Chain sequence(s) |
A: SKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFTTTVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGI
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 (00:02:43) [INFO] Auto_mut: Residue number 11 from chain A and a score of 1.240 (valine) selected for automated muatation (00:02:44) [INFO] Auto_mut: Residue number 229 from chain A and a score of 1.194 (isoleucine) selected for automated muatation (00:02:44) [INFO] Auto_mut: Residue number 39 from chain A and a score of 0.940 (tyrosine) selected for automated muatation (00:02:44) [INFO] Auto_mut: Residue number 10 from chain A and a score of 0.451 (glycine) selected for automated muatation (00:02:44) [INFO] Auto_mut: Residue number 176 from chain A and a score of 0.409 (valine) selected for automated muatation (00:02:44) [INFO] Auto_mut: Residue number 99 from chain A and a score of 0.371 (phenylalanine) selected for automated muatation (00:02:44) [INFO] Auto_mut: Mutating residue number 11 from chain A (valine) into glutamic acid (00:02:44) [INFO] Auto_mut: Mutating residue number 11 from chain A (valine) into aspartic acid (00:02:44) [INFO] Auto_mut: Mutating residue number 229 from chain A (isoleucine) into glutamic acid (00:02:44) [INFO] Auto_mut: Mutating residue number 11 from chain A (valine) into arginine (00:04:07) [INFO] Auto_mut: Mutating residue number 229 from chain A (isoleucine) into lysine (00:04:07) [INFO] Auto_mut: Mutating residue number 11 from chain A (valine) into lysine (00:04:10) [INFO] Auto_mut: Mutating residue number 229 from chain A (isoleucine) into aspartic acid (00:05:28) [INFO] Auto_mut: Mutating residue number 39 from chain A (tyrosine) into glutamic acid (00:05:28) [INFO] Auto_mut: Mutating residue number 39 from chain A (tyrosine) into aspartic acid (00:05:33) [INFO] Auto_mut: Mutating residue number 229 from chain A (isoleucine) into arginine (00:06:50) [INFO] Auto_mut: Mutating residue number 39 from chain A (tyrosine) into arginine (00:06:52) [INFO] Auto_mut: Mutating residue number 39 from chain A (tyrosine) into lysine (00:06:54) [INFO] Auto_mut: Mutating residue number 10 from chain A (glycine) into glutamic acid (00:08:15) [INFO] Auto_mut: Mutating residue number 10 from chain A (glycine) into aspartic acid (00:08:16) [INFO] Auto_mut: Mutating residue number 176 from chain A (valine) into glutamic acid (00:08:25) [INFO] Auto_mut: Mutating residue number 10 from chain A (glycine) into arginine (00:09:39) [INFO] Auto_mut: Mutating residue number 10 from chain A (glycine) into lysine (00:09:39) [INFO] Auto_mut: Mutating residue number 176 from chain A (valine) into lysine (00:09:49) [INFO] Auto_mut: Mutating residue number 176 from chain A (valine) into aspartic acid (00:11:07) [INFO] Auto_mut: Mutating residue number 99 from chain A (phenylalanine) into glutamic acid Mutating residue number 99 from chain A (phenylalanine) into glutamic acid (00:11:07) [INFO] Auto_mut: Mutating residue number 99 from chain A (phenylalanine) into aspartic acid Mutating residue number 99 from chain A (phenylalanine) into aspartic acid (00:11:18) [INFO] Auto_mut: Mutating residue number 176 from chain A (valine) into arginine (00:12:30) [INFO] Auto_mut: Mutating residue number 99 from chain A (phenylalanine) into lysine (00:12:36) [INFO] Auto_mut: Mutating residue number 99 from chain A (phenylalanine) into arginine (00:12:48) [INFO] Auto_mut: Effect of mutation residue number 11 from chain A (valine) into glutamic acid: Energy difference: 0.8226 kcal/mol, Difference in average score from the base case: -0.0456 