Project name: VHL_N78Y

Status: done

Started: 2026-01-10 20:34:24
Chain sequence(s) A: MEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVYQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD
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.                                                (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:05)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/a76490391298efd/tmp/folded.pdb                (00:03:05)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:06)
Show buried residues
Minimal score value
-4.0859
Maximal score value
1.8614
Average score
-1.0483
Total score value
-167.7316
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 0.1280
2 E A -1.7391
3 A A -1.2624
4 G A -2.1189
5 R A -2.9802
6 P A -2.0695
7 R A -2.6595
8 P A -1.4902
9 V A -0.4060
10 L A 0.0000
11 R A -0.7784
12 S A 0.0000
13 V A 0.6923
14 N A -1.0145
15 S A -1.6841
16 R A -2.6915
17 E A -2.4692
18 P A -1.7491
19 S A 0.0000
20 Q A -1.3032
21 V A 0.0000
22 I A -0.6255
23 F A 0.0000
24 C A -1.1139
25 N A 0.0000
26 R A -2.2687
27 S A 0.0000
28 P A -0.9981
29 R A -1.0149
30 V A -0.2279
31 V A 0.0000
32 L A 0.0312
33 P A 0.0000
34 V A 0.0000
35 W A -0.2963
36 L A 0.0000
37 N A -1.0542
38 F A -0.7206
39 D A -2.2171
40 G A -1.7792
41 E A -2.6440
42 P A -1.5344
43 Q A -0.9730
44 P A -0.4372
45 Y A 0.1748
46 P A -0.1572
47 T A 0.0074
48 L A 0.0000
49 P A -0.6130
50 P A -1.1023
51 G A -1.2939
52 T A -0.9949
53 G A -1.5114
54 R A -1.8446
55 R A -2.3005
56 I A -1.4688
57 H A -1.5380
58 S A 0.0000
59 Y A -1.2603
60 R A -1.5882
61 G A -0.1963
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 -0.3763
70 G A -0.6169
71 T A -0.9221
72 H A -1.0609
73 D A -0.9452
74 G A -0.4103
75 L A 0.0000
76 L A 0.1644
77 V A 0.0000
78 Y A 0.6805
79 Q A -0.6247
80 T A -0.3372
81 E A -0.4261
82 L A 0.4266
83 F A 0.0000
84 V A 1.5485
85 P A 0.0000
86 S A 0.0891
87 L A -0.1018
88 N A -0.4577
89 V A 0.4773
90 D A -1.5099
91 G A -1.3895
92 Q A -1.3412
93 P A -0.5568
94 I A 0.5249
95 F A 0.8834
96 A A 0.0000
97 N A -0.5062
98 I A 0.0000
99 T A -0.4059
100 L A 0.3461
101 P A 0.9035
102 V A 1.8614
103 Y A 0.5120
104 T A 0.0944
105 L A 0.3994
106 K A -1.2720
107 E A -1.5386
108 R A -1.3815
109 C A -0.5026
110 L A 0.0000
111 Q A -0.4746
112 V A 0.4647
113 V A 0.5547
114 R A -0.3644
115 S A 0.4971
116 L A 1.3491
117 V A -0.4389
118 K A -2.1934
119 P A -2.8046
120 E A -3.6499
121 N A -3.3907
122 Y A 0.0000
123 R A -3.9607
124 R A -3.4524
125 L A -1.8541
126 D A -1.9001
127 I A -0.0757
128 V A 0.7912
129 R A -1.6299
130 S A -0.8426
131 L A -1.1404
132 Y A 0.0000
133 E A -3.6980
134 D A -3.0126
135 L A 0.0000
136 E A -4.0859
137 D A -3.7389
138 H A -2.8769
139 P A -2.1529
140 N A -2.5655
141 V A -2.1444
142 Q A -3.2368
143 K A -3.6965
144 D A -2.9083
145 L A 0.0000
146 E A -3.9209
147 R A -3.7396
148 L A -2.6053
149 T A -2.5087
150 Q A -3.1832
151 E A -3.5431
152 R A -3.3980
153 I A -1.8279
154 A A -2.2382
155 H A -3.0250
156 Q A -3.3065
157 R A -2.9571
158 M A -1.2305
159 G A -2.0299
160 D A -2.6570
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 -1.0194 2.4291 View CSV PDB
4.5 -1.0912 2.4291 View CSV PDB
5.0 -1.1818 2.4291 View CSV PDB
5.5 -1.2734 2.4291 View CSV PDB
6.0 -1.3506 2.4291 View CSV PDB
6.5 -1.4064 2.4291 View CSV PDB
7.0 -1.4423 2.429 View CSV PDB
7.5 -1.464 2.429 View CSV PDB
8.0 -1.477 2.4289 View CSV PDB
8.5 -1.4836 2.4286 View CSV PDB
9.0 -1.483 2.4275 View CSV PDB