Project name: VHL_D73Y

Status: done

Started: 2026-01-10 20:25:39
Chain sequence(s) A: MEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHYGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD
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]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[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]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:42)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/ce3194fd5818708/tmp/folded.pdb                (00:03:42)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:41)
Show buried residues
Minimal score value
-4.3932
Maximal score value
1.8862
Average score
-1.1418
Total score value
-182.6811
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 M A 0.1223
2 E A -1.7251
3 A A -1.2567
4 G A -2.1210
5 R A -2.9697
6 P A -2.0375
7 R A -2.5947
8 P A -1.3543
9 V A -0.0749
10 L A 0.0000
11 R A -0.6779
12 S A 0.0000
13 V A 0.6346
14 N A -1.1099
15 S A -1.9095
16 R A -2.9956
17 E A -3.0923
18 P A -2.1780
19 S A 0.0000
20 Q A -1.7610
21 V A 0.0000
22 I A -1.0689
23 F A 0.0000
24 C A -1.3006
25 N A 0.0000
26 R A -2.2056
27 S A 0.0000
28 P A -0.9890
29 R A -0.9479
30 V A -0.1529
31 V A 0.0000
32 L A 0.0815
33 P A 0.0000
34 V A 0.0000
35 W A -0.2971
36 L A 0.0000
37 N A -1.0444
38 F A -0.7404
39 D A -2.1881
40 G A -1.7191
41 E A -2.6282
42 P A -1.5152
43 Q A -0.9454
44 P A -0.4181
45 Y A 0.1937
46 P A -0.2464
47 T A -0.0751
48 L A 0.0000
49 P A -0.6237
50 P A -1.0905
51 G A -1.2984
52 T A -1.1878
53 G A -1.9683
54 R A -2.7680
55 R A -2.8658
56 I A -1.8150
57 H A -1.7518
58 S A 0.0000
59 Y A -1.6203
60 R A -2.0462
61 G A -0.4347
62 H A 0.0000
63 L A 0.0000
64 W A 0.0000
65 L A 0.0000
66 F A 0.0000
67 R A 0.0000
68 D A 0.0000
69 A A -0.3025
70 G A -0.5365
71 T A -0.7672
72 H A -0.8490
73 Y A -0.5549
74 G A -0.5099
75 L A 0.0000
76 L A -0.7206
77 V A 0.0000
78 N A -1.6320
79 Q A -1.8847
80 T A -1.5897
81 E A -1.8719
82 L A 0.0000
83 F A 0.0000
84 V A 1.1970
85 P A 0.0000
86 S A -0.2013
87 L A -0.4306
88 N A -0.7602
89 V A 0.4075
90 D A -1.5452
91 G A -1.4872
92 Q A -1.4715
93 P A -0.7872
94 I A 0.3095
95 F A 0.3030
96 A A 0.0000
97 N A -0.9874
98 I A 0.0000
99 T A -0.7318
100 L A 0.4064
101 P A 0.8424
102 V A 1.8862
103 Y A 0.6004
104 T A 0.1543
105 L A 0.4484
106 K A -1.2082
107 E A -1.3801
108 R A -1.2969
109 C A -0.5438
110 L A 0.0000
111 Q A -0.4213
112 V A 0.4363
113 V A 0.5203
114 R A -0.2120
115 S A 0.4923
116 L A 1.3515
117 V A -0.2500
118 K A -2.1702
119 P A -2.4626
120 E A -3.4910
121 N A -3.1565
122 Y A 0.0000
123 R A -3.2338
124 R A -3.1157
125 L A -1.6661
126 D A -1.8171
127 I A -0.0866
128 V A 0.7707
129 R A -1.5899
130 S A -0.9425
131 L A -1.2555
132 Y A 0.0000
133 E A -3.6966
134 D A -3.1312
135 L A 0.0000
136 E A -4.0715
137 D A -3.8046
138 H A -2.9061
139 P A -2.0098
140 N A -2.3012
141 V A -2.0866
142 Q A -3.2625
143 K A -3.8359
144 D A -3.2739
145 L A 0.0000
146 E A -4.2357
147 R A -4.3932
148 L A -3.0570
149 T A -2.6172
150 Q A -3.3948
151 E A -3.8455
152 R A -3.2352
153 I A -1.6847
154 A A -2.2273
155 H A -2.9809
156 Q A -3.2480
157 R A -2.9005
158 M A -1.2260
159 G A -2.0269
160 D A -2.6545
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 partially or entirely disordered. Average score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 -1.1059 2.4522 View CSV PDB
4.5 -1.1826 2.4171 View CSV PDB
5.0 -1.2812 2.3985 View CSV PDB
5.5 -1.3825 2.3985 View CSV PDB
6.0 -1.4681 2.3985 View CSV PDB
6.5 -1.5299 2.3985 View CSV PDB
7.0 -1.5695 2.3985 View CSV PDB
7.5 -1.5933 2.3984 View CSV PDB
8.0 -1.6076 2.3982 View CSV PDB
8.5 -1.6153 2.3974 View CSV PDB
9.0 -1.6155 2.3951 View CSV PDB