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Table 1 The average values of SASA, VDW energies and the average number of protein-protein (intramolecular) and protein-solvent H-bonds in 1URX and 3WZ1 at different temperatures

From: Thermostability mechanisms of β-agarase by analyzing its structure through molecular dynamics simulation

  300 K 400 K 500 K
1URX
 RMSD 1.34 2.47 3.94
 RMSF 1.27 2.10 3.55
 SASA 109.33 130.17 190.38
 Protein–protein H-bond 69.94 54.55 45.88
 Protein-solvent H-bond 199.77 145.02 97.32
 VDW-force (protein) − 1072.66 − 924.63 − 717.41
 VDW-force (protein-water) − 459.07 − 427.31 − 394.84
3WZ1
 RMSD 1.80 1.97 4.74
 RMSF 3.19 1.96 4.22
 SASA 120.91 146.69 209.96
 Protein–protein H-bond 76.83 61.18 47.85
 Protein-solvent H-bond 216.39 155.81 112.68
 VDW-force (protein) − 1027.51 − 875.258 − 662.48
 VDW-force (protein-water) − 474.68 − 418.29 − 426.44
  1. SASA, H-bonds, VDW-force denote solvent accessible surface area, hydrogen bonds and Van Der Waals force, respectively. The values of SASA and VDW-force are given in Å and kcal/mol respectively