Workbench
Simulation report and files
General information
Name: Fully-glycosylated S protein (head) in open-closed-closed state in complex with antibody s309
Included proteins: Spike
Uniprot ID: P0DTC2
Species: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2)
PDB ID: 6WPT
Submitted by: Lehigh University, Bethlehem (CHARMM-GUI)
Submission date: May 20, 2021
System setup
Ligands: None
Membrane composition: None
Solvent type: TIP3P (water was filtered out of the simulation output)
Total number of atoms: 74769
Simulation details
Software and version: GROMACS 2018.6
Forcefield and version: CHARMM36(m) -
Time step : 4.0 fs
Delta : 1.0 ns
Replicates: 1
Accumulated simulation time: 0.5210 µs
References
Cao, Y.; Choi, Y.K.; Frank, M.; Woo, H.; Park, S.-J.; Yeom, M.S.; Seok, C.; Im, W. Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies. bioRxiv 2021, 2021.05.10.443519. DOI: 10.1101/2021.05.10.443519
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Viewer
Fully-glycosylated S protein (head) in open-closed-closed state in complex with antibody s309
( 6WPT)
Selection
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RMSF
Trajectory:
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Protein alpha carbons
Protein CA, CB, C, N, O
Non-hydrogen protein atoms
All protein atoms
Variant impact
Select a variant from the sequence to obtain its impact score as well as mutation effect and time-dependent descriptors:
Display isolate:
All isolates
Spike
AA
Seq. pos.
PDB resID
A
27
27
Y
28
28
T
29
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N
30
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S
31
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F
32
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T
33
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R
34
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G
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V
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Y
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Y
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P
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D
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K
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F
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R
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S
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S
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V
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L
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H
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S
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T
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Q
52
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D
53
53
L
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F
55
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L
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56
P
57
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F
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F
59
59
S
60
60
N
61
61
V
62
62
T
63
63
W
64
64
F
65
65
H
69
69
N
81
81
P
82
82
V
83
83
L
84
84
P
85
85
F
86
86
N
87
87
D
88
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G
89
89
V
90
90
Y
91
91
F
92
92
A
93
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S
94
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T
95
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E
96
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K
97
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S
98
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N
99
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I
100
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I
101
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R
102
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G
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W
104
