Project name: Ttt

Status: done

Started: 2025-04-13 15:36:07
Settings
Chain sequence(s) H: SEVQLVESGGGLVQPGGSLRLSCAASGFNVYYSSIHWVRQAPGKGLEWVASIYSYYGYTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARNVGYGMDYWGQGTLVTVSSASTKGPSVFPLAPAATAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTYICNVNHKPSNTKVDKKVE
L: SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQYIYGLITFGQGTKVEIKRTVAAPSVFIFPPSAKSGTASVVCLLNNFYPREAKVQWAAASQESVTEQDSKDSTYSLSSTLTLYEKHKVYACEVTHQGLSSPVTK
input PDB
Selected Chain(s) H,L
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode No
Automated mutations Yes
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with all chain(s) selected           (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:02:49)
[INFO]       Auto_mut: Residue number 57 from chain H and a score of 2.309 omitted from automated  
                       muatation (excluded by the user).                                           (00:02:52)
[INFO]       Auto_mut: Residue number 58 from chain H and a score of 2.139 omitted from automated  
                       muatation (excluded by the user).                                           (00:02:52)
[INFO]       Auto_mut: Residue number 34 from chain H and a score of 1.946 (tyrosine) selected for 
                       automated muatation                                                         (00:02:52)
[INFO]       Auto_mut: Residue number 94 from chain L and a score of 1.724 (tyrosine) selected for 
                       automated muatation                                                         (00:02:52)
[INFO]       Auto_mut: Residue number 30 from chain L and a score of 1.669 (valine) selected for   
                       automated muatation                                                         (00:02:52)
[INFO]       Auto_mut: Residue number 182 from chain L and a score of 1.441 (leucine) selected for 
                       automated muatation                                                         (00:02:52)
[INFO]       Auto_mut: Residue number 55 from chain H and a score of 1.433 (tyrosine) selected for 
                       automated muatation                                                         (00:02:52)
[INFO]       Auto_mut: Residue number 56 from chain H and a score of 1.343 (serine) selected for   
                       automated muatation                                                         (00:02:52)
[INFO]       Auto_mut: Mutating residue number 34 from chain H (tyrosine) into glutamic acid       (00:02:52)
[INFO]       Auto_mut: Mutating residue number 34 from chain H (tyrosine) into aspartic acid       (00:02:52)
[INFO]       Auto_mut: Mutating residue number 94 from chain L (tyrosine) into glutamic acid       (00:02:52)
[INFO]       Auto_mut: Mutating residue number 34 from chain H (tyrosine) into arginine            (00:04:21)
[INFO]       Auto_mut: Mutating residue number 94 from chain L (tyrosine) into lysine              (00:04:22)
[INFO]       Auto_mut: Mutating residue number 34 from chain H (tyrosine) into lysine              (00:04:24)
[INFO]       Auto_mut: Mutating residue number 94 from chain L (tyrosine) into aspartic acid       (00:06:00)
[INFO]       Auto_mut: Mutating residue number 30 from chain L (valine) into glutamic acid         (00:06:09)
[INFO]       Auto_mut: Mutating residue number 30 from chain L (valine) into aspartic acid         (00:06:13)
[INFO]       Auto_mut: Mutating residue number 94 from chain L (tyrosine) into arginine            (00:07:27)
[INFO]       Auto_mut: Mutating residue number 30 from chain L (valine) into lysine                (00:07:38)
[INFO]       Auto_mut: Mutating residue number 30 from chain L (valine) into arginine              (00:07:38)
[INFO]       Auto_mut: Mutating residue number 182 from chain L (leucine) into glutamic acid       (00:09:00)
[INFO]       Auto_mut: Mutating residue number 182 from chain L (leucine) into aspartic acid       (00:09:09)
