Table 1.
Comparison of predicted and experimental contacts from the Se and CHeB models. Interactions were computed with default setting in the Protein Interactions calculator server [19]. Chymotrypsin numbering system as in 1NL8 (pdb of Ss) is used for SP domains of FVIIa and FXa. Bold residues correspond to experimental contacts [20–32]. Abbreviations: HI, hydrophobic; HB, hydrogen bond; MS, main chain-side chain; SS, side chain-side chain; LC, light chain of FVIIa and FXa for residues over EGF-2 domain in light chain. Italic residues designate residues adjacent to residues involved in experimental contact.
| CHeB | Se | |
|---|---|---|
| TF/fXa | Glu24TF@OE1,OE2 ∷ Gly66fXa.EGF-1@O (MS-HB) | |
| Lys41TF ∷ Glu77fXa.EGF-1 (Ionic interaction) | ||
| Thr70TF@OG1 ∷ Gln58fXa.EGF-1@OE1 (SS-HB) | ||
| Glu99TF@N ∷ Glu77fXa.EGF-1@OE1 (MS-HB) | Glu99TF@OE1∷ Gln58fXa.EGF-1@NE2(SS-HB) | |
| Glu105TF ∷ Lys79fXa.EGF-1 (Ionic interaction) | ||
| Glu105TF@N ∷ Lys79fXa.EGF-1@OE2 (MS-HB) | ||
| Lys165TF@NZ ∷ Asp35fXa.Gla@OD2 (SS-HB) | ||
| Lys165TF ∷ Asp35fXa.Gla (Ionic interaction) | ||
| Lys166TF ∷ Gla32fXa.Gla (Ionic interaction) | ||
| Thr197TF@OG1∷ Cys61fXa.EGF-1@N (MS-HB) | ||
| Val198TF ∷ Pro54fXa.EGF-1 (HI) | ||
| Asn199TF@OD1∷ Ser53fXa.EGF-1@OG (SS-HB) | ||
| Arg200TF ∷ Gla39fXa.Gla (Ionic interaction) | ||
| Arg200TF ∷ Asp48fXa.EGF-1 (Ionic interaction) | ||
| Lys201TF@NZ ∷ Glu51fXa.EGF-1@OE2 (SS-HB) | ||
| Lys201TF ∷ Glu51fXa.EGF-1 (Ionic interaction) | ||
| Asp204TF ∷ Lys43fXa.Gla (Ionic interaction) | ||
| Asp204TF@OD1,OD2 ∷ Lys43fXa.Gla@NZ (SS-HB) | ||
| fVIIa/fXa | Ala34fVIIa.Gla ∷ Met18fXa.Gla (HI) | |
| Gla35fVIIa.Gla ∷ Lys36fXa.Gla (Ionic interaction) | ||
| Gla35fVIIa.Gla@N ∷ Met18fXa.Gla@SD (MS-HB) | ||
| Arg36fVIIa.Gla ∷ Gla14fXa.Gla (Ionic interaction) | ||
| Arg36fVIIa.Gla@NH1,NH2 ∷ Gla14fXa.Gla@OE1,OE2 (SS-HB) | ||
| Leu39fVIIa.Gla ∷ Phe31fXa.Gla (HI) | ||
| Leu39fVIIa.Gla ∷ Phe40fXa.Gla (HI) | ||
| Trp41fVIIa.Gla ∷ Met18fXa.Gla (HI) | ||
| Ile42fVIIa.Gla ∷ Met18fXa.Gla (HI) | ||
| Ile42fVIIa.Gla ∷ Phe40fXa.Gla (HI) | ||
| Ile42fVIIa.Gla ∷ Tyr44fXa.Gla (HI) | ||
| Gln150fVIIa.LC@O ∷ Lys134fXa.SP@NZ(MS-HB) | ||
| Arg152fVIIa.LC@O ∷ Lys134fXa.SP@NZ (MS-HB) | ||
| Lys20fVIIa.SP@NZ ∷ Tyr162fXa.SP@O (MS-HB) | Lys20fVIIa.SP ∷ Glu159fXa.SP (Ionic interaction) | |
| Lys20fVIIa.SP@NZ ∷ Glu159fXa.SP@OE1 (MS-HB) | ||
| Val21fVIIa.SP ∷ Pro161fXa.SP (HI) | ||
| Val21fVIIa.SP ∷ Tyr185fXa.SP (HI) | Val21fVIIa.SP ∷ Tyr185fXa.SP (HI) | |
| Glu26fVIIa.SP@OE1 ∷ Thr185BfXa.SP@OG1 (SS-HB) | ||
| Asp72fVIIa.SP ∷ Lys186fXa.SP (Ionic interaction) | ||
| Glu75fVIIa.SP ∷ Lys223fXa.SP (Ionic interaction) | ||
| Leu145fVIIa.SP ∷ Ile137fXa.SP (HI) | ||
| Leu145fVIIa.SP ∷ Met157fXa.SP (HI) | ||
| Leu145fVIIa.SP ∷ Tyr207fXa.SP (HI) | ||
| Asp146fVIIa.SP ∷ Arg202fXa.SP (Ionic interaction) | ||
| Arg147fVIIa.SP@NH1,NH2 ∷ Glu138fXa.LC@OE1,OE2 (SS-HB) | ||
| Arg147fVIIa.SP ∷ Glu138fXa.LC (Ionic interaction) | ||
| Leu153fVIIa.SP@N ∷ Gln20fXa.SP@OE1 (MS-HB) | ||
| Glu154fVIIa.SP@OE1,OE2 ∷ Tyr185fXa.SP@OH (SS-HB) | ||
| Glu154fVIIa.SP ∷ Lys186fXa.SP (Ionic interaction) | Glu154fVIIa.SP ∷ Lys186fXa.SP (Ionic interaction) | |
| Glu154fVIIa.SP@OE1 ∷ Lys186fXa.SP@OH (SS-HB) | Glu154fVIIa.SP@OE2 ∷ Lys186fXa.SP@NZ (SS-HB) | |
| Lys170DfVIIa.SP ∷ Glu74fXa.EGF-1 (Ionic interaction) | ||
| Lys170DfVIIa.SP@NZ ∷ Glu74fXa.EGF-1@OE1,OE2 (SS-HB) | ||
| Lys170DfVIIa.SP ∷ Asp92fXa.EGF-2 (Ionic interaction) | Arg170CfVIIa.SP ∷ Asp92fXa.EGF-2 (Ionic interaction) | |
| Lys170DfVIIa.SP ∷ Asp95fXa.EGF-2 (Ionic interaction) | Arg170CfVIIa.SP ∷ Asp95fXa.EGF-2 (Ionic interaction) | |
| Arg170CfVIIa.SP@NH1,NH2 ∷ Asp95fXa.EGF-2@OD1 (SS-HB) | ||
| Tyr184fVIIa.SP ∷ Lys134fXa.SP (Cation-Pi interaction) | ||
| Asp186fVIIa.SP ∷ Lys134fXa.SP (Ionic interaction) | ||
| Asp186fVIIa.SP@OD1 ∷ Lys134fXa.SP@NZ (SS-HB) | ||
| Ser188AfVIIa.SP@OG ∷ Lys204fXa.SP@N (MS-HB) | Ser188AfVIIa.SP@O ∷ Arg202fXa.SP@NH2 (MS-HB) | |