Project name: MUT_L426-660 TSA-1

Status: done

Started: 2025-02-10 19:01:08
Settings
Chain sequence(s) A: MARVGFLSNTTSSGDTWIDGYRSMNATVTKAAKVENGFKFTGPGSRATWPVNSRWDIKQYGFVDYNFTIVAMATIHQVPSESTPLLGASLRGNKRTKLIGLSYGAGGKWETVYDGTKTVQGGTWEPGREYQVALMLQDGNKGFVYVDGRLVGNPAMLPTPEERWTEFSHFYFGGDEGDSGSDATLTDVFLYNRPLSRGELKMIKEVED
input PDB
Selected Chain(s) A
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 A 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                                          (00:02:53)
[INFO]       Auto_mut: Residue number 119 from chain A and a score of 0.915 (valine) selected for  
                       automated muatation                                                         (00:02:54)
[INFO]       Auto_mut: Residue number 1 from chain A and a score of 0.847 omitted from automated   
                       muatation (excluded by the user).                                           (00:02:54)
[INFO]       Auto_mut: Residue number 57 from chain A and a score of 0.844 (isoleucine) selected   
                       for automated muatation                                                     (00:02:54)
[INFO]       Auto_mut: Residue number 156 from chain A and a score of 0.354 (methionine) selected  
                       for automated muatation                                                     (00:02:54)
[INFO]       Auto_mut: Residue number 189 from chain A and a score of 0.281 (phenylalanine)        
                       selected for automated muatation                                            (00:02:54)
[INFO]       Auto_mut: Residue number 6 from chain A and a score of 0.244 (phenylalanine) selected 
                       for automated muatation                                                     (00:02:54)
[INFO]       Auto_mut: Residue number 62 from chain A and a score of 0.163 (phenylalanine)         
                       selected for automated muatation                                            (00:02:54)
[INFO]       Auto_mut: Mutating residue number 119 from chain A (valine) into glutamic acid        (00:02:54)
[INFO]       Auto_mut: Mutating residue number 57 from chain A (isoleucine) into glutamic acid     (00:02:54)
[INFO]       Auto_mut: Mutating residue number 119 from chain A (valine) into aspartic acid        (00:02:54)
[INFO]       Auto_mut: Mutating residue number 119 from chain A (valine) into lysine               (00:04:13)
[INFO]       Auto_mut: Mutating residue number 119 from chain A (valine) into arginine             (00:04:17)
[INFO]       Auto_mut: Mutating residue number 57 from chain A (isoleucine) into lysine            (00:04:19)
[INFO]       Auto_mut: Mutating residue number 57 from chain A (isoleucine) into aspartic acid     (00:05:46)
[INFO]       Auto_mut: Mutating residue number 156 from chain A (methionine) into glutamic acid    (00:05:53)
[INFO]       Auto_mut: Mutating residue number 156 from chain A (methionine) into aspartic acid    (00:05:53)
[INFO]       Auto_mut: Mutating residue number 57 from chain A (isoleucine) into arginine          (00:06:59)
[INFO]       Auto_mut: Mutating residue number 156 from chain A (methionine) into arginine         (00:07:11)
[INFO]       Auto_mut: Mutating residue number 156 from chain A (methionine) into lysine           (00:07:22)
[INFO]       Auto_mut: Mutating residue number 189 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 189 from chain A (phenylalanine) into glutamic acid (00:08:26)
[INFO]       Auto_mut: Mutating residue number 189 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 189 from chain A (phenylalanine) into aspartic acid (00:08:47)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (phenylalanine) into glutamic acid   (00:08:58)
[INFO]       Auto_mut: Mutating residue number 189 from chain A (phenylalanine) into lysine        (00:09:50)
[INFO]       Auto_mut: Mutating residue number 189 from chain A (phenylalanine) into arginine      (00:10:07)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (phenylalanine) into lysine          (00:10:10)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (phenylalanine) into aspartic acid   (00:11:28)
[INFO]       Auto_mut: Mutating residue number 62 from chain A (phenylalanine) into glutamic acid  
                       Mutating residue number 62 from chain A (phenylalanine) into glutamic acid  (00:11:37)
[INFO]       Auto_mut: Mutating residue number 62 from chain A (phenylalanine) into aspartic acid  
                       Mutating residue number 62 from chain A (phenylalanine) into aspartic acid  (00:11:39)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (phenylalanine) into arginine        (00:12:43)
[INFO]       Auto_mut: Mutating residue number 62 from chain A (phenylalanine) into lysine         (00:12:57)
[INFO]       Auto_mut: Mutating residue number 62 from chain A (phenylalanine) into arginine       (00:12:57)
[INFO]       Auto_mut: Effect of mutation residue number 119 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.3532 kcal/mol, Difference in average score from  
                       the base case: -0.0104                                                      (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 119 from chain A (valine) into lysine:    
                       Energy difference: -0.7263 kcal/mol, Difference in average score from the   
