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Table 1 Change in binding free energy related to mutations in receptor-binding domain of the spike protein

From: Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein

Wild type Position Mutant type Mutants Distance to interface ΔΔGwild-mutation (kcal/mol) Affinity
From 26 December, 2019 to 8 March, 2020
 ARG 509 LYS R509K 15.117 -0.78 Decreasing
 PHE 338 LEU F338L 25.998 -0.776 Decreasing
 TYR 508 HIS Y508H 8.916 -0.595 Decreasing
 GLU 516 GLN E516Q 32.457 -0.556 Decreasing
 HIS 519 PRO H519P 40.899 -0.534 Decreasing
 HIS 519 GLN H519Q 40.899 -0.502 Decreasing
 GLY 476 SER G476S 3.806 -0.433 Decreasing
 ASN 439 LYS N439K 7.234 -0.331 Decreasing
 ASP 467 VAL D467V 14.986 -0.291 Decreasing
 VAL 510 LEU V510L 16.548 -0.27 Decreasing
 GLN 409 GLU Q409E 9.46 -0.253 Decreasing
 LYS 378 ARG K378R 19.35 -0.245 Decreasing
 ARG 408 ILE R408I 10.586 -0.199 Decreasing
 ASP 405 VAL D405V 7.48 -0.196 Decreasing
 ILE 468 THR I468T 14.973 -0.177 Decreasing
 ILE 472 VAL I472V 8.123 -0.177 Decreasing
 SER 477 GLY S477G 4.97 -0.172 Decreasing
 GLY 446 VAL G446V 3.279 -0.158 Decreasing
 GLN 414 ALA Q414A 15.173 -0.118 Decreasing
 LYS 458 ASN K458N 9.745 -0.089 Decreasing
 VAL 483 ALA V483A 9.719 -0.053 Decreasing
 SER 438 PHE S438F 11.54 -0.039 Decreasing
 VAL 483 ILE V483I 9.719 -0.026 Decreasing
 ALA 372 SER A372S 15.674 -0.023 Decreasing
 ASP 364 TYR D364Y 28.736 -0.021 Decreasing
 ALA 475 VAL A475V 2.813 -0.001 Decreasing
 ALA 522 VAL A522V 41.819 0.024 Increasing
 PRO 491 ARG P491R 6.013 0.033 Increasing
 LYS 458 ARG K458R 9.745 0.042 Increasing
 VAL 341 ILE V341I 23.363 0.045 Increasing
 ALA 522 SER A522S 41.819 0.088 Increasing
 ALA 435 SER A435S 15.197 0.148 Increasing
 ASN 354 ASP N354D 20.704 0.168 Increasing
 ALA 520 SER A520S 42.138 0.177 Increasing
 ALA 348 THR A367T 16.047 0.204 Increasing
 VAL 367 PHE V367F 23.608 0.235 Increasing
 GLN 414 GLU Q414E 15.173 0.252 Increasing
 ILE 468 PHE I468F 14.973 0.256 Increasing
From 9 March, 2020 to 30 November, 2020
 PHE 490 LEU F490L 3.825 -0.791 Decreasing
 LYS 417 ARG K417R 2.862 -0.487 Decreasing
 ASN 439 LYS N439K§ 7.234 -0.331 Decreasing
 ASN 354 LYS N354K 20.704 -0.294 Decreasing
 PHE 490 SER F490S 3.825 -0.239 Decreasing
 SER 373 LEU S373L 14.013 -0.203 Decreasing
 VAL 382 LEU V382L 30.232 -0.202 Decreasing
 GLU 484 LYS E484K 4.184 -0.154 Decreasing
 THR 385 ILE T385I 28.446 -0.128 Decreasing
 ARG 408 LYS R408K 10.586 -0.127 Decreasing
 SER 494 PRO S494P 6.031 -0.095 Decreasing
 VAL 483 ALA V483A 9.719 -0.053 Decreasing
 THR 478 LYS T478K 7.571 -0.028 Decreasing
 ALA 475 VAL A475V§ 2.813 -0.001 Decreasing
 PRO 384 SER P384S 26.132 0.01 Increasing
 SER 469 PRO S469P 12.248 0.02 Increasing
 SER 459 TYR S459Y 11.205 0.02 Increasing
 ARG 346 LYS R346K 16.314 0.022 Increasing
 ASN 354 SER N354S 20.704 0.033 Increasing
 PRO 521 ARG P521R 42.427 0.036 Increasing
 SER 514 PHE S514F 26.529 0.041 Increasing
 ALA 522 SER A522S§ 41.819 0.088 Increasing
 SER 477 ASN S477N 4.97 0.227 Increasing
 VAL 367 PHE V367F§ 23.608 0.235 Increasing
 ALA 522 GLU A522E 41.819 0.409 Increasing
 ASN 501 THR N501T 3.115 0.87 Increasing
  1. §These four mutations were also predicted in early stage