Project name: mut3

Status: done

Started: 2025-02-18 03:37:38
Settings
Chain sequence(s) A: STTQIPQIQKTEISFRPNDPKSYEAYVLNIVRFLEKYKDSAQRDDMIFEDCGDSPSEPKERGDFNHERGERKVCRFKLEWLGNCSGLNDETYGYKEGKPCIIIKLNRVSGFKPKPPKNESLETYTSMKYNPNVLPVDCTGKRDEDKDKVGNVEYFGLGNSPGFPLQYYPYYGKDLQPKYLQPLLAVQFTNLTMDTEIRIECKAYGENIGYSEKDRFQGRFDVKIEVKS
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]                                                (00:00:01)
[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]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:04:41)
[INFO]       Auto_mut: Residue number 124 from chain A and a score of 0.669 (tyrosine) selected    
                       for automated muatation                                                     (00:04:42)
[INFO]       Auto_mut: Residue number 108 from chain A and a score of 0.496 (valine) selected for  
                       automated muatation                                                         (00:04:42)
[INFO]       Auto_mut: Residue number 109 from chain A and a score of -0.140 (serine) selected for 
                       automated muatation                                                         (00:04:42)
[INFO]       Auto_mut: Mutating residue number 124 from chain A (tyrosine) into glutamic acid      (00:04:42)
[INFO]       Auto_mut: Mutating residue number 124 from chain A (tyrosine) into aspartic acid      (00:04:42)
[INFO]       Auto_mut: Mutating residue number 124 from chain A (tyrosine) into lysine             (00:04:42)
[INFO]       Auto_mut: Mutating residue number 124 from chain A (tyrosine) into arginine           (00:06:50)
[INFO]       Auto_mut: Mutating residue number 108 from chain A (valine) into glutamic acid        (00:06:51)
[INFO]       Auto_mut: Mutating residue number 108 from chain A (valine) into lysine               (00:07:25)
[INFO]       Auto_mut: Mutating residue number 108 from chain A (valine) into aspartic acid        (00:08:58)
[INFO]       Auto_mut: Mutating residue number 108 from chain A (valine) into arginine             (00:09:22)
[INFO]       Auto_mut: Mutating residue number 109 from chain A (serine) into glutamic acid        (00:09:54)
[INFO]       Auto_mut: Mutating residue number 109 from chain A (serine) into lysine               (00:11:04)
[INFO]       Auto_mut: Mutating residue number 109 from chain A (serine) into aspartic acid        (00:11:37)
[INFO]       Auto_mut: Mutating residue number 109 from chain A (serine) into arginine             (00:12:06)
[INFO]       Auto_mut: Effect of mutation residue number 124 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: -0.0934 kcal/mol, Difference in average score from 
                       the base case: -0.0654                                                      (00:14:17)
[INFO]       Auto_mut: Effect of mutation residue number 124 from chain A (tyrosine) into lysine:  
                       Energy difference: -1.0376 kcal/mol, Difference in average score from the   
                       base case: -0.0417                                                          (00:14:17)
[INFO]       Auto_mut: Effect of mutation residue number 124 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 0.0997 kcal/mol, Difference in average score from  
                       the base case: -0.0736                                                      (00:14:17)