                       base case: -0.0327                                                          (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 119 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.3042 kcal/mol, Difference in average score from 
                       the base case: -0.0348                                                      (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 119 from chain A (valine) into arginine:  
                       Energy difference: -1.2598 kcal/mol, Difference in average score from the   
                       base case: -0.0335                                                          (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 57 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: -0.4376 kcal/mol, Difference in average   
                       score from the base case: -0.0028                                           (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 57 from chain A (isoleucine) into lysine: 
                       Energy difference: -0.4416 kcal/mol, Difference in average score from the   
                       base case: 0.0026                                                           (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 57 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: -1.3249 kcal/mol, Difference in average   
                       score from the base case: -0.0059                                           (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 57 from chain A (isoleucine) into         
                       arginine: Energy difference: -0.4665 kcal/mol, Difference in average score  
                       from the base case: 0.0002                                                  (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 156 from chain A (methionine) into        
                       glutamic acid: Energy difference: 0.3061 kcal/mol, Difference in average    
                       score from the base case: -0.0247                                           (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 156 from chain A (methionine) into        
                       lysine: Energy difference: -0.0539 kcal/mol, Difference in average score    
                       from the base case: -0.0229                                                 (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 156 from chain A (methionine) into        
                       aspartic acid: Energy difference: 0.1951 kcal/mol, Difference in average    
                       score from the base case: -0.0267                                           (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 156 from chain A (methionine) into        
                       arginine: Energy difference: -0.2372 kcal/mol, Difference in average score  
                       from the base case: -0.0282                                                 (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 189 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 3.9230 kcal/mol, Difference in average    
                       score from the base case: 0.0341                                            (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 189 from chain A (phenylalanine) into     
                       lysine: Energy difference: 2.1675 kcal/mol, Difference in average score     
                       from the base case: 0.0445                                                  (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 189 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 3.6861 kcal/mol, Difference in average    
                       score from the base case: 0.0200                                            (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 189 from chain A (phenylalanine) into     
                       arginine: Energy difference: 1.5835 kcal/mol, Difference in average score   
                       from the base case: 0.0458                                                  (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (phenylalanine) into       
                       glutamic acid: Energy difference: 0.6042 kcal/mol, Difference in average    
                       score from the base case: 0.0325                                            (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (phenylalanine) into       
                       lysine: Energy difference: -0.8071 kcal/mol, Difference in average score    
                       from the base case: 0.0262                                                  (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (phenylalanine) into       
                       aspartic acid: Energy difference: 2.6387 kcal/mol, Difference in average    
                       score from the base case: 0.0322                                            (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (phenylalanine) into       
                       arginine: Energy difference: -0.1235 kcal/mol, Difference in average score  
                       from the base case: 0.0270                                                  (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 62 from chain A (phenylalanine) into      
                       glutamic acid: Energy difference: 1.8628 kcal/mol, Difference in average    
