbors of given FOD class members)—the true positive results. Parenthesis denotes gratuitous prediction (1 a difference in the sequence). Numbers given in bold distinguish actual FOD class members present on the \(T\) vs. \(O\) map (before clustering). Underline marks \(D_{1}/B_{1}\) class members and their nearest neighbors inside the combined \(D_{2}+D_{1}/B_{2}+B_{1}\) clusters (i.e., residues appearing in the results due to union with level 1).  
\end{table} 
Table 4: Comparison of residues engaged in native P-P and P-L interactions in FdI (1 FXR) with results of their prediction. There are two clusters constructed from members of class \(D_{2}\), two from \(D_{2}+D_{1}\) class union and one from \(B_{2}+B_{1}\) class union. \begin{table}
\begin{tabular}{c c c c} \hline \hline \multirow{2}{*}{**Class**} & \multirow{2}{*}{**Cluster**} & **Native P-P Contacts** & **Native P-L Contacts** \\ \cline{3-4}  & & 3, 23, 24, 25, 26, 32, 37 & 8, 9, 10, 11, 12, 13, 14, 31, 55, 50 \\ \hline \multirow{3}{*}{\(D_{2}+D_{1}\)} & 2, 8, **9**, 10, 11, 50, 51, **52**, 53, 54 & \(\emptyset\) & 8, 9, 10, 11, (12), 50, (55) \\  & 4, 5, 6, 8, 24, 25, 28, 29, **30**, 31, 32 & (3), (23), 24, 25, (26), 32 & 8, (9), 31 \\ \multirow{3}{*}{\(B_{2}+B_{1}\)} & 1, 2, **3**, 4**, 5, 6, 8, 10, 11, **12**, 13, 14, 15, 16, & 3, (23), 24, 25, (26), 32 & 8, (9), 10, 11, 12, 13, 14, 31, 55 \\  & 24, 25, 28, 29, 30, 31, 32, 54, 55, 56, 58 & \(\emptyset\) & \\ \hline \hline \end{tabular}
\end{table} 
Table 5: Comparison of residues engaged in native P-P and P-L interaction in FdII (1 FXD) with results of their prediction.