[INFO]       Auto_mut: Effect of mutation residue number 124 from chain A (tyrosine) into          
                       arginine: Energy difference: -0.5258 kcal/mol, Difference in average score  
                       from the base case: -0.0405                                                 (00:14:17)
[INFO]       Auto_mut: Effect of mutation residue number 108 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.1208 kcal/mol, Difference in average score from 
                       the base case: -0.0660                                                      (00:14:17)
[INFO]       Auto_mut: Effect of mutation residue number 108 from chain A (valine) into lysine:    
                       Energy difference: -0.1511 kcal/mol, Difference in average score from the   
                       base case: -0.0625                                                          (00:14:17)
[INFO]       Auto_mut: Effect of mutation residue number 108 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.1823 kcal/mol, Difference in average score from  
                       the base case: -0.0619                                                      (00:14:17)
[INFO]       Auto_mut: Effect of mutation residue number 108 from chain A (valine) into arginine:  
                       Energy difference: -0.9735 kcal/mol, Difference in average score from the   
                       base case: -0.0527                                                          (00:14:17)
[INFO]       Auto_mut: Effect of mutation residue number 109 from chain A (serine) into glutamic   
                       acid: Energy difference: -1.0504 kcal/mol, Difference in average score from 
                       the base case: -0.0398                                                      (00:14:17)
[INFO]       Auto_mut: Effect of mutation residue number 109 from chain A (serine) into lysine:    
                       Energy difference: -1.2794 kcal/mol, Difference in average score from the   
                       base case: -0.0294                                                          (00:14:17)
[INFO]       Auto_mut: Effect of mutation residue number 109 from chain A (serine) into aspartic   
                       acid: Energy difference: -0.3726 kcal/mol, Difference in average score from 
                       the base case: -0.0338                                                      (00:14:17)
[INFO]       Auto_mut: Effect of mutation residue number 109 from chain A (serine) into arginine:  
                       Energy difference: -1.9688 kcal/mol, Difference in average score from the   
                       base case: -0.0194                                                          (00:14:17)
[INFO]       Main:     Simulation completed successfully.                                          (00:14:20)
Show buried residues
Minimal score value
-4.3347
Maximal score value
0.6687
Average score
-1.2871
Total score value
-293.4685
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 S A -0.7424
2 T A 0.0000
3 T A -0.4800
4 Q A 0.0000
5 I A 0.0000
6 P A 0.0000
7 Q A -1.5939
8 I A -1.5352
9 Q A -2.3251
10 K A -2.6555
11 T A 0.0000
12 E A -2.1834
13 I A 0.0000
14 S A -1.1109
15 F A 0.0000
16 R A -2.7144
17 P A -2.8089
18 N A -2.7249
19 D A -2.3906
20 P A -2.4751
21 K A -2.8015
22 S A -1.9559
23 Y A 0.0000
24 E A -2.4051
25 A A -0.9292
26 Y A -0.5270
27 V A 0.0000
28 L A -0.2057
29 N A -0.6484
30 I A 0.0000
