Project name: a5e1072d8be80ef

Status: done

Started: 2025-02-23 19:37:56
Settings
Chain sequence(s) H: EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSAITWNSGHIDYADSVEGRFTISRDNAKNSLYLDMNSLRAEDTAVYYCAKVSYLSTASSLDYWGQGTLVTVSSASTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKI
L: DIQMTQSPSSLSASVGDRVTITCRASQGIRNYLAWYQQKPGKAPKLLIYAASTLQSGVPSRFSGSGSGTDFTLTISSLQPEDVATYYCQRYNRAPYTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE
input PDB
Selected Chain(s) H,L
Distance of aggregation 5 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                                        (00:00:00)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:03:36)
[INFO]       Auto_mut: Residue number 5 from chain H and a score of 1.773 (valine) selected for    
                       automated muatation                                                         (00:03:39)
[INFO]       Auto_mut: Residue number 101 from chain H and a score of 1.541 (tyrosine) selected    
                       for automated muatation                                                     (00:03:39)
[INFO]       Auto_mut: Residue number 102 from chain H and a score of 1.497 (leucine) selected for 
                       automated muatation                                                         (00:03:39)
[INFO]       Auto_mut: Residue number 154 from chain L and a score of 1.484 (leucine) selected for 
                       automated muatation                                                         (00:03:39)
[INFO]       Auto_mut: Residue number 178 from chain H and a score of 1.400 (leucine) selected for 
                       automated muatation                                                         (00:03:39)
[INFO]       Auto_mut: Residue number 110 from chain L and a score of 1.145 (valine) selected for  
                       automated muatation                                                         (00:03:39)
[INFO]       Auto_mut: Mutating residue number 5 from chain H (valine) into glutamic acid          (00:03:39)
[INFO]       Auto_mut: Mutating residue number 5 from chain H (valine) into aspartic acid          (00:03:39)
[INFO]       Auto_mut: Mutating residue number 101 from chain H (tyrosine) into glutamic acid      (00:03:39)
[INFO]       Auto_mut: Mutating residue number 5 from chain H (valine) into arginine               (00:05:21)
[INFO]       Auto_mut: Mutating residue number 5 from chain H (valine) into lysine                 (00:05:23)
[INFO]       Auto_mut: Mutating residue number 101 from chain H (tyrosine) into lysine             (00:05:32)
[INFO]       Auto_mut: Mutating residue number 101 from chain H (tyrosine) into aspartic acid      (00:07:13)
[INFO]       Auto_mut: Mutating residue number 102 from chain H (leucine) into glutamic acid       (00:07:27)
[INFO]       Auto_mut: Mutating residue number 102 from chain H (leucine) into aspartic acid       (00:07:43)
[INFO]       Auto_mut: Mutating residue number 101 from chain H (tyrosine) into arginine           (00:09:01)
[INFO]       Auto_mut: Mutating residue number 102 from chain H (leucine) into lysine              (00:09:17)
[INFO]       Auto_mut: Mutating residue number 102 from chain H (leucine) into arginine            (00:09:27)
[INFO]       Auto_mut: Mutating residue number 154 from chain L (leucine) into glutamic acid       (00:10:52)
[INFO]       Auto_mut: Mutating residue number 154 from chain L (leucine) into aspartic acid       (00:11:20)
[INFO]       Auto_mut: Mutating residue number 178 from chain H (leucine) into glutamic acid       (00:11:21)
[INFO]       Auto_mut: Mutating residue number 154 from chain L (leucine) into lysine              (00:12:49)
[INFO]       Auto_mut: Mutating residue number 178 from chain H (leucine) into lysine              (00:13:03)