[INFO]       Auto_mut: Mutating residue number 55 from chain H (tyrosine) into glutamic acid       (00:09:22)
[INFO]       Auto_mut: Mutating residue number 182 from chain L (leucine) into lysine              (00:10:31)
[INFO]       Auto_mut: Mutating residue number 182 from chain L (leucine) into arginine            (00:10:39)
[INFO]       Auto_mut: Mutating residue number 55 from chain H (tyrosine) into lysine              (00:11:01)
[INFO]       Auto_mut: Mutating residue number 55 from chain H (tyrosine) into aspartic acid       (00:12:09)
[INFO]       Auto_mut: Mutating residue number 56 from chain H (serine) into glutamic acid         (00:12:09)
[INFO]       Auto_mut: Mutating residue number 56 from chain H (serine) into aspartic acid         (00:13:05)
[INFO]       Auto_mut: Mutating residue number 56 from chain H (serine) into lysine                (00:13:36)
[INFO]       Auto_mut: Mutating residue number 55 from chain H (tyrosine) into arginine            (00:13:37)
[INFO]       Auto_mut: Mutating residue number 56 from chain H (serine) into arginine              (00:14:34)
[INFO]       Auto_mut: Effect of mutation residue number 34 from chain H (tyrosine) into glutamic  
                       acid: Energy difference: 0.0536 kcal/mol, Difference in average score from  
                       the base case: -0.0291                                                      (00:16:02)
[INFO]       Auto_mut: Effect of mutation residue number 34 from chain H (tyrosine) into lysine:   
                       Energy difference: 0.2855 kcal/mol, Difference in average score from the    
                       base case: -0.0161                                                          (00:16:02)
[INFO]       Auto_mut: Effect of mutation residue number 34 from chain H (tyrosine) into aspartic  
                       acid: Energy difference: 0.3709 kcal/mol, Difference in average score from  
                       the base case: -0.0241                                                      (00:16:02)
[INFO]       Auto_mut: Effect of mutation residue number 34 from chain H (tyrosine) into arginine: 
                       Energy difference: -1.2736 kcal/mol, Difference in average score from the   
                       base case: -0.0276                                                          (00:16:02)
[INFO]       Auto_mut: Effect of mutation residue number 94 from chain L (tyrosine) into glutamic  
                       acid: Energy difference: 0.9301 kcal/mol, Difference in average score from  
                       the base case: -0.0111                                                      (00:16:02)
[INFO]       Auto_mut: Effect of mutation residue number 94 from chain L (tyrosine) into lysine:   
                       Energy difference: 0.2434 kcal/mol, Difference in average score from the    
                       base case: -0.0069                                                          (00:16:02)
[INFO]       Auto_mut: Effect of mutation residue number 94 from chain L (tyrosine) into aspartic  
                       acid: Energy difference: 0.8231 kcal/mol, Difference in average score from  
                       the base case: -0.0120                                                      (00:16:02)
[INFO]       Auto_mut: Effect of mutation residue number 94 from chain L (tyrosine) into arginine: 
                       Energy difference: 0.6186 kcal/mol, Difference in average score from the    
                       base case: -0.0089                                                          (00:16:02)
[INFO]       Auto_mut: Effect of mutation residue number 30 from chain L (valine) into glutamic    
                       acid: Energy difference: -0.8606 kcal/mol, Difference in average score from 
                       the base case: -0.0202                                                      (00:16:02)
[INFO]       Auto_mut: Effect of mutation residue number 30 from chain L (valine) into lysine:     
                       Energy difference: -0.4755 kcal/mol, Difference in average score from the   