                       score from the base case: 0.0257                                            (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 62 from chain A (phenylalanine) into      
                       lysine: Energy difference: 2.0057 kcal/mol, Difference in average score     
                       from the base case: -0.0072                                                 (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 62 from chain A (phenylalanine) into      
                       aspartic acid: Energy difference: 2.6723 kcal/mol, Difference in average    
                       score from the base case: 0.0185                                            (00:14:53)
[INFO]       Auto_mut: Effect of mutation residue number 62 from chain A (phenylalanine) into      
                       arginine: Energy difference: 1.9105 kcal/mol, Difference in average score   
                       from the base case: 0.0312                                                  (00:14:53)
[INFO]       Main:     Simulation completed successfully.                                          (00:14:58)
Show buried residues
Aggrescan3D profile | MUT_L426-660 TSA-1 | Chain AM1N25D56N93T123P158D187-4-2024ResidueScore
Minimal score value
-3.9033
Maximal score value
0.9149
Average score
-0.8521
Total score value
-177.2266
Download the table (csv)

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

Show chain Show residues from to
residue index residue name chain Aggrescan3D score mutation
residue index
residue name
chain
Aggrescan3D score
mutation
1 M A 0.8471
2 A A 0.1379
3 R A -0.0105
4 V A 0.0063
5 G A 0.0000
6 F A 0.2437
7 L A 0.0000
8 S A -1.0046
9 N A -1.9572
10 T A -1.7023
11 T A -1.0400
12 S A -0.9883
13 S A -1.1247
14 G A -1.7726
15 D A -2.4552
16 T A -1.3798
17 W A 0.0000
18 I A -0.6180
19 D A 0.0000
20 G A -0.4360
21 Y A 0.1085
22 R A -1.4447
23 S A -0.8922
24 M A -0.6699
25 N A -0.8859
26 A A 0.0000
27 T A -0.6808
28 V A 0.0000
29 T A -1.4609
30 K A -2.4239
31 A A -1.9329
32 A A -1.6362
33 K A -2.8957
34 V A -1.9706
35 E A -2.7594
36 N A -2.2524
37 G A 0.0000
38 F A 0.0000
39 K A -1.7975
40 F A 0.0000
41 T A -1.1883
42 G A 0.0000
43 P A -1.5164
44 G A -1.9573
45 S A 0.0000
46 R A -1.6006
47 A A 0.0000
48 T A -0.5144
49 W A 0.0000
50 P A -0.2189
51 V A 0.0000
52 N A 0.0000
53 S A -1.0182
54 R A -1.5151
55 W A 0.0388
56 D A -0.3307
57 I A 0.8436
58 K A -0.7048
59 Q A -0.6654
60 Y A 0.0000
61 G A -0.1636
62 F A 0.1628
63 V A 0.0000
64 D A 0.0000
65 Y A -0.0751
66 N A -0.8670
67 F A 0.0000
68 T A 0.0000
69 I A 0.0000
70 V A 0.0000
71 A A 0.0000
72 M A -0.5818
73 A A 0.0000
74 T A -1.7494
75 I A 0.0000
76 H A -1.6943
77 Q A -1.1695
78 V A 0.1581
79 P A -0.4868
80 S A -0.9260
81 E A -1.7863
82 S A -0.9594
83 T A 0.0000
84 P A -0.4541
85 L A 0.0000
86 L A 0.0000
87 G A 0.0000
88 A A 0.0000
89 S A 0.0000
90 L A 0.0000
91 R A -2.5346
92 G A -2.5803
93 N A -3.0106
94 K A -3.6100
95 R A -3.9033
96 T A -2.7711
97 K A -2.2759
98 L A 0.0000
99 I A 0.0000
100 G A 0.0000
101 L A 0.0000
102 S A 0.0000
103 Y A 0.0000
104 G A 0.0000
105 A A -0.5962
106 G A -0.6238
107 G A -0.9322
108 K A -1.3518
109 W A 0.0000
110 E A 0.0000
111 T A 0.0000
112 V A -0.6952
113 Y A -0.9551
114 D A -1.9153
115 G A -1.9587
116 T A -1.3339
117 K A -1.1864
118 T A 0.1303
119 V A 0.9149
120 Q A -0.2917
121 G A -0.8414
122 G A -1.0861
123 T A -1.3220
124 W A 0.0000
125 E A -2.6047
126 P A -1.9827
127 G A -2.1359
128 R A -2.5312
129 E A -2.6016
130 Y A 0.0000
131 Q A 0.0000
132 V A 0.0000
133 A A 0.0000
134 L A 0.0000
135 M A 0.0000
136 L A 0.0000
137 Q A -1.4369
138 D A -2.0781
139 G A 0.0000
140 N A -0.9828
141 K A -0.9510
142 G A 0.0000
143 F A -0.1400
144 V A 0.0000
145 Y A 0.0000
146 V A 0.0000
147 D A -1.5788
148 G A -2.2485
149 R A -2.4405
150 L A -1.2503
151 V A 0.0000
152 G A -0.9774
153 N A -1.2719
154 P A -0.5291
155 A A -0.2254
156 M A 0.3542
157 L A 0.0000
158 P A -1.0982
159 T A -1.3633
160 P A -1.5249
161 E A -2.5218
162 E A -2.4973
163 R A -1.5417
164 W A -0.4221
165 T A -1.0382
166 E A -1.1430
167 F A 0.0000
168 S A -1.1887
169 H A -0.6650
170 F A 0.0000
171 Y A 0.0000
172 F A 0.0000
173 G A 0.0000
174 G A 0.0000
175 D A -1.9708
176 E A -2.9471
177 G A -2.4481
178 D A -2.6802
179 S A -2.0454
180 G A -1.6055
181 S A 0.0000
182 D A -1.1437
183 A A 0.0000
184 T A -0.9551
185 L A 0.0000
186 T A -0.7432
187 D A -0.9562
188 V A 0.0000
189 F A 0.2808
190 L A 0.0000
191 Y A 0.0000
192 N A -0.7962
193 R A -1.1320
194 P A -1.1099
195 L A 0.0000
196 S A -1.6110
197 R A -2.9784
198 G A -2.0456
199 E A -1.5612
200 L A 0.0000
201 K A -2.8609
202 M A -1.3848
203 I A 0.0000
204 K A -2.0287
205 E A -2.3211
206 V A -0.4796
207 E A -1.9934
208 D A -2.5733
residue index residue name chain Aggrescan3D score
mutation
Download PDB file
View in 3Dmol
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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
VR119A -1.2598 -0.0335 View CSV PDB
VK119A -0.7263 -0.0327 View CSV PDB
MR156A -0.2372 -0.0282 View CSV PDB
MK156A -0.0539 -0.0229 View CSV PDB
ID57A -1.3249 -0.0059 View CSV PDB
IE57A -0.4376 -0.0028 View CSV PDB
FK62A 2.0057 -0.0072 View CSV PDB
FK6A -0.8071 0.0262 View CSV PDB
FR6A -0.1235 0.027 View CSV PDB
FD62A 2.6723 0.0185 View CSV PDB
FD189A 3.6861 0.02 View CSV PDB
FR189A 1.5835 0.0458 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018