Project name: phlamhtrimer [mutate: LR73C, FH74D] [mutate: LT56B] [mutate: IK45B] [mutate: VK3D] [mutate: TL56B] [mutate: LS56B] [mutate: SL56B, NA53B] [mutate: AN53B]

Status: done

Started: 2025-04-25 14:19:08
Chain sequence(s) C: DARRKAEMLQNEAKTLLAQANSKLQLLKDLERKYEDNQRYLEDKAQELARLEGEVRSLLKDISQKVAVYSTCR
B: ENVERWQGQYEGLRGQDLGQAVLDAGHSVSTLEKTLPQLLAKLSKLENRGVHAASLALSASIGRVRELCAQARGAASKVKV
D: DTKDLNKLNEIEGTLNKAKDEMKVSDLDRKVSDLENEAKKQEAAIMDYNRDIEEIMKCIRNLEDIRKTLPSGCHNTPSIEKP
input PDB
Selected Chain(s) B,C,D
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage No
Dynamic mode No
Automated mutations No
Mutated residues AN53B
Energy difference between WT (input) and mutated protein (by FoldX) -0.828852 kcal/mol
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with all chain(s) selected           (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       PDB-Info: The input structure is partially or entirely disordered. Average score is   
                       recommended for pH analysis.                                                (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       FoldX:    Building mutant model                                                       (00:01:44)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:46)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/c954b515945db98/tmp/folded.pdb                (00:01:46)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:53)
Show buried residues
Minimal score value
-4.4218
Maximal score value
1.226
Average score
-1.692
Total score value
-399.3031
Download the table (csv)

