Project name: R6mu_2

Status: done

Started: 2026-02-28 23:18:26
Chain sequence(s) A: SMLESLVGKILNLLTQVRLTGQNIDDLYADLVLVYEAGTLGQIETYRNQFMQLLAQLLMLLDELLRLIRELMRFIKENNVSENLLIILKLMLTALDEYKWIFQQANALFTQLLIGLATGTLTQEQLDAIIAQLEALRKLGEQVSHLIDSLMNKIKEELYE
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                                          (00:03:59)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/62d4c8a036d1c44/tmp/folded.pdb                (00:03:59)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:10)
Show buried residues
Minimal score value
-3.9403
Maximal score value
1.2589
Average score
-0.9643
Total score value
-154.2856
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 S A -0.2858
2 M A 0.4922
3 L A -0.0690
4 E A -1.7280
5 S A -1.0573
6 L A -0.8062
7 V A 0.0000
8 G A -1.5060
9 K A -2.1633
10 I A 0.0000
11 L A -1.1026
12 N A -1.8437
13 L A -0.9852
14 L A 0.0000
15 T A -0.7179
16 Q A -0.6574
17 V A 0.0000
18 R A -1.1592
19 L A 0.1145
20 T A 0.0000
21 G A 0.0000
22 Q A -2.0617
23 N A -2.1679
24 I A 0.0000
25 D A -2.6061
26 D A -2.8444
27 L A -1.7277
28 Y A 0.0000
29 A A -0.9858
30 D A -0.8722
31 L A 0.0000
32 V A 0.6843
33 L A 1.2589
34 V A 0.3914
35 Y A -0.1509
36 E A -1.2735
37 A A -0.4483
38 G A -0.3163
39 T A -0.5550
40 L A -0.1733
41 G A -1.0353
42 Q A -1.3692
43 I A 0.0000
44 E A -1.9067
45 T A -1.6170
46 Y A -1.4906
47 R A -1.8252
48 N A -2.3168
49 Q A -1.9165
50 F A 0.0000
51 M A -0.9918
52 Q A -1.6078
53 L A -0.8767
54 L A 0.0000
55 A A -0.1488
56 Q A -0.2778
57 L A 0.0000
58 L A -0.0909
59 M A 0.3190
60 L A 0.0000
61 L A 0.0000
62 D A -2.0716
63 E A -1.5646
64 L A 0.0000
65 L A -1.6953
66 R A -2.2194
67 L A 0.0000
68 I A 0.0000
69 R A -2.2594
70 E A -2.1297
71 L A 0.0000
72 M A 0.0000
73 R A -3.5618
74 F A -2.2510
75 I A 0.0000
76 K A -3.9403
77 E A -3.7627
78 N A -2.9510
79 N A -2.9300
80 V A -1.1362
81 S A -1.3834
82 E A -2.1276
83 N A -1.5306
84 L A 0.0000
85 L A -0.4905
86 I A 0.9814
87 I A 0.0000
88 L A 0.0000
89 K A -0.3850
90 L A 0.6142
91 M A 0.0000
92 L A -0.8876
93 T A -0.9804
94 A A 0.0000
95 L A 0.0000
96 D A -2.3079
97 E A -1.8212
98 Y A 0.0000
99 K A -1.4134
100 W A -0.5671
101 I A 0.0000
102 F A 0.0000
103 Q A -0.8710
104 Q A -0.7237
105 A A -0.7877
106 N A -0.5426
107 A A -0.5044
108 L A -0.2582
109 F A 0.0000
110 T A -0.1303
111 Q A 0.0053
112 L A 0.0000
113 L A 0.0000
114 I A 1.1800
115 G A 0.0000
116 L A 0.5273
117 A A 0.4434
118 T A 0.2538
119 G A -0.2482
120 T A -0.1139
121 L A -0.7430
122 T A -1.6782
123 Q A -2.7619
124 E A -3.3017
125 Q A -2.4904
126 L A 0.0000
127 D A -2.8194
128 A A -1.8662
129 I A 0.0000
130 I A -0.9157
131 A A -1.0638
132 Q A -1.4185
133 L A 0.0000
134 E A -1.6722
135 A A -1.3752
136 L A 0.0000
137 R A -2.9114
138 K A -3.2467
139 L A -2.0123
140 G A -2.4167
141 E A -3.5404
142 Q A -2.7157
143 V A 0.0000
144 S A -1.8299
145 H A -1.7562
146 L A -0.6757
147 I A 0.0000
148 D A -1.2592
149 S A -1.0052
150 L A 0.0000
151 M A -1.3900
152 N A -2.5190
153 K A -2.7735
154 I A 0.0000
155 K A -2.3019
156 E A -3.1648
157 E A -2.3761
158 L A -0.9554
159 Y A -0.3633
160 E A -1.9482
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 -0.6018 2.3766 View CSV PDB
4.5 -0.6876 2.3634 View CSV PDB
5.0 -0.8007 2.3407 View CSV PDB
5.5 -0.9225 2.3114 View CSV PDB
6.0 -1.0334 2.2804 View CSV PDB
6.5 -1.1163 2.2523 View CSV PDB
7.0 -1.1633 2.232 View CSV PDB
7.5 -1.1809 2.2212 View CSV PDB
8.0 -1.1814 2.2167 View CSV PDB
8.5 -1.1715 2.2152 View CSV PDB
9.0 -1.1515 2.2147 View CSV PDB