## 3 Results
### Sequence Analysis  
To measure the sequence and structure similarities between FdI and FdII, their PDB structures were submitted to Matras server, which is known to be among the best tools for 3D structure alignment [54; 55]. Based on data received from Matras, sequence similarity between FdI and FdII is measured at 41.4% after the introduction of six insertions in the shorter sequence (FdII): one between N5 and D6, one between D37 and S38 and two padding residues at each chain terminus. This alignment, as well as the secondary structure composition and non-bonded contacts is presented in Figure 2. Secondary structure similarity between FdI and FdII is determined to be 91.4%, with 100% of beta sheet match. Figure 2: Sequence comparison of FdI (IFXR) and FdII (IFXD) after sequence alignment, split into 1–32 (**a**) and 33–64 (**b**) segments. Six insertions in FdII sequence are marked in the central (unlabeled) row with a star, sequence identity with pipe, similar intrinsic hydrophobicity values (\(H\) parameter difference \(\leq\) 0.2) with tilde and highly different intrinsic hydrophobicity values. hydrophobicity values (\(H\) parameter difference > 0.4) with cross. Horizontal bars denote secondary structure motifs: pink--helix, amber--sheet, purple triangles--P-P interaction, teal triangles--P-L interaction and white diamonds--ligand-coordinating cysteines. \(H\) parameter values are expressed by colors of the circles with amino acid codes: closer to blue--more hydrophilic, closer to red--more hydrophobic and closer to green--towards the middle of hydrophobicity scale. FOD model takes hydrophobicity as the most important characteristic of amino acid sequence during structure formation. Due to sequence and structure similarities between FdI and FdII, a comparison of their intrinsic hydrophobicity (\(H\)) is relevant. Their \(H\) parameter profiles can be visually compared in Figures 2 and 3. In all, 25 out of 64 residues in the aligned sequences match exactly (same amino acid), while 16 from the rest have similar value of \(H\) parameter--no more than 0.2 difference (20% when measured on FOD hydrophobicity scale--between 0 and 1). Moreover, 10 out of those 25 matching residues inhabit the two helical regions present in both proteins. FdI vs. FdII \(H\) parameter correlation coefficient--with six residues omitted due to insertions--is equal to 0.67. There are however nine outliers (Figure 3), determined as pairs of residues with \(H\) parameter difference higher than 0.4 (40% of the length of FOD hydrophobicity scale). These are: Y5-E3, A21-C18, A26-E23, K37-134, V39-P36, Q44-L40, E46-C42, C58-A54 and W61-R57 (first residue from FdI, second residue from FdII). Elimination of those outliers increases the correlation coefficient to 0.92. This suggests rather high similarity of intrinsic hydrophobicity distribution along the two chains. On Figures 2 and 3 one can see that almost all residues engaged in P-P interaction (apart from E46 from FdI) are located in the loop regions. Residues in the vicinity of the ligand are also mostly outside the secondary structure or--with the sole exception of C17-C14 pair--they stay at extremities of helices and strands. Ligands appear to be located in mostly \(H\)-wise hydrophobic pockets (11-17 and 54-59 in FdI numbers), while the other unstructured fragments (7-10, 28-32 and 37-42 in FdI numbers) exhibit mostly non-hydrophobic status. That is where protein-protein interacting residues are located. The exceptions are: M24 and V32 in FdII and V39 surrounded by P-P contacts in FdI. This above situation is interesting because it seems to contradict the expectations of FOD model. An example where hydrophobicity plays a significant role in quaternary structure formation are monomers with exposed significant hydrophobic patches (causing  
Figure 3: Comparison of hydrophobicity parameter values of FdI (1 FXR) and FdII (1 FXD) after sequence alignment, in 1-D (**a**) and in 2-D (**b**).