[INFO]       Auto_mut: Mutating residue number 154 from chain L (leucine) into arginine            (00:13:09)
[INFO]       Auto_mut: Mutating residue number 178 from chain H (leucine) into aspartic acid       (00:14:47)
[INFO]       Auto_mut: Mutating residue number 110 from chain L (valine) into glutamic acid        (00:15:02)
[INFO]       Auto_mut: Mutating residue number 110 from chain L (valine) into aspartic acid        (00:15:08)
[INFO]       Auto_mut: Mutating residue number 178 from chain H (leucine) into arginine            (00:16:33)
[INFO]       Auto_mut: Mutating residue number 110 from chain L (valine) into lysine               (00:16:40)
[INFO]       Auto_mut: Mutating residue number 110 from chain L (valine) into arginine             (00:16:53)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain H (valine) into glutamic     
                       acid: Energy difference: -0.0334 kcal/mol, Difference in average score from 
                       the base case: -0.0099                                                      (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain H (valine) into lysine:      
                       Energy difference: -0.1877 kcal/mol, Difference in average score from the   
                       base case: -0.0076                                                          (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain H (valine) into aspartic     
                       acid: Energy difference: 0.2161 kcal/mol, Difference in average score from  
                       the base case: -0.0091                                                      (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain H (valine) into arginine:    
                       Energy difference: -1.0110 kcal/mol, Difference in average score from the   
                       base case: -0.0081                                                          (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 101 from chain H (tyrosine) into glutamic 
                       acid: Energy difference: 0.5030 kcal/mol, Difference in average score from  
                       the base case: -0.0094                                                      (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 101 from chain H (tyrosine) into lysine:  
                       Energy difference: 0.0102 kcal/mol, Difference in average score from the    
                       base case: -0.0091                                                          (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 101 from chain H (tyrosine) into aspartic 
                       acid: Energy difference: -0.4267 kcal/mol, Difference in average score from 
                       the base case: -0.0094                                                      (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 101 from chain H (tyrosine) into          
                       arginine: Energy difference: -0.2973 kcal/mol, Difference in average score  
                       from the base case: -0.0095                                                 (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 102 from chain H (leucine) into glutamic  
                       acid: Energy difference: 0.3954 kcal/mol, Difference in average score from  
                       the base case: -0.0111                                                      (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 102 from chain H (leucine) into lysine:   
                       Energy difference: 0.3396 kcal/mol, Difference in average score from the    
                       base case: -0.0056                                                          (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 102 from chain H (leucine) into aspartic  