                       base case: -0.0174                                                          (00:16:02)
[INFO]       Auto_mut: Effect of mutation residue number 30 from chain L (valine) into aspartic    
                       acid: Energy difference: -0.4789 kcal/mol, Difference in average score from 
                       the base case: -0.0199                                                      (00:16:02)
[INFO]       Auto_mut: Effect of mutation residue number 30 from chain L (valine) into arginine:   
                       Energy difference: -0.1807 kcal/mol, Difference in average score from the   
                       base case: -0.0134                                                          (00:16:02)
[INFO]       Auto_mut: Effect of mutation residue number 182 from chain L (leucine) into glutamic  
                       acid: Energy difference: 1.5578 kcal/mol, Difference in average score from  
                       the base case: -0.0238                                                      (00:16:02)
[INFO]       Auto_mut: Effect of mutation residue number 182 from chain L (leucine) into lysine:   
                       Energy difference: 1.2586 kcal/mol, Difference in average score from the    
                       base case: -0.0219                                                          (00:16:02)
[INFO]       Auto_mut: Effect of mutation residue number 182 from chain L (leucine) into aspartic  
                       acid: Energy difference: 1.8475 kcal/mol, Difference in average score from  
                       the base case: -0.0233                                                      (00:16:03)
[INFO]       Auto_mut: Effect of mutation residue number 182 from chain L (leucine) into arginine: 
                       Energy difference: 0.8041 kcal/mol, Difference in average score from the    
                       base case: -0.0239                                                          (00:16:03)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain H (tyrosine) into glutamic  
                       acid: Energy difference: 0.4107 kcal/mol, Difference in average score from  
                       the base case: 0.0010                                                       (00:16:03)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain H (tyrosine) into lysine:   
                       Energy difference: 0.1278 kcal/mol, Difference in average score from the    
                       base case: 0.0105                                                           (00:16:03)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain H (tyrosine) into aspartic  
                       acid: Energy difference: 0.6256 kcal/mol, Difference in average score from  
                       the base case: 0.0015                                                       (00:16:03)
[INFO]       Auto_mut: Effect of mutation residue number 55 from chain H (tyrosine) into arginine: 
                       Energy difference: -0.5013 kcal/mol, Difference in average score from the   
                       base case: -0.0036                                                          (00:16:03)
[INFO]       Auto_mut: Effect of mutation residue number 56 from chain H (serine) into glutamic    
                       acid: Energy difference: 1.8543 kcal/mol, Difference in average score from  
                       the base case: 0.0029                                                       (00:16:03)
[INFO]       Auto_mut: Effect of mutation residue number 56 from chain H (serine) into lysine:     
                       Energy difference: 0.1172 kcal/mol, Difference in average score from the    
                       base case: 0.0050                                                           (00:16:03)
[INFO]       Auto_mut: Effect of mutation residue number 56 from chain H (serine) into aspartic    
                       acid: Energy difference: 0.9433 kcal/mol, Difference in average score from  
