Document: The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/418830 doi: bioRxiv preprint because P10 is homogeneous and is therefore omitted later) with residues W3, N4, I7, D8, M11, A12, C16, Q17, S29, V30, W31, A32, A33, V34, P35, and K115 (62.5% hydrophobic). Category II (mode3, mode6, mode10) utilizes a mixed hydrophobic/hydrophilic binding interface, consisting of Y24, K25, D26, S27, P28, D41, T43, P44, A45, E46, V47, G48, V49, V51, G52, K53, D54, S57, F58, N61, G62, L63, T64, and G67 (37.5% hydrophobic). Category III (mode4, mode5, mode7) is also featured by a mixed hydrophobic/hydrophilic binding interface, but consisting of a different set of residues Y59, S61, V72, I73, R74, D86, R88, A95, P96, T97, N99, E116, G117, V118, H119, G120, G121, N124, and K125 (31.6% hydrophobic). Finally, Category IV (mode9, mode11) makes the use of the binding groove from the crystal structure between the N-terminal α helix and C-terminal α helix, mainly contributed by G2, W3, N4, Y6, D26, S27, S29, W31, H133, L134, S137, and Y139 (41.7% hydrophobic). Since both the highest scores mode1 and mode2 are in Category I, GRAMM-X seems to prefer a more hydrophobic binding interface for PFN1-P10, although it also picks out mixed binding interfaces, including the co-crystal binding interface -mode9 in Category IV.
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