                       acid: Energy difference: 0.7538 kcal/mol, Difference in average score from  
                       the base case: -0.0123                                                      (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 102 from chain H (leucine) into arginine: 
                       Energy difference: -1.1506 kcal/mol, Difference in average score from the   
                       base case: -0.0084                                                          (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 154 from chain L (leucine) into glutamic  
                       acid: Energy difference: 0.2287 kcal/mol, Difference in average score from  
                       the base case: -0.0118                                                      (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 154 from chain L (leucine) into lysine:   
                       Energy difference: 0.1506 kcal/mol, Difference in average score from the    
                       base case: -0.0108                                                          (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 154 from chain L (leucine) into aspartic  
                       acid: Energy difference: 0.1969 kcal/mol, Difference in average score from  
                       the base case: -0.0119                                                      (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 154 from chain L (leucine) into arginine: 
                       Energy difference: 0.3515 kcal/mol, Difference in average score from the    
                       base case: -0.0121                                                          (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 178 from chain H (leucine) into glutamic  
                       acid: Energy difference: -0.0744 kcal/mol, Difference in average score from 
                       the base case: -0.0112                                                      (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 178 from chain H (leucine) into lysine:   
                       Energy difference: 0.1541 kcal/mol, Difference in average score from the    
                       base case: -0.0101                                                          (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 178 from chain H (leucine) into aspartic  
                       acid: Energy difference: 0.7791 kcal/mol, Difference in average score from  
                       the base case: -0.0114                                                      (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 178 from chain H (leucine) into arginine: 
                       Energy difference: 0.0920 kcal/mol, Difference in average score from the    
                       base case: -0.0110                                                          (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 110 from chain L (valine) into glutamic   
                       acid: Energy difference: 0.5490 kcal/mol, Difference in average score from  
                       the base case: -0.0118                                                      (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 110 from chain L (valine) into lysine:    
                       Energy difference: 0.6324 kcal/mol, Difference in average score from the    
                       base case: -0.0109                                                          (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 110 from chain L (valine) into aspartic   
                       acid: Energy difference: 0.7857 kcal/mol, Difference in average score from  
                       the base case: -0.0117                                                      (00:18:36)
