Project name: TruncatedIgYCH1CH2

Status: done

Started: 2026-03-28 21:48:47
Chain sequence(s) A: APSVFPISSCCGSTQQQPVVGCLATGYIPGPATFSWSGASGATSVTVPETHGVGPHKRASFLRPPHAGSGDFFTCSVNHQATRTSLTQNVEGCVAGGEPTPPEVQVLHSSVCSTLGDDSVELLCVITGFSPPPVEVEWLVDGAPAHLVATMTRPQREAGSKTYMATSQTNVSREDWKAGKAFTCRVKHPATGGTAQGHARF
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 globular. Max 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                                          (00:01:28)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/b67a7531e9303ae/tmp/folded.pdb                (00:01:28)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:05)
Show buried residues
Minimal score value
-3.364
Maximal score value
2.0852
Average score
-0.6866
Total score value
-138.0146
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 -0.2644
2 P A 0.0000
3 S A 0.3008
4 V A 1.1229
5 F A 2.0852
6 P A 0.9321
7 I A 1.1645
8 S A 0.8895
9 S A 0.5045
10 C A 0.8302
11 C A -0.1040
12 G A -0.9834
13 S A -1.0021
14 T A -1.0777
15 Q A -1.6375
16 Q A -2.1260
17 Q A -1.7188
18 P A 0.0000
19 V A 0.0349
20 V A 0.0000
21 G A 0.0000
22 C A 0.0000
23 L A 1.1188
24 A A 0.0000
25 T A -0.2078
26 G A -0.4411
27 Y A 0.0000
28 I A 1.0076
29 P A 0.2838
30 G A -0.5197
31 P A -0.7650
32 A A 0.0000
33 T A -0.6275
34 F A 0.0245
35 S A -0.2661
36 W A -0.2830
37 S A -0.3494
38 G A -0.4609
39 A A -0.6384
40 S A -0.7066
41 G A -0.9421
42 A A -0.9634
43 T A -0.4011
44 S A 0.1762
45 V A 0.9667
46 T A 0.7556
47 V A 0.6863
48 P A -0.4033
49 E A -1.2958
50 T A -1.1278
51 H A -1.3167
52 G A -0.3148
53 V A 1.1204
54 G A 0.1895
55 P A -0.1915
56 H A -0.8717
57 K A -1.4135
58 R A -0.8502
59 A A 0.5146
60 S A 0.0000
61 F A 0.8938
62 L A 0.0000
63 R A -1.1556
64 P A 0.0000
65 P A -1.2760
66 H A -1.8027
67 A A -1.2184
68 G A -0.9488
69 S A -0.4356
70 G A -0.5417
71 D A -0.6114
72 F A 0.5800
73 F A 0.0000
74 T A -0.4603
75 C A 0.0000
76 S A -0.4502
77 V A 0.0000
78 N A -1.5486
79 H A 0.0000
80 Q A -2.2549
81 A A -1.0447
82 T A -1.1921
83 R A -2.5068
84 T A -1.4379
85 S A -1.0121
86 L A -0.0284
87 T A -0.2646
88 Q A -0.2676
89 N A -0.8652
90 V A 0.0000
91 E A -0.1728
92 G A 0.0000
93 C A 0.0000
94 V A 0.9290
95 A A 0.0467
96 G A -0.6891
97 G A -1.5296
98 E A -2.3139
99 P A -1.4442
100 T A -1.2534
101 P A -1.1959
102 P A 0.0000
103 E A -2.2848
104 V A 0.0000
105 Q A -1.6654
106 V A 0.0000
107 L A -0.0650
108 H A -0.7543
109 S A -0.5221
110 S A -0.0131
111 V A 0.1191
112 C A 0.8263
113 S A 0.1582
114 T A 0.5018
115 L A 0.6500
116 G A -1.0925
117 D A -2.5400
118 D A -3.1956
119 S A -2.7135
120 V A 0.0000
121 E A -1.8919
122 L A 0.0000
123 L A -0.1698
124 C A 0.0000
125 V A -0.0444
126 I A 0.0000
127 T A -0.9709
128 G A -1.0521
129 F A 0.0000
130 S A -1.0623
131 P A -0.8127
132 P A -0.9060
133 P A -0.9695
134 V A -1.2384
135 E A -2.2743
136 V A -1.4905
137 E A -1.9174
138 W A 0.0000
139 L A -1.0891
140 V A -1.1621
141 D A -2.3498
142 G A -1.4102
143 A A -0.8078
144 P A -0.9775
145 A A -0.5392
146 H A -0.5203
147 L A 0.3747
148 V A 1.4126
149 A A 0.5152
150 T A 0.3225
151 M A -0.2504
152 T A -0.9732
153 R A -2.1924
154 P A -1.7284
155 Q A -2.3208
156 R A -2.6596
157 E A -1.7751
158 A A -1.1017
159 G A -1.1372
160 S A -1.5285
161 K A -2.3069
162 T A -1.6089
163 Y A -1.4666
164 M A -0.9344
165 A A 0.0000
166 T A -0.2420
167 S A 0.0000
168 Q A -0.3242
169 T A 0.0000
170 N A -1.7193
171 V A 0.0000
172 S A -2.5078
173 R A -2.9528
174 E A -3.3640
175 D A -2.4603
176 W A 0.0000
177 K A -2.4654
178 A A -1.7118
179 G A -1.4954
180 K A -2.0390
181 A A -1.6398
182 F A 0.0000
183 T A -1.9418
184 C A 0.0000
185 R A -2.5831
186 V A 0.0000
187 K A -2.2033
188 H A 0.0000
189 P A -1.0694
190 A A -0.7760
191 T A -0.8762
192 G A -0.8783
193 G A -0.7796
194 T A -1.5399
195 A A -1.7137
196 Q A -2.6068
197 G A -1.8756
198 H A -2.1224
199 A A 0.0000
200 R A -1.7948
201 F A 0.3100
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 -0.2611 4.4892 View CSV PDB
4.5 -0.3073 4.4892 View CSV PDB
5.0 -0.3658 4.4892 View CSV PDB
5.5 -0.424 4.4892 View CSV PDB
6.0 -0.4695 4.4892 View CSV PDB
6.5 -0.4942 4.4892 View CSV PDB
7.0 -0.5011 4.4892 View CSV PDB
7.5 -0.4998 4.4892 View CSV PDB
8.0 -0.4959 4.4892 View CSV PDB
8.5 -0.4898 4.4892 View CSV PDB
9.0 -0.4788 4.4892 View CSV PDB