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Table 6 Energetics of docking complex formed between epitopes and PBG of MHCs along with their conservation, accessibility and conformational stability values

From: Insight into SNPs and epitopes of E protein of newly emerged genotype-I isolates of JEV from Midnapur, West Bengal, India

IEDB Server Analyses Shannon Variability NACCESS
Analysis
Peptide
Analysis
Docking Analyses of MHCs-Peptides
(Energy in Kcal Mol−1)
  SL. NO. Amino acid Position Peptide Average
Shannon Entropy
Average side-chain Accessibility CGE GE VDWa ACE HB
MHC-I 1 59 YYYHASVTD 0.02 23.5 −4.70 −42.89 −16.11 −5.89 −4.74
2 95 GFTDRGWGK 0.03 50.4 −6.61 −28.87 −21.69 −4.29 −2.42
3 382 YIVVGRKDK 0.01 32.0 −5.52 −29.36 −11.13 −4.13 −1.95
4 394 HHRHKAGST 0.03 64.3 −5.84 −39.03 −14.41 −2.02 −7.97
MHC-II 1 55 EVRSYYYHASVTDIS 0.04 24.7 −16.96 −48.65 −15.18 −9.98 −2.92
2 95 GFTDRGWGKGCGLFG 0.02 57.9 −17.23 −46.57 −14.25 −5.75 −4.75
3 380 DSYIVVGRKDKQINH 0.04 34.9 −16.07 −53.97 −22.96 −1.11 −5.02
  4 383 IVVGRKDKQINHHRH 0.00 36.8 −15.34 −52.90 −13.06 −3.63 −2.61
  1. aVDW is the net stabilization due to Van der Waals interactions i.e. (attractive VDW – repulsive VDW); GE global stabilization energy, ACE atomic contact energy, HB hydrogen bond, CGE coarse-grained free-energy of peptide-structure used for docking [49]