31 V A -1.0237
32 R A -2.1958
33 F A -1.4904
34 L A 0.0000
35 E A -3.5992
36 K A -3.5460
37 Y A 0.0000
38 K A -3.5715
39 D A -3.7531
40 S A -2.5133
41 A A -2.6392
42 Q A 0.0000
43 R A -3.1506
44 D A -2.0237
45 D A -2.4965
46 M A -0.5370
47 I A -1.1018
48 F A 0.0000
49 E A -2.3941
50 D A -2.9641
51 C A -1.7087
52 G A -2.0362
53 D A -2.5986
54 S A -1.6014
55 P A -1.4313
56 S A -1.5953
57 E A -2.5211
58 P A -2.1978
59 K A -2.2009
60 E A -2.9688
61 R A -2.1777
62 G A -2.0828
63 D A -2.3983
64 F A -0.5366
65 N A -2.0730
66 H A -3.2495
67 E A -3.6959
68 R A -3.7975
69 G A -3.2918
70 E A -3.4454
71 R A 0.0000
72 K A -1.9117
73 V A 0.0000
74 C A 0.0000
75 R A -2.2493
76 F A 0.0000
77 K A -2.4905
78 L A 0.0000
79 E A -2.3653
80 W A -1.6401
81 L A 0.0000
82 G A -1.3155
83 N A -1.7580
84 C A 0.0000
85 S A 0.0000
86 G A -1.0421
87 L A -0.3348
88 N A -1.6753
89 D A -2.2028
90 E A -2.1893
91 T A -2.0346
92 Y A 0.0000
93 G A 0.0000
94 Y A 0.0000
95 K A -3.5154
96 E A -3.1543
97 G A -2.3673
98 K A -1.8595
99 P A 0.0000
100 C A 0.0000
101 I A 0.0000
102 I A 0.0000
103 I A 0.0000
104 K A -0.6820
105 L A 0.0000
106 N A -1.1601
107 R A -1.4859
108 V A 0.4958
109 S A -0.1404
110 G A -0.5018
111 F A -0.4579
112 K A -1.9038
113 P A 0.0000
114 K A -2.6845
115 P A 0.0000
116 P A 0.0000
117 K A -3.5395
118 N A -3.3641
119 E A -3.2883
120 S A -2.1160
121 L A 0.0000
122 E A -2.4644
123 T A -0.7535
124 Y A 0.6687
125 T A -0.2734
126 S A -0.7694
127 M A -0.9303
128 K A -1.9942
129 Y A -1.7829
130 N A -1.2286
131 P A -1.4715
132 N A -1.3185
133 V A 0.0000
134 L A 0.0000
135 P A 0.0000
136 V A 0.0000
137 D A -0.2686
138 C A 0.0000
139 T A -1.5568
140 G A 0.0000
141 K A -2.7416
142 R A -3.2467
143 D A -4.0015
144 E A -4.0029
145 D A 0.0000
146 K A -4.3347
147 D A -3.8433
148 K A -3.0948
149 V A 0.0000
150 G A -1.9300
151 N A -1.4872
152 V A -0.7819
153 E A -0.8859
154 Y A -0.4806
155 F A -0.6975
156 G A 0.0000
157 L A 0.0000
158 G A -1.5507
159 N A -1.4143
160 S A -1.0522
161 P A -0.7062
162 G A 0.0000
163 F A 0.0000
164 P A 0.0000
165 L A 0.0000
166 Q A 0.0000
167 Y A 0.0000
168 Y A 0.0000
169 P A 0.0000
170 Y A 0.0000
171 Y A 0.0000
172 G A -1.4576
173 K A -3.2716
174 D A -3.3565
175 L A 0.0000
176 Q A 0.0000
177 P A -2.2918
178 K A -2.1742
179 Y A -1.4206
180 L A 0.0000
181 Q A -0.7534
182 P A 0.0000
183 L A 0.0000
184 L A 0.0000
185 A A 0.0000
186 V A 0.0000
187 Q A 0.0000
188 F A 0.0000
189 T A -1.5034
190 N A -1.6937
191 L A 0.0000
192 T A -1.3394
193 M A -1.2660
194 D A -2.3694
195 T A -1.9203
196 E A -2.5482
197 I A 0.0000
198 R A -2.7059
199 I A 0.0000
200 E A -1.4190
201 C A 0.0000
202 K A -0.5555
203 A A 0.0000
204 Y A -0.4157
205 G A -1.8758
206 E A -2.8877
207 N A -2.0294
208 I A -1.0400
209 G A -0.4474
210 Y A -0.2559
211 S A -1.6737
212 E A -2.9168
213 K A -3.0700
214 D A -2.4826
215 R A -2.5739
216 F A -1.2884
217 Q A -1.4308
218 G A 0.0000
219 R A -0.9088
220 F A 0.0000
221 D A -1.5026
222 V A 0.0000
223 K A -2.0280
224 I A 0.0000
225 E A -1.9533
226 V A 0.0000
227 K A -2.0949
228 S A -1.3949
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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
VR108A -0.9735 -0.0527 View CSV PDB
YK124A -1.0376 -0.0417 View CSV PDB
SE109A -1.0504 -0.0398 View CSV PDB
SK109A -1.2794 -0.0294 View CSV PDB
YR124A -0.5258 -0.0405 View CSV PDB
VE108A -0.1208 -0.066 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018