## 3 Results
### Hydrophobicity Characteristic--Monomers  
The status of monomers of FdI and FdII and their selected fragments (ordered secondary structure and residues engaged in P-P interaction and ligand binding) is given in Table 2. \(T\) and \(O\) hydrophobicity density profiles are shown in Figure 4. Profiles for FdII have two modes: normal (Figure 4c) and aligned with FdI (Figure 4b). \begin{table}
\begin{tabular}{c c c c c c c c c c c} \hline \hline \multirow{2}{*}{**Fragment**} & \multicolumn{2}{c}{**Residues**} & \multicolumn{2}{c}{**RD**} & \multicolumn{2}{c}{**TvH**} & \multicolumn{2}{c}{**OvT**} & \multicolumn{2}{c}{**OvH**} \\ \cline{2-11}  & **FdI** & **FdII** & **FdII** & **FdII** & **FdII** & **FdII** & **FdII** & **FdII** & **FdII** & **FdII** \\ \hline monomer & chain A & chain A & **0.33** & **0.27** & 0.56 & 0.60 & 0.72 & 0.78 & 0.79 & 0.86 \\ strand A.1 & 3–6 & 1–4 & **0.18** & **0.25** & 0.91 & 0.70 & 0.98 & 0.86 & 0.86 & 0.97 \\ strand A.2 & 59–62 & 55–58 & **0.19** & **0.15** & 0.82 & 0.79 & 0.99 & 0.95 & 0.76 & 0.93 \\ sheet A & strand A.1 + A.2 & strand A.1 + A.2 & **0.21** & **0.18** & 0.83 & 0.69 & 0.94 & 0.91 & 0.77 & 0.87 \\ strand B.1 & 25–27 & 22–24 & **0.04** & **0.18** & 0.46 & 0.71 & 1.00 & 0.97 & 0.49 & 0.86 \\ strand B.2 & 34–36 & 31–33 & 0.83 & 0.89 & \(-\)0.48 & \(-\)1.00 & 0.84 & \(-\)0.99 & \(-\)0.88 & 0.99 \\ sheet B & strand B.1 + B.2 & strand B.1 + B.2 & **0.32** & **0.26** & 0.20 & 0.53 & 0.73 & 0.83 & 0.45 & 0.86 \\ all sheets & sheet A + B & sheet A + B & **0.23** & **0.19** & 0.73 & 0.64 & 0.90 & 0.90 & 0.71 & 0.84 \\ no sheets &!(sheet A + B) &!(sheet A + B) & **0.33** & **0.26** & 0.45 & 0.57 & 0.72 & 0.81 & 0.80 & 0.87 \\ helix 1 & 15–21 & 13–17 & **0.23** & **0.18** & 0.85 & 0.81 & 0.97 & 0.94 & 0.88 & 0.96 \\ helix 2 & 43–54 & 41–49 & **0.35** & **0.28** & 0.59 & 0.70 & 0.71 & 0.82 & 0.93 & 0.92 \\ all helices & helix 1 + 2 & helix 1 + 2 & **0.31** & **0.25** & 0.70 & 0.76 & 0.81 & 0.88 & 0.90 & 0.94 \\ no helices &!(helix 1 + 2) &!(helix 1 + 2) & **0.34** & **0.29** & 0.55 & 0.56 & 0.70 & 0.74 & 0.74 & 0.84 \\ P-P & FdI(P-P) & FdII(P-P) & **0.46** & **0.18** & 0.24 & 0.65 & 0.33 & 0.87 & 0.92 & 0.91 \\ no P-P &!(FdI(P-P)) &!(FdI(P-P)) & **0.31** & **0.28** & 0.56 & 0.59 & 0.75 & 0.77 & 0.79 & 0.85 \\ P-L & FdI(P-L) & FdIII(P-L) & **0.40** & **0.45** & 0.37 & 0.07 & 0.67 & 0.63 & 0.84 & 0.69 \\ no P-L &!(FdI(P-L)) &!(FdII(P-L)) & **0.30** & **0.27** & 0.62 & 0.66 & 0.75 & 0.79 & 0.73 & 0.87 \\ catalytic & 11,14,17,54 & 8,14,50 & **0.25** & **0.27** & n/a & n/a & 0.90 & 0.92 & n/a & n/a \\ no catalytic &!(11,14,17,54) &!(8,14,50) & **0.33** & **0.28** & 0.58 & 0.59 & 0.72 & 0.77 & 0.76 & 0.85 \\ S-S bond & n/a & 18–42 & n/a & **0.25** & n/a & 0.62 & n/a & 0.78 & n/a & 0.90 \\ no S-S bond & n/a &!(18–42) & n/a & **0.30** & n/a & 0.58 & n/a & 0.78 & n/a & 0.83 \\ \hline \hline \end{tabular} Note: P-P denotes residues engaged in protein–protein interaction. P-L denotes residues engaged in ligand binding. “Catalytic” denotes ligand-coordinating cysteines. S-S bond denotes chain segment between residues forming the disulfide bond. “No” before name of a fragment and an exclamation mark around data in Residues column means that _RD_ and correlation coefficients (_TvH_, _OvT_ and _OrH_) were obtained for all residues except those presented in Residues column (i.e., everything except P-P contacts). Values given in bold distinguish status of accordance with the model (_RD_ < 0.5). Underlined values exhibit correlation coefficient difference between the proteins higher than 0.5. _TvH_ and _OvH_ are unavailable for catalytic residues due to all of them having same \(H\) value (all cysteines).  
\end{table} 
Table 2: Hydrophobicity status of monomers of FdI (1 FXR) and FdII (1 FXD) and their selected fragments. Figure 4: Hydrophobicity density profiles of monomers of FdI (1 FXR) (**a**) and FdII (1 FXD) (**b**,**c**). Profile on (**b**) is the profile from (**c**) after sequence alignment (six insertions: two at each terminus and two within the chain, marked by distribution  
discontinuities).