[INFO]       Auto_mut: Effect of mutation residue number 110 from chain L (valine) into arginine:  
                       Energy difference: 0.7427 kcal/mol, Difference in average score from the    
                       base case: -0.0114                                                          (00:18:36)
[INFO]       Main:     Simulation completed successfully.                                          (00:18:42)
Show buried residues
Minimal score value
-2.132
Maximal score value
1.7728
Average score
-0.2849
Total score value
-121.6505
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
1 E H -1.8405
2 V H -0.3707
3 Q H -0.8862
4 L H 0.0000
5 V H 1.7728
6 E H 0.0000
7 S H -0.2632
8 G H -0.3487
9 G H -0.2671
10 G H -0.0740
11 L H 0.2685
12 V H 0.0000
13 Q H -0.7896
14 P H -0.3325
15 G H -0.8523
16 R H -1.9565
17 S H -0.5093
18 L H -0.1566
19 R H -1.8639
20 L H 0.0000
21 S H -0.0076
22 C H 0.0000
23 A H 0.0362
24 A H 0.0000
25 S H -0.2988
26 G H -0.6476
27 F H 0.1971
28 T H -0.0165
29 F H 0.0000
30 D H -1.3954
31 D H -1.9399
32 Y H 0.1182
33 A H 0.0000
34 M H 0.0000
35 H H 0.0000
36 W H 0.0000
37 V H 0.0000
38 R H 0.0000
39 Q H -0.1414
40 A H -0.0634
41 P H -0.3390
42 G H -0.7438
43 K H -1.3586
44 G H -0.3186
45 L H 0.0000
46 E H -0.4232
47 W H 0.0000
48 V H 0.0000
49 S H 0.0000
50 A H 0.0000
51 I H 0.0000
52 T H 0.0950
53 W H 0.4483
54 N H -1.1786
55 S H -0.4735
56 G H -0.6475
57 H H -0.7604
58 I H 0.5566
59 D H -0.1000
60 Y H 0.1319
61 A H 0.0000
62 D H -1.8185
63 S H -0.4424
64 V H -0.1726
65 E H -1.8695
66 G H -0.8354
67 R H -0.3388
68 F H 0.0000
69 T H -0.0458
70 I H 0.0000
71 S H -0.1452
72 R H -0.3027
73 D H -0.5544
74 N H -0.4986
75 A H -0.3203
76 K H -1.7826
77 N H -0.8675
78 S H 0.0000
79 L H 0.0000
80 Y H 0.3365
81 L H 0.0000
82 D H -0.6722
83 M H 0.0000
84 N H -0.5819
85 S H -0.3300
86 L H 0.0000
87 R H -1.3384
88 A H -0.5208
89 E H -1.8091
90 D H 0.0000
91 T H -0.0118
92 A H 0.0000
93 V H 0.4092
94 Y H 0.0000
95 Y H 0.0000
96 C H 0.0000
97 A H 0.0000
98 K H 0.0000
99 V H 0.0000
100 S H 0.0000
101 Y H 1.5411
102 L H 1.4971
103 S H 0.1225
104 T H 0.0000
105 A H 0.0098
106 S H 0.0000
107 S H 0.0000
108 L H 0.0000
109 D H -0.2611
110 Y H 0.4600
111 W H 0.0000
112 G H 0.0000
113 Q H -1.1983
114 G H 0.0000
115 T H 0.0334
116 L H 0.2814
117 V H 0.0000
118 T H 0.0233
119 V H 0.0000
120 S H -0.0824
121 S H -0.2950
122 A H -0.0289
123 S H -0.2122
124 T H -0.2150
125 K H -0.7434
126 G H -0.2810
127 P H -0.0675
128 S H -0.0793
129 V H 0.0000
130 F H 0.1846
131 P H 0.0061
132 L H 0.0000
133 A H 0.0200
134 P H -0.1020
135 S H -0.2640
136 S H -0.2514
142 G H -0.4793
143 T H -0.1537
144 A H 0.0007
145 A H 0.0000
146 L H 0.0000
147 G H 0.0000
148 C H 0.0000
149 L H 0.0000
150 V H 0.0000
151 K H 0.0000
152 D H -0.5717
153 Y H 0.0000
154 F H 0.1910
155 P H 0.0000
156 E H -0.5199
157 P H -0.3110
158 V H 0.0000
159 T H -0.0357
160 V H 0.1599
161 S H -0.0660
162 W H 0.0000
163 N H -0.2461
164 S H -0.3374
165 G H -0.4491
166 A H 0.0281
167 L H 0.2580
168 T H -0.0618
169 S H -0.2546
170 G H -0.1305
171 V H 0.2991
172 H H -0.0443
173 T H -0.0525
174 F H 0.0000
175 P H -0.0990
176 A H 0.0502
177 V H 0.5408
178 L H 1.3999
179 Q H 0.0169
180 S H -0.2877
181 S H -0.3016
182 G H -0.2636
183 L H 0.2344
184 Y H 0.4066
185 S H 0.0161
186 L H 0.0000
187 S H 0.0000
188 S H 0.0000
189 V H 0.0000
190 V H 0.0000
191 T H -0.0156
192 V H 0.0000
193 P H -0.2937
194 S H -0.2982
195 S H -0.2657
196 S H -0.0218
197 L H 0.3312
198 G H -0.3851
199 T H -0.2859
200 Q H -0.6898
201 T H -0.1996
202 Y H 0.0000
203 I H 0.2101
204 C H 0.0000
205 N H -0.4942
206 V H 0.0000
207 N H -0.3717
208 H H 0.0000
209 K H -1.8843
210 P H -0.4054
211 S H -0.2894
212 N H -1.5117
213 T H -0.5746
214 K H -1.6292
215 V H -0.1223