The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan4D score mutation
1 E B -2.8742
2 N B -2.3304
3 V B -0.8251
4 E B -2.9698
5 R B -3.2786
6 W B -1.2831
7 Q B -1.9276
8 G B -2.4674
9 Q B -2.0528
10 Y B -1.6049
11 E B -2.8831
12 G B -1.9511
13 L B -1.0148
14 R B -2.7222
15 G B -2.7607
16 Q B -2.3271
17 D B -2.3274
18 L B -2.3795
19 G B -1.7864
20 Q B -1.7560
21 A B 0.0000
22 V B 0.0000
23 L B -0.0086
24 D B -1.1080
25 A B 0.0000
26 G B -1.0039
27 H B -1.2924
28 S B -1.4210
29 V B 0.0000
30 S B -1.3321
31 T B -1.4045
32 L B 0.0000
33 E B -2.3460
34 K B -2.3667
35 T B -1.4962
36 L B 0.0000
37 P B -1.2943
38 Q B -1.3620
39 L B 0.0000
40 L B -0.5552
41 A B -0.9697
42 K B -1.6788
43 L B 0.0000
44 S B -2.0443
45 K B -2.9725
46 L B 0.0000
47 E B -3.2636
48 N B -2.6777
49 R B -1.9026
50 G B -0.9007
51 V B 0.8677
52 H B -0.3088
53 N B -0.7131 mutated: AN53B
54 A B 0.0000
55 S B 0.2591
56 L B 1.2260
57 A B 0.2735
58 L B 0.0000
59 S B 0.1347
60 A B -0.0394
61 S B -0.7012
62 I B 0.0000
63 G B -1.8687
64 R B -2.3554
65 V B 0.0000
66 R B -2.7964
67 E B -3.2244
68 L B 0.0000
69 C B 0.0000
70 A B -1.9867
71 Q B -2.2788
72 A B 0.0000
73 R B -2.3664
74 G B -1.6820
75 A B -1.7689
76 A B -1.4627
77 S B -1.6474
78 K B -2.2344
79 V B 0.0000
80 K B -1.2777
81 V B 0.6643
1 D C -2.8246
2 A C -2.2976
3 R C -3.3124
4 R C -3.4357
5 K C -2.7288
6 A C 0.0000
7 E C -2.4558
8 M C -1.5637
9 L C 0.0000
10 Q C -2.1544
11 N C -2.4593
12 E C -1.9674
13 A C 0.0000
14 K C -2.3355
15 T C -1.5608
16 L C -1.0340
17 L C -1.3431
18 A C -0.9505
19 Q C -1.2562
20 A C 0.0000
21 N C -1.4070
22 S C -1.1774
23 K C -1.4510
24 L C -1.2650
25 Q C -1.6299
26 L C -1.2938
27 L C 0.0000
28 K C -2.3212
29 D C -2.5220
30 L C 0.0000
31 E C -3.5198
32 R C -4.2395
33 K C -4.0713
34 Y C 0.0000
35 E C -4.4218
36 D C -4.3344
37 N C -3.3069
38 Q C -3.0423
39 R C -3.5401
40 Y C -2.0820
41 L C 0.0000
42 E C -2.7202
43 D C -2.4831
44 K C -2.0461
45 A C -1.6201
46 Q C -2.2387
47 E C -2.3475
48 L C 0.0000
49 A C -1.8449
50 R C -2.7543
51 L C -1.9060
52 E C -2.2440
53 G C -2.2194
54 E C -2.6558
55 V C 0.0000
56 R C -2.7966
57 S C -2.2332
58 L C 0.0000
59 L C -2.5369
60 K C -3.1112
61 D C -2.8156
62 I C 0.0000
63 S C -2.1515
64 Q C -2.1087
65 K C -1.5807
66 V C 0.0000
67 A C -0.5524
68 V C -0.0556
69 Y C -0.6186
70 S C -0.8456
71 T C -0.5602
72 C C -0.8932
73 R C -2.0650
1 D D -2.4898
2 T D -2.0197
3 K D -2.8527
4 D D -2.4372
5 L D -1.9342
6 N D -3.1587
7 K D -2.8474
8 L D 0.0000
9 N D -3.1092
10 E D -3.3770
11 I D 0.0000
12 E D -2.4638
13 G D -2.3198
14 T D -2.1615
15 L D 0.0000
16 N D -2.4327
17 K D -3.3492
18 A D 0.0000
19 K D -2.5868
20 D D -3.2259
21 E D -2.5333
22 M D -1.9449
23 K D -2.3844
24 V D -0.0608
25 S D -1.0155
26 D D -1.8863
27 L D 0.0000
28 D D -3.6199
29 R D -3.8628
30 K D -3.4415
31 V D 0.0000
32 S D -3.2199
33 D D -4.3039
34 L D 0.0000
35 E D -3.6876
36 N D -4.2125
37 E D -4.3538
38 A D 0.0000
39 K D -4.4164
40 K D -3.9672
41 Q D -3.1914
42 E D -3.0966
43 A D -2.0205
44 A D -1.7029
45 I D 0.0000
46 M D -1.1323
47 D D -2.4731
48 Y D -1.8667
49 N D -2.0161
50 R D -3.3552
51 D D -3.0247
52 I D 0.0000
53 E D -3.2368
54 E D -3.3790
55 I D 0.0000
56 M D -2.1328
57 K D -2.9268
58 C D -2.4579
59 I D 0.0000
60 R D -3.4682
61 N D -3.0457
62 L D 0.0000
63 E D -3.4175
64 D D -3.4985
65 I D -2.3361
66 R D -2.6465
67 K D -2.6917
68 T D -1.2446
69 L D -0.8039
70 P D -0.3015
71 S D -0.5175
72 G D -0.4612
73 C D -0.8806
74 H D -1.6863
75 N D -2.1327
76 T D -0.9769
77 P D -0.7362
78 S D -0.3630
79 I D 0.3722
80 E D -1.8395
81 K D -2.1345
82 P D -1.2832
Download PDB file
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Calculations for various pH values

This page contains details and comparisons for all models calculated at different pH points.
Please find suggestions on interpreting the results below. More details can be found in the Tutorial.
The input structure is partially or entirely disordered. Average score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 -1.8109 1.5942 View CSV PDB
4.5 -1.9289 1.5963 View CSV PDB
5.0 -2.075 1.602 View CSV PDB
5.5 -2.2205 1.6146 View CSV PDB
6.0 -2.3348 1.6337 View CSV PDB
6.5 -2.397 1.6522 View CSV PDB
7.0 -2.4055 1.6637 View CSV PDB
7.5 -2.3759 1.6687 View CSV PDB
8.0 -2.3249 1.6705 View CSV PDB
8.5 -2.2585 1.6711 View CSV PDB
9.0 -2.1755 1.6835 View CSV PDB