Project name: VHL pH 6

Status: done

Started: 2026-04-27 10:53:02
Chain sequence(s) C: LRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQE
input PDB
Selected Chain(s) C
Distance of aggregation 5 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 C 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                                          (00:03:04)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/db3d653b2f4009d/tmp/folded.pdb                (00:03:04)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:58)
Show buried residues
Minimal score value
-2.2869
Maximal score value
1.797
Average score
-0.3516
Total score value
-49.9299
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
63 L C 0.9382
64 R C -1.6254
65 S C 0.0000
66 V C 1.5995
67 N C -0.6233
68 S C -0.5688
69 R C -2.0064
70 E C -1.2337
71 P C -0.3147
72 S C 0.0000
73 Q C -0.5088
74 V C 0.0000
75 I C 0.0244
76 F C 0.0000
77 C C 0.1050
78 N C 0.0000
79 R C -1.8441
80 S C 0.0000
81 P C -0.3009
82 R C -0.1463
83 V C 0.8385
84 V C 0.0000
85 L C 0.1699
86 P C 0.0000
87 V C 0.0000
88 W C 0.0954
89 L C 0.0000
90 N C -0.5320
91 F C 0.2873
92 D C -1.7126
93 G C -1.0580
94 E C -1.8771
95 P C -0.4803
96 Q C -0.5783
97 P C -0.1946
98 Y C 0.4878
99 P C -0.1609
100 T C -0.0615
101 L C 0.0000
102 P C -0.0862
103 P C -0.1981
104 G C -0.5014
105 T C -0.1799
106 G C -0.4137
107 R C -0.9868
108 R C -1.8666
109 I C -0.2586
110 H C -0.9853
111 S C 0.0000
112 Y C 0.3367
113 R C -0.7081
114 G C -0.2344
115 H C 0.0000
116 L C 0.2622
117 W C 0.0000
118 L C 0.0000
119 F C 0.0000
120 R C 0.0000
121 D C 0.0000
122 A C -0.0491
123 G C -0.4682
124 T C -0.1743
125 H C -0.3400
126 D C 0.0000
127 G C -0.1788
128 L C 0.0000
129 L C 0.2832
130 V C 0.0000
131 N C -0.9243
132 Q C -1.3368
133 T C -0.6071
134 E C -1.7826
135 L C -0.0821
136 F C 0.0000
137 V C 0.9904
138 P C 0.0000
139 S C 0.0381
140 L C 1.5180
141 N C 0.0000
142 V C 1.3878
143 D C -1.6181
144 G C -0.8982
145 Q C -0.6392
146 P C -0.0841
147 I C 0.6607
148 F C 1.3597
149 A C 0.0000
150 N C -0.3665
151 I C 0.0000
152 T C 0.0719
153 L C 0.5257
154 P C 0.3684
155 V C 1.7970
156 Y C 0.5009
157 T C 0.2600
158 L C 1.1162
159 K C -1.6415
160 E C -1.6927
161 R C -1.0474
162 C C 0.2263
163 L C 0.2216
164 Q C 0.0000
165 V C 0.9041
166 V C 0.6851
167 R C -0.1318
168 S C 0.0340
169 L C 1.5526
170 V C 0.2168
171 K C -1.7007
172 P C -0.8825
173 E C -1.9306
174 N C -0.6979
175 Y C 0.0000
176 R C -2.1770
177 R C -2.0980
178 L C -0.2464
179 D C -1.5776
180 I C 0.7114
181 V C 1.5587
182 R C -1.5321
183 S C -0.3836
184 L C 0.2680
185 Y C -0.0231
186 E C -1.9991
187 D C -1.5220
188 L C 0.0000
189 E C -2.1530
190 D C -2.2230
191 H C -0.8572
192 P C -0.3102
193 N C -0.8425
194 V C 0.0000
195 Q C -1.4937
196 K C -1.9875
197 D C -0.8886
198 L C 0.0000
199 E C -2.1584
200 R C -2.2869
201 L C -0.0455
202 T C -0.2352
203 Q C -1.7315
204 E C -2.0380
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 -0.2683 2.8813 View CSV PDB
4.5 -0.3015 2.8813 View CSV PDB
5.0 -0.3447 2.8813 View CSV PDB
5.5 -0.3897 2.8813 View CSV PDB
6.0 -0.4293 2.8813 View CSV PDB
6.5 -0.4592 2.8813 View CSV PDB
7.0 -0.4786 2.8813 View CSV PDB
7.5 -0.4901 2.8813 View CSV PDB
8.0 -0.4972 2.8813 View CSV PDB
8.5 -0.5015 2.8813 View CSV PDB
9.0 -0.5027 2.8813 View CSV PDB