216 D H -1.7786
217 K H -0.9410
218 K H -1.6270
219 I H 0.1265
1 D L -1.7500
2 I L -0.3248
3 Q L -1.1565
4 M L 0.0000
5 T L -0.0272
6 Q L 0.0000
7 S L -0.2420
8 P L -0.2013
9 S L -0.2709
10 S L -0.4018
11 L L 0.1682
12 S L -0.2020
13 A L -0.0357
14 S L -0.0932
15 V L 0.8977
16 G L -0.4180
17 D L -1.5498
18 R L -2.0766
19 V L 0.0000
20 T L -0.0519
21 I L 0.0000
22 T L -0.0340
23 C L 0.0000
24 R L -2.0532
25 A L 0.0000
26 S L -0.3179
27 Q L -0.6925
28 G L -0.5892
29 I L 0.0000
30 R L -1.9601
31 N L -0.7931
32 Y L 0.4410
33 L L 0.0000
34 A L 0.0000
35 W L 0.0000
36 Y L 0.0000
37 Q L 0.0000
38 Q L 0.0000
39 K L -0.4932
40 P L -0.2618
41 G L -0.7973
42 K L -1.7831
43 A L -0.2910
44 P L 0.0000
45 K L -1.1206
46 L L 0.0000
47 L L 0.0000
48 I L 0.0000
49 Y L 0.2012
50 A L 0.0059
51 A L 0.0000
52 S L -0.1893
53 T L 0.0059
54 L L 0.3835
55 Q L -0.1432
56 S L -0.3328
57 G L -0.5058
58 V L 0.0000
59 P L -0.1750
60 S L -0.2979
61 R L -0.3661
62 F L 0.0000
63 S L -0.1157
64 G L 0.0000
65 S L -0.2161
66 G L -0.2478
67 S L -0.2647
68 G L -0.4591
69 T L -0.4066
70 D L -1.9379
71 F L 0.0000
72 T L -0.0219
73 L L 0.0000
74 T L -0.0295
75 I L 0.0000
76 S L -0.3428
77 S L -0.3791
78 L L 0.0000
79 Q L -0.3457
80 P L -0.3141
81 E L -1.1371
82 D L 0.0000
83 V L 0.0000
84 A L 0.0000
85 T L 0.0000
86 Y L 0.0000
87 Y L 0.0000
88 C L 0.0000
89 Q L 0.0000
90 R L 0.0000
91 Y L 0.0000
92 N L -0.9337
93 R L -1.9599
94 A L -0.3505
95 P L -0.0567
96 Y L 0.0000
97 T L -0.0180
98 F L 0.0000
99 G L 0.0000
100 Q L -0.9578
101 G L 0.0000
102 T L 0.0000
103 K L -1.7245
104 V L 0.0000
105 E L -0.3217
106 I L 0.0000
107 K L -1.8011
108 R L -0.8488
109 T L 0.0468
110 V L 1.1448
111 A L 0.2467
112 A L 0.0082
113 P L 0.0000
114 S L -0.1710
115 V L 0.0000
116 F L 0.3053
117 I L 0.0000
118 F L 0.0000
119 P L -0.1141
120 P L -0.0500
121 S L -0.3617
122 D L -1.9659
123 E L -1.6109
124 Q L 0.0000
125 L L -0.2111
126 K L -1.8007
127 S L -0.5605
128 G L -0.3178
129 T L -0.1740
130 A L 0.0000
131 S L 0.0000
132 V L 0.0000
133 V L 0.0000
134 C L 0.0000
135 L L 0.0000
136 L L 0.0000
137 N L 0.0000
138 N L -0.5250
139 F L 0.0000
140 Y L 0.1515
141 P L -0.1913
142 R L -1.4286
143 E L -2.0161
144 A L -0.5965
145 K L -1.4410
146 V L -0.1072
147 Q L -0.2922
148 W L 0.0000
149 K L 0.0131
150 V L 0.0000
151 D L -1.4623
152 N L -1.4896
153 A L 0.0939
154 L L 1.4835
155 Q L 0.0165
156 S L -0.3427
157 G L -0.7415
158 N L -1.3735
159 S L -0.4552
160 Q L -1.1221
161 E L -1.7924
162 S L -0.2377
163 V L 0.4788
164 T L -0.2103
165 E L -1.5499
166 Q L 0.0000
167 D L -0.5601
168 S L -0.7465
169 K L -1.8025
170 D L -0.6681
171 S L 0.0000
172 T L 0.0000
173 Y L 0.0000
174 S L 0.0000
175 L L 0.0000
176 S L 0.0000
177 S L 0.0000
178 T L -0.0119
179 L L 0.0000
180 T L -0.0171
181 L L 0.0000
182 S L -0.2784
183 K L -0.7711
184 A L -0.1846
185 D L -0.5822
186 Y L 0.0000
187 E L -2.1320
188 K L -2.0711
189 H L -0.7903
190 K L -1.4682
191 V L 0.1427
192 Y L 0.0000
193 A L 0.0000
194 C L 0.0000
195 E L -0.4050
196 V L 0.0000
197 T L -0.0472
198 H L 0.0000
199 Q L -1.2333
200 G L -0.3641
201 L L 0.1473
202 S L -0.2110
203 S L -0.2827
204 P L -0.1187
205 V L 0.4582
206 T L -0.1414
207 K L -0.8031
208 S L -0.3164
209 F L 0.0361
210 N L -0.6554
211 R L -0.5576
212 G L -0.8635
213 E L -1.9053
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
LR102H -1.1506 -0.0084 View CSV PDB
VR5H -1.011 -0.0081 View CSV PDB
YD101H -0.4267 -0.0094 View CSV PDB
YR101H -0.2973 -0.0095 View CSV PDB
LE178H -0.0744 -0.0112 View CSV PDB
VE5H -0.0334 -0.0099 View CSV PDB
LR178H 0.092 -0.011 View CSV PDB
LK154L 0.1506 -0.0108 View CSV PDB
LD154L 0.1969 -0.0119 View CSV PDB
LE102H 0.3954 -0.0111 View CSV PDB
VE110L 0.549 -0.0118 View CSV PDB
VK110L 0.6324 -0.0109 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018