104
I
105
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F
106
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G
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T
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T
109
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L
110
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D
111
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S
112
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K
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T
114
114
Q
115
115
S
116
116
L
117
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L
118
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I
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V
120
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N
121
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N
122
122
A
123
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T
124
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N
125
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V
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V
127
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I
128
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K
129
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V
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C
131
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E
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F
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Q
134
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F
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C
136
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N
137
137
D
138
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P
139
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F
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L
141
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G
142
142
V
159
159
N
165
165
C
166
166
T
167
167
F
168
168
E
169
169
Y
170
170
V
171
171
S
172
172
F
186
186
K
187
187
N
188
188
L
189
189
R
190
190
E
191
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F
192
192
V
193
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F
194
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K
195
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N
196
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I
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D
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G
199
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Y
200
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F
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K
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I
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Y
204
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S
205
205
K
206
206
H
207
207
T
208
208
P
209
209
I
210
2
N
211
211
L
212
212
V
213
3
R
214
214
D
215
215
L
216
4
P(T)
217
5
Q
218
6
G
219
219
F
220
220
S
221
7
A
222
222
L
223
11
E
224
224
P(S)
225
12
L
226
13
V
227
227
D
228
228
L(S)
229
14
P
230
15
I
231
231
G
232
16
I
233
233
N
234
234
I
235
235
T(E)
236
17
R
237
18
F
238
238
Q(A)
239
19
T
240
20
L
242
21
L(S)
244
22
H(C)
245
23
R
246
24
S
247
26
L(Q)
249
27
T
250
28
S(V)
254
29
S
255
30
S
256
31
T
259
32
G(S)
261
33
A(L)
262
34
A
263
35
A(W)
264
36
Y
265
37
Y(Q)
266
38
V(Q)
267
39
G
268
42
Y
269
269
L
270
270
Q
271
43
P
272
45
R
273
46
T
274
274
F
275
275
L
276
47
L
277
48
K(I)
278
49
Y
279
50
N
280
280
E
281
281
N
282
282
G
283
51
T
284
284
I
285
2
T
286
286
D
287
287
A
288
288
V
289
3
D
290
290
C
291
291
A
292
52
L
293
293
D
294
294
P
295
295
L
296
4
S
297
53
E
298
298
T
299
5
K(Q)
300
6
C(S)
301
7
T
302
10
L
303
11
K(I)
304
59
S
305
12
F
306
63
T
307
307
V(S)
308
64
E(G)
309
65
K(S)
310
66
G
311
67
I
312
312
Y(S)
313
68
Q(G)
314
69
T(L)
315
13
S
316
14
N(D)
317
71
F
318
72
R(L)
319
4
V
320
5
Q
321
6
P
322
15
T(G)
323
16
E
324
17
S(T)
325
75
I
326
76
V(S)
327