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 11 from chain A (valine) into lysine: Energy difference: -0.5527 kcal/mol, Difference in average score from the base case: -0.0314 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 11 from chain A (valine) into aspartic acid: Energy difference: 0.9895 kcal/mol, Difference in average score from the base case: -0.0457 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 11 from chain A (valine) into arginine: Energy difference: -0.4208 kcal/mol, Difference in average score from the base case: -0.0351 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 229 from chain A (isoleucine) into glutamic acid: Energy difference: 1.4456 kcal/mol, Difference in average score from the base case: -0.0312 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 229 from chain A (isoleucine) into lysine: Energy difference: -0.3903 kcal/mol, Difference in average score from the base case: -0.0266 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 229 from chain A (isoleucine) into aspartic acid: Energy difference: 2.2401 kcal/mol, Difference in average score from the base case: -0.0313 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 229 from chain A (isoleucine) into arginine: Energy difference: 0.6123 kcal/mol, Difference in average score from the base case: -0.0282 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 39 from chain A (tyrosine) into glutamic acid: Energy difference: 0.2602 kcal/mol, Difference in average score from the base case: -0.0250 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 39 from chain A (tyrosine) into lysine: Energy difference: -0.7179 kcal/mol, Difference in average score from the base case: -0.0227 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 39 from chain A (tyrosine) into aspartic acid: Energy difference: 0.1447 kcal/mol, Difference in average score from the base case: -0.0244 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 39 from chain A (tyrosine) into arginine: Energy difference: -0.4954 kcal/mol, Difference in average score from the base case: -0.0254 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 10 from chain A (glycine) into glutamic acid: Energy difference: 1.8000 kcal/mol, Difference in average score from the base case: -0.0218 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 10 from chain A (glycine) into lysine: Energy difference: 0.2667 kcal/mol, Difference in average score from the base case: -0.0172 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 10 from chain A (glycine) into aspartic acid: Energy difference: -0.2034 kcal/mol, Difference in average score from the base case: -0.0206 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 10 from chain A (glycine) into arginine: Energy difference: 0.0640 kcal/mol, Difference in average score from the base case: -0.0191 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 176 from chain A (valine) into glutamic acid: Energy difference: 0.6690 kcal/mol, Difference in average score from the base case: -0.0409 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 176 from chain A (valine) into lysine: Energy difference: -0.0001 kcal/mol, Difference in average score from the base case: -0.0395 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 176 from chain A (valine) into aspartic acid: Energy difference: 1.3387 kcal/mol, Difference in average score from the base case: -0.0451 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 176 from chain A (valine) into arginine: Energy difference: 0.0948 kcal/mol, Difference in average score from the base case: -0.0427 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 99 from chain A (phenylalanine) into glutamic acid: Energy difference: 1.6068 kcal/mol, Difference in average score from the base case: -0.0313 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 99 from chain A (phenylalanine) into lysine: Energy difference: 0.8000 kcal/mol, Difference in average score from the base case: -0.0277 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 99 from chain A (phenylalanine) into aspartic acid: Energy difference: 2.1780 kcal/mol, Difference in average score from the base case: -0.0321 (00:14:29) [INFO] Auto_mut: Effect of mutation residue number 99 from chain A (phenylalanine) into arginine: Energy difference: 1.4532 kcal/mol, Difference in average score from the base case: -0.0252 (00:14:29) [INFO] Main: Simulation completed successfully. (00:14:35) |
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 | |
2 | S | A | -1.7480 | |
3 | K | A | -1.9266 | |
4 | G | A | 0.0000 | |
5 | E | A | -2.6551 | |
6 | E | A | -2.5822 | |
7 | L | A | -1.1964 | |
8 | F | A | 0.0000 | |
9 | T | A | -0.6278 | |
10 | G | A | 0.4512 | |
11 | V | A | 1.2396 | |
12 | V | A | 0.0000 | |
13 | P | A | -0.9752 | |
14 | I | A | 0.0000 | |
15 | L | A | -0.9862 | |
16 | V | A | 0.0000 | |
17 | E | A | -1.9305 | |
18 | L | A | 0.0000 | |
19 | D | A | -3.3361 | |
20 | G | A | 0.0000 | |
21 | D | A | -2.4363 | |
22 | V | A | 0.0000 | |
23 | N | A | -2.0751 | |
24 | G | A | -1.6314 | |
25 | H | A | -2.1611 | |
26 | K | A | -2.8459 | |
27 | F | A | 0.0000 | |
28 | S | A | -1.6658 | |
29 | V | A | 0.0000 | |
30 | S | A | -0.9663 | |
31 | G | A | 0.0000 | |
32 | E | A | -2.1402 | |
33 | G | A | -1.4854 | |
34 | E | A | -1.5504 | |
35 | G | A | 0.0000 | |
36 | D | A | 0.0545 | |
37 | A | A | 0.0000 | |
38 | T | A | 0.2714 | |
39 | Y | A | 0.9402 | |
40 | G | A | 0.0000 | |
41 | K | A | -0.3884 | |
42 | L | A | 0.0000 | |
43 | T | A | -0.7581 | |
44 | L | A | 0.0000 | |
45 | K | A | -0.9364 | |
46 | F | A | 0.0000 | |
47 | I | A | -1.0400 | |
48 | C | A | 0.0000 | |
49 | T | A | -0.7814 | |
50 | T | A | -1.2946 | |
51 | G | A | -1.6006 | |
52 | K | A | -2.2497 | |
53 | L | A | 0.0000 | |
54 | P | A | -1.1990 | |
55 | V | A | 0.0000 | |
56 | P | A | 0.0000 | |
57 | W | A | 0.0000 | |
58 | P | A | 0.0000 | |
59 | T | A | 0.0000 | |
60 | L | A | 0.0000 | |
61 | V | A | 0.0000 | |
62 | T | A | -0.0037 | |
63 | T | A | 0.0000 | |
64 | F | A | 0.0000 | |
68 | V | A | -0.0527 | |
69 | Q | A | -0.2169 | |
70 | C | A | 0.0000 | |
71 | F | A | 0.0000 | |
72 | S | A | 0.0000 | |
73 | R | A | -1.1774 | |
74 | Y | A | 0.0000 | |
75 | P | A | -1.8004 | |
76 | D | A | -3.0657 | |
77 | H | A | -2.2846 | |
78 | M | A | 0.0000 | |
79 | K | A | -3.3140 | |
80 | R | A | -3.0544 | |
81 | H | A | -1.7645 | |
82 | D | A | 0.0000 | |
83 | F | A | 0.0000 | |
84 | F | A | 0.0000 | |
85 | K | A | -1.1575 | |
86 | S | A | 0.0000 | |
87 | A | A | 0.0000 | |
88 | M | A | 0.0000 | |
89 | P | A | -1.8367 | |
90 | E | A | -2.5061 | |
91 | G | A | 0.0000 | |
92 | Y | A | 0.0000 | |
93 | V | A | -0.9173 | |
94 | Q | A | 0.0000 | |
95 | E | A | -2.5636 | |
96 | R | A | 0.0000 | |
97 | T | A | -0.5103 | |
98 | I | A | 0.0000 | |
99 | F | A | 0.3706 | |
100 | F | A | 0.0000 | |
101 | K | A | -1.5851 | |
102 | D | A | -2.5554 | |
103 | D | A | -2.4961 | |
104 | G | A | 0.0000 | |
105 | N | A | -0.7386 | |
106 | Y | A | 0.0000 | |
107 | K | A | -1.8764 | |
108 | T | A | 0.0000 | |
109 | R | A | -3.1202 | |
110 | A | A | 0.0000 | |
111 | E | A | -2.2195 | |
112 | V | A | 0.0000 | |
113 | K | A | -1.9659 | |