                       the base case: 0.0017                                                       (00:16:03)
[INFO]       Auto_mut: Effect of mutation residue number 56 from chain H (serine) into arginine:   
                       Energy difference: 1.2002 kcal/mol, Difference in average score from the    
                       base case: 0.0015                                                           (00:16:03)
[INFO]       Main:     Simulation completed successfully.                                          (00:16:11)
Show buried residues
Minimal score value
-3.2191
Maximal score value
2.3086
Average score
-0.5378
Total score value
-216.7511
Download the table (csv)

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
3 S H -1.1989
4 E H -2.0250
5 V H -1.0111
6 Q H -0.8281
7 L H 0.0000
8 V H 0.6435
9 E H 0.0000
10 S H -0.4430
11 G H -0.6981
12 G H -0.3457
13 G H -0.0256
14 L H -0.0044
15 V H 0.0000
16 Q H -1.6665
17 P H -1.9390
18 G H -1.6746
19 G H -1.3374
20 S H -1.3143
21 L H -1.0559
22 R H -1.6818
23 L H 0.0000
24 S H -0.3748
25 C H 0.0000
26 A H -0.1625
27 A H -0.3464
28 S H -0.6930
29 G H -1.1039
30 F H -0.2246
31 N H -0.4289
32 V H 0.0000
33 Y H 1.3020
34 Y H 1.9464
35 S H 0.0000
36 S H 0.0000
37 I H 0.0000
38 H H 0.0000
39 W H 0.0000
40 V H 0.0000
41 R H 0.0000
42 Q H -0.7815
43 A H -1.1479
44 P H -0.9301
45 G H -1.4872
46 K H -2.3525
47 G H -1.6112
48 L H 0.0000
49 E H -1.1956
50 W H 0.0000
51 V H 0.0000
52 A H 0.0000
53 S H 0.0000
54 I H 0.0000
55 Y H 1.4325
56 S H 1.3425
57 Y H 2.3086
58 Y H 2.1390
59 G H 0.9651
60 Y H 1.1796
61 T H 0.5188
62 S H 0.0000
63 Y H -0.8843
64 A H -1.4224
65 D H -2.5604
66 S H -1.8363
67 V H 0.0000
68 K H -2.6839
69 G H -1.9341
70 R H -1.8804
71 F H 0.0000
72 T H -0.9764
73 I H 0.0000
74 S H -0.2793
75 A H -0.5248
76 D H -1.3770
77 T H -0.8541
78 S H -1.3679
79 K H -2.2185
80 N H -1.4527
81 T H 0.0000
82 A H 0.0000
83 Y H 0.0000
84 L H 0.0000
85 Q H -1.2907
86 M H 0.0000
87 N H -2.1665
88 S H -1.7122
89 L H 0.0000
90 R H -2.9876
91 A H -2.0439
92 E H -2.4748
93 D H 0.0000
94 T H -0.8097
95 A H 0.0000
96 V H 0.2545
97 Y H 0.0000
98 Y H 0.0000
99 C H 0.0000
100 A H 0.0000
101 R H 0.0000
102 N H 0.5002
103 V H 1.1054
104 G H 0.5279
105 Y H 1.2575
106 G H 0.5963
107 M H 0.0000
108 D H 0.2871
109 Y H 0.1913
110 W H -0.2118
111 G H 0.0000
112 Q H -1.3380
113 G H -0.6128
114 T H -0.0305
115 L H 0.3093
116 V H 0.0000
117 T H -0.4764
118 V H 0.0000
119 S H -1.0384
120 S H -0.6344
121 A H -0.4977
122 S H -0.6752
123 T H -0.9466
124 K H -1.6776
125 G H -1.6789
126 P H 0.0000
127 S H -0.2168
128 V H 0.0000
129 F H -0.1301
130 P H -0.5192
131 L H 0.0000
132 A H -0.6348
133 P H -0.2619
134 A H -0.1127
135 A H 0.0487
142 T H -0.2665
143 A H -0.1838
144 A H 0.0000
145 L H 0.0000
146 G H 0.0000
147 C H 0.0000
148 L H 0.0000
149 V H 0.0000
150 K H 0.0000
151 D H -0.4765
152 Y H 0.0000
153 F H 0.0000
154 P H 0.0000
155 E H -0.8338
156 P H -0.8512
157 V H -0.8550
158 T H -0.7416
159 V H -0.4800
160 S H -0.4999
161 W H 0.0000
162 N H -0.8979
163 S H -0.7601
164 G H -0.6289
165 A H -0.3046
166 L H -0.0342
167 T H -0.2201
168 S H -0.2257
169 G H -0.3835
170 V H 0.1053
171 H H -0.4249
172 T H -0.2184
173 F H 0.0000
174 P H -0.3990
175 A H 0.0889
176 V H 0.3253
177 L H 0.8736
178 Q H 0.1579
179 S H -0.1043
180 S H -0.2426
181 G H -0.0101
182 L H -0.0352
183 Y H 0.2294
184 S H 0.0000
185 L H 0.0000
186 S H 0.0000
187 S H 0.0000
188 V H 0.0000
189 V H 0.0000
190 T H -0.2117
191 V H 0.0000
192 P H -0.2862
193 S H -0.2130
194 S H -0.0885
195 S H 0.2744
196 L H 0.8596
197 G H 0.0211
200 T H -0.4095
201 Y H -0.4686
202 I H -1.0787
203 C H 0.0000
204 N H -1.6882
205 V H 0.0000
206 N H -2.2993
207 H H 0.0000
208 K H -2.8862
209 P H -1.7187
210 S H -2.0343
211 N H -2.7067
212 T H -2.2485
213 K H -2.8849
214 V H -1.7818
215 D H -2.7040
216 K H -2.2581
217 K H -2.2870
218 V H 0.0000
219 E H -1.9267
1 S L -1.3644
2 D L -2.2010
3 I L -1.1540
4 Q L -2.1145
5 M L 0.0000
6 T L -1.3897
7 Q L 0.0000
8 S L -0.9183
9 P L -0.6222
10 S L -0.9494
11 S L -0.9028