77
R
328
18
F
329
329
P
330
330
N
331
331
I(A)
332
19
T
333
20
N
334
334
L
335
21
C
336
23
P
337
81
F
338
338
G
339
8
E
340
82
V
341
11
F
342
342
N
343
343
A(K)
344
12
T(K)
345
13
R
346
24
F
347
84
A
348
25
S
349
26
V
350
29
Y
351
87
A
352
352
W
353
353
N
354
354
R
355
355
K
356
19
R
357
357
I
358
358
S
359
30
N(Y)
360
88
C
361
89
V(Q)
362
90
A(Q)
363
91
D(S)
364
31
Y(T)
365
32
S
366
33
V
367
367
L
368
34
Y
369
369
N(C)
370
22
S(K)
371
23
A
372
35
S
373
373
F(W)
374
36
S(Y)
375
37
T(Q)
376
38
F(Q)
377
39
K
378
40
C
379
379
Y(P)
380
41
G
381
42
V(Q)
382
43
S(A)
383
44
P
384
45
T
385
102
K(R)
386
46
L
387
47
N
388
388
D
389
389
L
390
48
C
391
391
F
392
29
T
393
30
N
394
394
V(I)
395
49
Y
396
50
A
397
52
D
398
398
S
399
53
Y
400
32
V
401
104
I
402
34
R
403
403
G
404
404
D(S)
405
35
E
406
105
V(S)
407
54
R
408
55
Q
409
39
I
410
410
A
411
56
P
412
41
G
413
42
Q
414
43
T
415
57
G
416
58
K
417
417
I
418
59
A
419
419
D
420
420
Y
421
421
N
422
422
Y
423
423
K
424
424
L
425
45
P
426
60
D
427
61
D(R)
428
62
F
429
63
T(S)
430
64
G
431
65
C
432
432
V
433
433
I
434
434
A(E)
435
46
W
436
47
N
437
437
S
438
66
N
439
439
N
440
440
L
441
441
D(G)
442
67
S
443
68
K
444
444
G(M)
446
48
G
447
69
N
448
448
Y
449
449
N
450
450
Y(T)
451
70
L(D)
452
71
Y(F)
453
72
R(T)
454
73
L
455
74
R(T)
457
75
K(I)
458
76
S
459
77
N(R)
460
78
L
461
79
K(E)
462
80
P
463
81
F
464
464
E
465
82
R
466
466
D
467
83
I
468
51
S
469
52
T
470
53
I
472
472
Y
473
54
Q(F)
474
84
A
475
85
S
477
477
T
478
478
N
481
55
G
482
56
V
483
86
G(N)
485
57
F(T)
486
58
N
487
59
Y
489
87
P
491
491
L(A)
492
61
Q
493
62
S
494
494
Y
495
88
G(K)
496
63
C
497
89
Q
498
90
P
499
499
T
500
500
N
501
501
G
502
502
V
503
503
G
504
66
Y
505
505
Q
506
91
P
507
507
Y
508
508
R
509
67
V
510
510
V
511
511
V
512
68
L
513
513
S
514
514
F
515
515
E
516
516
L
517
517
L
518
518
H
519
92
A
520
520
P
521
521
A(D)
522
93
T
523
94
V
524
524
C(M)
525
70
T
526
71
P(T)
527
72
K(D)
528
73
K(T)
529
74
S
530
95
T
531
76
N
532
532
L
533
96
V
534
534
K
535
535
N
536
536
K
537
537
C
538
538
V
539
539
N
540
540
F
541
541
N(T)
542
97
F
543
98
N
544
544
G
545
99
L
546
546
T
547
77
G
548
100
T
549
78
G
550
101
V
551
551
L(Y)
552
80
T(M)
553
81
E
554
82
S
555
555
N
556
556
K
557
557
K
558
558
F
559
559
L
560
83
P
561
561
F
562
562
Q
563
563
Q(R)
564
84
F(R)
565
85
G(L)
566
86
R
567
87
D
568
89
I
569
569
A
570
570
D
571
90
T
572
572
T
573
91
D
574
574
A
575
92
V
576
93
R
577
98
D
578
99
P
579
579
Q(Y)
580
100
T
581
101
L
582
582
E
583
583
I
584
584
L
585
585
D
586
586
I
587
587
T(R)
588
102
P(G)
589
103
C(A)
590
104
S(W)
591
105
F
592
106
G
593
593
G
594
107
V(E)
595
108
S
596
109
V(L)
597
110
I
598
111
T
599
599
P(G)
600
112
G
601
113
T(F)
602
114
N
603
116
T
604
604
S(W)
605
117
N(G)
606
118
Q
607
119
V
608
608
A(G)
609
120
V(T)
610
121
L
611
122
Y
612
612
Q
613
613
D
614
614
V
615
123
N
616
616
C
617
617
T
618
124
E
619
619
V
635
635
N
641
641
V
642
642
F
643
643
Q
644
644
T
645
645
R
646
646
A
647
647
G
648
648
C
649
649
L
650
650
I
651
651
G
652
652
A
653
653
E
654
654
H
655
655
V
656
656
N
657
657
N
658
658
S
659
659
Y
660
660
E
661
661
C
662
662
D
663
663
I
664
664
P
665
665
I
666
666
G
667
667
A
668
668
G
669
669
I
670
670
C
671
671
A
672
672
S
673
673
Y
674
674
Q
677
677
T
678
678
Q
690
690
S
691
691
I
692
692
I
693
693
A
694
694
Y
695
695
T
696
696
M
697
697
S
698
698
L
699
699
G
700
700
A
701
701
E
702
702
N
703
703
S
704
704
V
705
705
A
706
706
Y
707
707
S
708
708
N
709
709
N
710
710
S
711
711
I
712
712
A
713
713
I
714
714
P
715
715
T
716
716
N
717
717
F
718
718
T
719
719
I
720
720
S
721
721
V
722
722
T
723
723
T
724
724
E
725
725
I
726
726
L
727
727
P
728
728
V
729
729
S
730
730
M
731
731
T
732
732
K
733
733
T
734
734
S
735
735
V
736
736
D
737
737
C
738
738
T
739
739
M
740
740
Y
741
741
I
742
742
C
743
743
G
744
744
D
745
745
S
746
746
T
747
747
E
748
748
C
749
749
S
750
750
N
751
751
L
752
752
L
753
753
L
754
754
Q
755
755
Y
756
756
G
757
757
S
758
758
F
759