114 | F | A | -2.0041 | |
115 | E | A | -2.7630 | |
116 | G | A | -2.2840 | |
117 | D | A | -2.5449 | |
118 | T | A | -1.7283 | |
119 | L | A | 0.0000 | |
120 | V | A | 0.0000 | |
121 | N | A | 0.0000 | |
122 | R | A | -2.8747 | |
123 | I | A | 0.0000 | |
124 | E | A | -3.9529 | |
125 | L | A | 0.0000 | |
126 | K | A | -2.7094 | |
127 | G | A | 0.0000 | |
128 | I | A | -1.1789 | |
129 | D | A | -2.3003 | |
130 | F | A | 0.0000 | |
131 | K | A | -3.9622 | |
132 | E | A | -3.9904 | |
133 | D | A | -3.6067 | |
134 | G | A | -2.8039 | |
135 | N | A | -2.1472 | |
136 | I | A | 0.0000 | |
137 | L | A | -1.9260 | |
138 | G | A | -2.2856 | |
139 | H | A | -2.2238 | |
140 | K | A | -2.5262 | |
141 | L | A | 0.0000 | |
142 | E | A | -1.8498 | |
143 | Y | A | -0.6819 | |
144 | N | A | -0.6203 | |
145 | Y | A | -0.7041 | |
146 | N | A | -0.9709 | |
147 | S | A | -1.0619 | |
148 | H | A | 0.0000 | |
149 | N | A | -1.0828 | |
150 | V | A | 0.0000 | |
151 | Y | A | 0.0634 | |
152 | I | A | 0.0000 | |
153 | M | A | -0.9507 | |
154 | A | A | -1.7151 | |
155 | D | A | 0.0000 | |
156 | K | A | -3.1149 | |
157 | Q | A | -3.1357 | |
158 | K | A | -3.4573 | |
159 | N | A | -2.6641 | |
160 | G | A | 0.0000 | |
161 | I | A | 0.0000 | |
162 | K | A | -1.5315 | |
163 | V | A | 0.0000 | |
164 | N | A | -0.3613 | |
165 | F | A | 0.0000 | |
166 | K | A | -1.1632 | |
167 | I | A | 0.0000 | |
168 | R | A | -0.8515 | |
169 | H | A | 0.0000 | |
170 | N | A | -1.1601 | |
171 | I | A | 0.0000 | |
172 | E | A | -3.2753 | |
173 | D | A | -2.9818 | |
174 | G | A | -1.8027 | |
175 | S | A | -0.7058 | |
176 | V | A | 0.4094 | |
177 | Q | A | 0.0000 | |
178 | L | A | -0.4014 | |
179 | A | A | 0.0000 | |
180 | D | A | 0.0000 | |
181 | H | A | 0.0000 | |
182 | Y | A | 0.1868 | |
183 | Q | A | 0.0000 | |
184 | Q | A | -1.7438 | |
185 | N | A | 0.0000 | |
186 | T | A | -0.9755 | |
187 | P | A | -0.8470 | |
188 | I | A | -0.4057 | |
189 | G | A | -1.3325 | |
190 | D | A | -2.0301 | |
191 | G | A | -1.3720 | |
192 | P | A | -0.8415 | |
193 | V | A | -0.5890 | |
194 | L | A | -0.6668 | |
195 | L | A | -0.7930 | |
196 | P | A | 0.0000 | |
197 | D | A | -2.2076 | |
198 | N | A | -1.6201 | |
199 | H | A | 0.0000 | |
200 | Y | A | 0.1242 | |
201 | L | A | 0.0000 | |
202 | S | A | -0.6276 | |
203 | T | A | -0.8347 | |
204 | Q | A | -1.3131 | |
205 | S | A | -0.5628 | |
206 | A | A | -0.0198 | |
207 | L | A | -0.0167 | |
208 | S | A | -0.6496 | |
209 | K | A | -1.7214 | |
210 | D | A | -2.1751 | |
211 | P | A | -1.8352 | |
212 | N | A | -2.4809 | |
213 | E | A | -2.7245 | |
214 | K | A | -3.1977 | |
215 | R | A | -3.4038 | |
216 | D | A | -2.3139 | |
217 | H | A | 0.0000 | |
218 | M | A | 0.0000 | |
219 | V | A | -0.1304 | |
220 | L | A | 0.0000 | |
221 | L | A | 0.2860 | |
222 | E | A | -0.2495 | |
223 | F | A | -0.0424 | |
224 | V | A | 0.0000 | |
225 | T | A | -0.4465 | |
226 | A | A | 0.0000 | |
227 | A | A | 0.0830 | |
228 | G | A | 0.3013 | |
229 | I | A | 1.1944 |
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 |
|||
VK11A | -0.5527 | -0.0314 | View | CSV | PDB |
VR11A | -0.4208 | -0.0351 | View | CSV | PDB |
YK39A | -0.7179 | -0.0227 | View | CSV | PDB |
YR39A | -0.4954 | -0.0254 | View | CSV | PDB |
IK229A | -0.3903 | -0.0266 | View | CSV | PDB |
VK176A | -0.0001 | -0.0395 | View | CSV | PDB |
GD10A | -0.2034 | -0.0206 | View | CSV | PDB |
VR176A | 0.0948 | -0.0427 | View | CSV | PDB |
GR10A | 0.064 | -0.0191 | View | CSV | PDB |
IR229A | 0.6123 | -0.0282 | View | CSV | PDB |
FK99A | 0.8 | -0.0277 | View | CSV | PDB |
FE99A | 1.6068 | -0.0313 | View | CSV | PDB |