12 L L -0.5150
13 S L -0.8778
14 A L 0.0000
15 S L -0.6313
16 V L 0.1168
17 G L -0.7718
18 D L -1.4905
19 R L -2.2098
20 V L 0.0000
21 T L -0.5853
22 I L 0.0000
23 T L -0.8386
24 C L 0.0000
25 R L -2.5044
26 A L 0.0000
27 S L -1.2497
28 Q L -0.5829
29 S L 0.1344
30 V L 1.6695
31 S L 0.0000
32 S L 0.1205
33 A L 0.3373
34 V L 0.0000
35 A L 0.0000
36 W L 0.0000
37 Y L 0.0000
38 Q L 0.0000
39 Q L 0.0000
40 K L -1.6578
41 P L -1.5679
42 G L -1.6464
43 K L -2.5042
44 A L -1.4406
45 P L 0.0000
46 K L -0.9068
47 L L 0.0000
48 L L 0.0000
49 I L 0.0000
50 Y L 0.5064
51 S L 0.0894
52 A L 0.0000
53 S L -0.3357
54 S L 0.2919
55 L L 0.5526
56 Y L 0.4393
57 S L -0.0271
58 G L -0.3969
59 V L -0.1681
60 P L -0.3508
61 S L -0.4237
62 R L -0.8019
63 F L 0.0000
64 S L -0.2634
65 G L -0.3825
66 S L -0.8853
67 R L -1.5188
68 S L -1.2337
69 G L -1.0674
70 T L -1.1662
71 D L -1.7228
72 F L 0.0000
73 T L -0.7939
74 L L 0.0000
75 T L -0.6077
76 I L 0.0000
77 S L -1.3072
78 S L -1.1488
79 L L 0.0000
80 Q L -0.9974
81 P L -1.2217
82 E L -1.9397
83 D L 0.0000
84 F L -0.6855
85 A L 0.0000
86 T L -1.0012
87 Y L 0.0000
88 Y L 0.0000
89 C L 0.0000
90 Q L 0.0000
91 Q L 0.0000
92 Y L 0.9037
93 I L 0.0000
94 Y L 1.7236
95 G L 0.0000
96 L L 0.9477
97 I L 0.0000
98 T L -0.3587
99 F L 0.0000
100 G L 0.0000
101 Q L -1.8154
102 G L 0.0000
103 T L 0.0000
104 K L -1.8595
105 V L 0.0000
106 E L -1.3126
107 I L -0.6787
108 K L -1.5710
109 R L -1.2335
110 T L -0.1174
111 V L 0.4491
112 A L 0.2067
113 A L -0.1130
114 P L 0.0000
115 S L -0.1902
116 V L 0.0000
117 F L -0.0626
118 I L 0.0368
119 F L 0.0000
120 P L -0.2288
121 P L -0.4469
122 S L -0.5392
126 A L -0.8865
127 K L -1.9193
128 S L -1.2771
129 G L -0.8861
130 T L -0.3526
131 A L -0.1255
132 S L 0.1438
133 V L 0.0000
134 V L 0.0000
135 C L 0.0000
136 L L 0.0000
137 L L 0.0000
138 N L -0.4490
139 N L -1.0632
140 F L 0.0000
141 Y L -1.1062
142 P L -1.7227
143 R L -3.1051
144 E L -3.2191
145 A L -2.2333
146 K L -2.2611
147 V L -1.2241
148 Q L -1.2656
149 W L -0.3196
157 A L -0.0246
158 A L 0.0383
159 A L 0.2653
160 S L -0.5513
161 Q L -1.2649
162 E L -1.9632
163 S L -0.8917
164 V L -0.9207
165 T L -1.2697
166 E L -2.3525
167 Q L -1.9501
168 D L -1.9812
169 S L -1.9179
170 K L -2.2824
171 D L -1.7820
172 S L 0.0000
173 T L 0.0000
174 Y L 0.0000
175 S L 0.0000
176 L L 0.0000
177 S L 0.0000
178 S L 0.0000
179 T L -0.3484
180 L L 0.0502
181 T L 0.6523
182 L L 1.4412
187 Y L -0.2728
188 E L -2.4217
189 K L -3.0261
190 H L -2.6819
191 K L -2.4923
192 V L -1.4241
193 Y L -1.2353
194 A L -0.7560
195 C L 0.0000
196 E L -1.0781
197 V L 0.0000
198 T L -1.1731
199 H L 0.0000
200 Q L -1.5260
201 G L -0.3754
202 L L -0.2263
203 S L -0.4653
204 S L -0.4082
205 P L -0.5455
206 V L -0.0645
207 T L -0.8096
208 K L -1.4091
Download PDB file
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Automated mutations analysis

In the automated mutations mode, the server selects aggregation prone resides and each selected residue is mutated to glutamic acid, lysine, aspartic acid and arginine. The table below shows 2 best scored mutants for each mutated residue. Protein variants are ordered according to the mutation effect they had on protein stability (energetic effect) together with the difference in the average per-residue aggregation score between the wild type and the mutant (in the table green values indicate a positive change, grey are neutral, and orange/red mean destabilizing or more aggregation prone mutants).
Summary for all the mutants can be found in this CSV file.

Mutant
Energetic effect
Score comparison
YR34H -1.2736 -0.0276 View CSV PDB
VE30L -0.8606 -0.0202 View CSV PDB
VD30L -0.4789 -0.0199 View CSV PDB
YR55H -0.5013 -0.0036 View CSV PDB
YE34H 0.0536 -0.0291 View CSV PDB
LR182L 0.8041 -0.0239 View CSV PDB
YK94L 0.2434 -0.0069 View CSV PDB
LK182L 1.2586 -0.0219 View CSV PDB
YD94L 0.8231 -0.012 View CSV PDB
YE55H 0.4107 0.001 View CSV PDB
SD56H 0.9433 0.0017 View CSV PDB
SR56H 1.2002 0.0015 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018