759
C
760
760
T
761
761
Q
762
762
L
763
763
N
764
764
R
765
765
A
766
766
L
767
767
T
768
768
G
769
769
I
770
770
A
771
771
V
772
772
E
773
773
Q
774
774
D
775
775
K
776
776
N
777
777
T
778
778
Q
779
779
E
780
780
V
781
781
F
782
782
A
783
783
Q
784
784
V
785
785
K
786
786
Q
787
787
I
788
788
Y
789
789
K
790
790
T
791
791
P
792
792
P
793
793
I
794
794
K
795
795
D
796
796
F
797
797
G
798
798
G
799
799
F
800
800
N
801
801
F
802
802
S
803
803
Q
804
804
I
805
805
L
806
806
P
807
807
D
808
808
P
809
809
S
810
810
K
811
811
S
813
813
K
814
814
R
815
815
S
816
816
F
817
817
I
818
818
E
819
819
D
820
820
L
821
821
L
822
822
F
823
823
N
824
824
K
825
825
V
826
826
T
827
827
N
856
856
G
857
857
L
858
858
T
859
859
V
860
860
L
861
861
P
862
862
P
863
863
L
864
864
L
865
865
T
866
866
D
867
867
E
868
868
M
869
869
I
870
870
A
871
871
Q
872
872
Y
873
873
T
874
874
S
875
875
A
876
876
L
877
877
L
878
878
A
879
879
G
880
880
T
881
881
I
882
882
T
883
883
S
884
884
G
885
885
W
886
886
T
887
887
F
888
888
G
889
889
A
890
890
G
891
891
A
892
892
A
893
893
L
894
894
Q
895
895
I
896
896
P
897
897
F
898
898
A
899
899
M
900
900
Q
901
901
M
902
902
A
903
903
Y
904
904
R
905
905
F
906
906
N
907
907
G
908
908
I
909
909
G
910
910
V
911
911
T
912
912
Q
913
913
N
914
914
V
915
915
L
916
916
Y
917
917
E
918
918
N
919
919
Q
920
920
K
921
921
L
922
922
I
923
923
A
924
924
N
925
925
Q
926
926
F
927
927
N
928
928
S
929
929
A
930
930
I
931
931
G
932
932
K
933
933
I
934
934
Q
935
935
D
936
936
S
937
937
L
938
938
S
939
939
S
940
940
T
941
941
A
942
942
S
943
943
A
944
944
L
945
945
G
946
946
K
947
947
L
948
948
Q
949
949
D
950
950
V
951
951
V
952
952
N
953
953
Q
954
954
N
955
955
A
956
956
Q
957
957
A
958
958
L
959
959
N
960
960
T
961
961
L
962
962
V
963
963
K
964
964
Q
965
965
L
966
966
S
967
967
S
968
968
N
969
969
F
970
970
G
971
971
A
972
972
I
973
973
S
974
974
S
975
975
V
976
976
L
977
977
N
978
978
D
979
979
I
980
980
L
981
981
S
982
982
R
983
983
L
984
984
D
985
985
K
986
986
V
987
987
E
988
988
A
989
989
E
990
990
V
991
991
Q
992
992
I
993
993
D
994
994
R
995
995
L
996
996
I
997
997
T
998
998
G
999
999
R
1000
1000
L
1001
1001
Q
1002
1002
S
1003
1003
L
1004
1004
Q
1005
1005
T
1006
1006
Y
1007
1007
V
1008
1008
T
1009
1009
Q
1010
1010
Q
1011
1011
L
1012
1012
I
1013
1013
R
1014
1014
A
1015
1015
A
1016
1016
E
1017
1017
I
1018
1018
R
1019
1019
A
1020
1020
S
1021
1021
A
1022
1022
N
1023
1023
L
1024
1024
A
1025
1025
A
1026
1026
T
1027
1027
K
1028
1028
M
1029
1029
S
1030
1030
E
1031
1031
C
1032
1032
V
1033
1033
L
1034
1034
G
1035
1035
Q
1036
1036
S
1037
1037
K
1038
1038
R
1039
1039
V
1040
1040
D
1041
1041
F
1042
1042
C
1043
1043
G
1044
1044
K
1045
1045
G
1046
1046
Y
1047
1047
H
1048
1048
L
1049
1049
M
1050
1050
S
1051
1051
F
1052
1052
P
1053
1053
Q
1054
1054
S
1055
1055
A
1056
1056
P
1057
1057
H
1058
1058
G
1059
1059
V
1060
1060
V
1061
1061
F
1062
1062
L
1063
1063
H
1064
1064
V
1065
1065
T
1066
1066
Y
1067
1067
V
1068
1068
P
1069
1069
A
1070
1070
Q
1071
1071
E
1072
1072
K
1073
1073
N
1074
1074
F
1075
1075
T
1076
1076
T
1077
1077
A
1078
1078
P
1079
1079
A
1080
1080
I
1081
1081
C
1082
1082
H
1083
1083
D
1084
1084
G
1085
1085
K
1086
1086
A
1087
1087
H
1088
1088
F
1089
1089
P
1090
1090
R
1091
1091
E
1092
1092
G
1093
1093
V
1094
1094
F
1095
1095
V
1096
1096
S
1097
1097
N
1098
1098
G
1099
1099
T
1100
1100
H
1101
1101
W
1102
1102
F
1103
1103
V
1104
1104
T
1105
1105
Q
1106
1106
R
1107
1107
N
1108
1108
F
1109
1109
Y
1110
1110
E
1111
1111
P
1112
1112
Q
1113
1113
I
1114
1114
I
1115
1115
T
1116
1116
T
1117
1117
D
1118
1118
N
1119
1119
T
1120
1120
F
1121
1121
V
1122
1122
S
1123
1123
G
1124
1124
N
1125
1125
C
1126
1126
D
1127
1127
V
1128
1128
V
1129
1129
I
1130
1130
G
1131
1131
I
1132
1132
V
1133
1133
N
1134
1134
N
1135
1135
T
1136
1136
V
1137
1137
Y
1138
1138
D
1139
1139
P
1140
1140
Impact score
Select a variant from the sequence above to obtain its impact score as well as mutation effect and time-dependent descriptors.