Project name: phlamhtrimer [mutate: LR73C, FH74D] [mutate: LT56B] [mutate: IK45B] [mutate: VK3D] [mutate: TL56B] [mutate: LS56B] [mutate: SL56B, NA53B] [mutate: AN53B] [mutate: SK55B]

Status: done

Started: 2025-04-25 14:24:44
Chain sequence(s) C: DARRKAEMLQNEAKTLLAQANSKLQLLKDLERKYEDNQRYLEDKAQELARLEGEVRSLLKDISQKVAVYSTCR
B: ENVERWQGQYEGLRGQDLGQAVLDAGHSVSTLEKTLPQLLAKLSKLENRGVHNASLALSASIGRVRELCAQARGAASKVKV
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 SK55B
Energy difference between WT (input) and mutated protein (by FoldX) -0.471646 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                                                       (00:01:47)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:04)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/23025308bea3411/tmp/folded.pdb                (00:02:04)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:11)
Show buried residues
Minimal score value
-4.4346
Maximal score value
0.9559
Average score
-1.7009
Total score value
-401.4066
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 -2.7609
16 Q B -2.3271
17 D B -2.3274
18 L B -2.3797
19 G B -1.7863
20 Q B -1.7560
21 A B 0.0000
22 V B 0.0000
23 L B -0.0078
24 D B -1.1077
25 A B 0.0000
26 G B -1.0023
27 H B -1.2920
28 S B -1.4208
29 V B 0.0000
30 S B -1.3319
31 T B -1.4043
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 -2.0423
45 K B -2.9688
46 L B 0.0000
47 E B -3.2592
48 N B -2.6707
49 R B -1.8812
50 G B -0.8813
51 V B 0.8171
52 H B -0.3923
53 N B -0.8699
54 A B 0.0000
55 K B -0.2801 mutated: SK55B
56 L B 0.9559
57 A B 0.0980
58 L B 0.0000
59 S B -0.0132
60 A B -0.1185
61 S B -0.7585
62 I B 0.0000
63 G B -1.8687
64 R B -2.3554
65 V B 0.0000
66 R B -2.7985
67 E B -3.2285
68 L B 0.0000
69 C B 0.0000
70 A B -1.9940
71 Q B -2.2939
72 A B 0.0000
73 R B -2.3713
74 G B -1.6875
75 A B -1.7729
76 A B -1.4648
77 S B -1.6490
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 -2.2978
3 R C -3.3125
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 -2.1543
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 -3.5197
32 R C -4.2440
33 K C -4.0737
34 Y C 0.0000
35 E C -4.4346
36 D C -4.3512
37 N C -3.3222
38 Q C -3.1418
39 R C -3.5639
40 Y C -2.1018
41 L C 0.0000
42 E C -2.8344
43 D C -2.4985
44 K C -2.1202
45 A C -1.7177
46 Q C -2.2441
47 E C -2.3505
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 -2.2193
54 E C -2.6556
55 V C 0.0000
56 R C -2.7978
57 S C -2.2328
58 L C 0.0000
59 L C -2.5388
60 K C -3.1106
61 D C -2.8152
62 I C 0.0000
63 S C -2.1530
64 Q C -2.1085
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 -2.4902
2 T D -2.0195
3 K D -2.8521
4 D D -2.4369
5 L D -1.9334
6 N D -3.1568
7 K D -2.8431
8 L D 0.0000
9 N D -3.1078
10 E D -3.3753
11 I D 0.0000
12 E D -2.4630
13 G D -2.3193
14 T D -2.1614
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 -3.2211
33 D D -4.3061
34 L D 0.0000
35 E D -3.6852
36 N D -4.2094
37 E D -4.3486
38 A D 0.0000
39 K D -4.4031
40 K D -3.9461
41 Q D -3.2155
42 E D -3.0762
43 A D -2.0064
44 A D -1.7614
45 I D 0.0000
46 M D -1.1258
47 D D -2.4684
48 Y D -1.9355
49 N D -2.0159
50 R D -3.3551
51 D D -3.0243
52 I D 0.0000
53 E D -3.2367
54 E D -3.3789
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 -3.4174
64 D D -3.4985
65 I D -2.3361
66 R D -2.6464
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 -1.8261 1.5667 View CSV PDB
4.5 -1.9441 1.3794 View CSV PDB
5.0 -2.0899 1.1837 View CSV PDB
5.5 -2.235 1.1419 View CSV PDB
6.0 -2.3488 1.1932 View CSV PDB
6.5 -2.4099 1.2628 View CSV PDB
7.0 -2.4163 1.3441 View CSV PDB
7.5 -2.3842 1.4303 View CSV PDB
8.0 -2.3304 1.5182 View CSV PDB
8.5 -2.2615 1.6064 View CSV PDB
9.0 -2.176 1.6939 View CSV PDB