Project name: 330

Status: done

Started: 2026-05-07 13:59:16
Chain sequence(s) A: AAAAAAAYYAQALASIDEAATLVKAKKWEEAKDQVADAVENFCLGKNPDVTDLQTVLLDAATKEMFALADEAIAALDKQDEAAALDALAKMKALVTATAA
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage No
Dynamic mode No
Automated mutations No
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:03)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:10)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/125835c9589c6d9/tmp/folded.pdb                (00:02:10)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:37)
Show buried residues
Minimal score value
-4.016
Maximal score value
2.5547
Average score
-1.0611
Total score value
-106.1112
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 A A -0.2998
2 A A 0.0977
3 A A 0.1954
4 A A -0.0708
5 A A -0.2105
6 A A 0.1021
7 A A 0.0307
8 Y A -0.2277
9 Y A 0.0000
10 A A -0.2843
11 Q A -1.4096
12 A A 0.0000
13 L A -0.8863
14 A A -1.3944
15 S A -2.1039
16 I A 0.0000
17 D A -2.4872
18 E A -2.5796
19 A A 0.0000
20 A A -2.0255
21 T A -1.8777
22 L A -2.5483
23 V A 0.0000
24 K A -2.5464
25 A A -2.0360
26 K A -3.6786
27 K A -3.4364
28 W A -3.8900
29 E A -4.0160
30 E A -3.9620
31 A A 0.0000
32 K A -2.8497
33 D A -3.2626
34 Q A -2.9231
35 V A 0.0000
36 A A -1.7429
37 D A -2.2914
38 A A 0.0000
39 V A -0.7533
40 E A -2.0842
41 N A -1.3090
42 F A 0.0000
43 C A -0.2662
44 L A -0.4511
45 G A 0.0000
46 K A -0.1926
47 N A -0.4814
48 P A -0.5866
49 D A -1.4338
50 V A 0.0208
51 T A -0.5833
52 D A -1.1118
53 L A 0.4814
54 Q A -0.3962
55 T A 0.7546
56 V A 2.5547
57 L A 2.3984
58 L A 1.6558
59 D A -0.0834
60 A A -0.7933
61 A A -0.8280
62 T A 0.0000
63 K A -1.7931
64 E A -2.5647
65 M A 0.0000
66 F A -0.8082
67 A A -1.6508
68 L A 0.0000
69 A A -1.5712
70 D A -2.4040
71 E A -2.7415
72 A A 0.0000
73 I A -1.9854
74 A A -2.1791
75 A A 0.0000
76 L A 0.0000
77 D A -3.4926
78 K A -3.4949
79 Q A -3.8614
80 D A -2.9368
81 E A -2.7864
82 A A -1.4156
83 A A -1.6347
84 A A 0.0000
85 L A -1.5550
86 D A -2.4019
87 A A 0.0000
88 L A 0.0000
89 A A -1.6493
90 K A -2.2686
91 M A 0.0000
92 K A -1.4974
93 A A -0.6916
94 L A -0.6382
95 V A 0.0000
96 T A -0.2187
97 A A 0.0285
98 T A -0.0254
99 A A 0.1270
100 A A 0.1031
Download PDB file
View in 3Dmol

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 globular. Max score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 -0.1954 2.8943 View CSV PDB
4.5 -0.3554 2.8277 View CSV PDB
5.0 -0.5521 2.7885 View CSV PDB
5.5 -0.7548 2.7602 View CSV PDB
6.0 -0.9325 2.7333 View CSV PDB
6.5 -1.0605 2.7089 View CSV PDB
7.0 -1.1334 2.6873 View CSV PDB
7.5 -1.1667 2.6688 View CSV PDB
8.0 -1.1764 2.6551 View CSV PDB
8.5 -1.1654 2.6489 View CSV PDB
9.0 -1.1273 2.6621 View CSV PDB