Project name: alpha

Status: done

submitted: 2017-03-16 10:46:18, status changed: 2017-03-16 12:49:36
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Chain sequence(s) A: MDVFMKGLSKAKEGVVAAAEKTKQGVAEAAGKTKEGVLYVGSKTKEGVVHGVATVAEKTKEQVTNVGGAVVTGVTAVAQKTVEGAGSIAAATGFVKKDQLGKNEEGAPQEGILEDMPVDPDNEAYEMPSEEGYQDYEPEA
Distance of aggregation 10 Å
Dynamic mode Yes
Show buried residues

Minimal score value
-3.921
Maximal score value
3.0759
Average score
-0.6574
Total score value
-92.0406

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 M A 1.4792
2 D A 0.1958
3 V A 2.0950
4 F A 2.6963
5 M A 1.5302
6 K A -0.6321
7 G A -0.1062
8 L A 0.4992
9 S A -1.3010
10 K A -2.4039
11 A A -1.3562
12 K A -2.1506
13 E A -2.1926
14 G A -0.9402
15 V A 0.5487
16 V A 0.3694
17 A A -0.6636
18 A A -0.7369
19 A A -1.0084
20 E A -2.3236
21 K A -2.9116
22 T A -2.1924
23 K A -2.9984
24 Q A -3.0395
25 G A -2.0997
26 V A -0.4659
27 A A -1.4308
28 E A -2.9175
29 A A -1.7004
30 A A -1.5828
31 G A -2.3410
32 K A -2.8535
33 T A -1.7331
34 K A -2.0947
35 E A -1.2905
36 G A 0.2743
37 V A 1.8568
38 L A 2.1488
39 Y A 1.7266
40 V A 2.5149
41 G A 0.7787
42 S A -0.5160
43 K A -2.3611
44 T A -1.7342
45 K A -2.2459
46 E A -2.2973
47 G A -0.1188
48 V A 1.2605
49 V A 1.7383
50 H A 0.9378
51 G A 1.5172
52 V A 2.8518
53 A A 1.3904
54 T A 0.5149
55 V A 1.2816
56 A A -0.4767
57 E A -2.0667
58 K A -2.1423
59 T A -1.9366
60 K A -2.8011
61 E A -2.9555
62 Q A -2.1976
63 V A -0.0236
64 T A -0.7575
65 N A -0.6058
66 V A 1.5908
67 G A 1.2317
68 G A 1.2156
69 A A 1.8615
70 V A 3.0733
71 V A 3.0641
72 T A 2.1079
73 G A 1.9372
74 V A 3.0759
75 T A 1.6715
76 A A 0.9997
77 V A 1.7748
78 A A 0.9419
79 Q A -0.2454
80 K A -0.4878
81 T A 0.1864
82 V A 0.6435
83 E A -0.9268
84 G A -0.4950
85 A A -0.1683
86 G A -0.6828
87 S A -0.3744
88 I A 0.5051
89 A A 0.2918
90 A A 0.6337
91 A A 0.7617
92 T A 0.7445
93 G A 0.7825
94 F A 2.1066
95 V A 0.9103
96 K A -1.7266
97 K A -2.8810
98 D A -3.3766
99 Q A -2.5417
100 L A -1.2299
101 G A -2.2280
102 K A -3.1318
103 N A -3.4561
104 E A -3.6011
105 E A -3.9210
106 G A -3.0639
107 A A -2.4844
108 P A -2.3602
109 Q A -2.6843
110 E A -2.7302
111 G A -1.2731
112 I A 1.1887
113 L A 1.3784
114 E A -1.0002
115 D A -1.2316
116 M A 0.9392
117 P A 1.1597
118 V A 1.4113
119 D A -0.5326
120 P A -1.5826
121 D A -2.6987
122 N A -2.3406
123 E A -2.9631
124 A A -1.8600
125 Y A -2.0052
126 E A -3.0589
127 M A -1.4078
128 P A -1.3098
129 S A -1.7728
130 E A -2.8465
131 E A -3.1534
132 G A -1.6991
133 Y A -0.6025
134 Q A -1.8760
135 D A -1.6000
136 Y A -0.2459
137 E A -1.4580
138 P A -1.4547
139 E A -2.1389
140 A A -0.8232

Above is the comparison between the input structure and the most aggregation prone model (predicted in the flexibility simulations, download both models in the PDB file format , download table with rmsd values ). The picture presents the most aggregation prone model (in blue) superimposed on the input structure (in red). The plot shows rmsd profile (distances between residues of the superimposed structures).

Dynamic mode uses CABS-flex simulations of protein structure fluctuations. The structure fluctuations may have impact on the size and extent of aggregation "hot-spots" on the protein surface. The dynamic mode uses the following pipeline: (1) based on the input structure, CABS-flex predicts a set of different models reflecting protein dynamics in solution; (2) for each of these models A3D score is calculated; (3) finally, the most aggregation prone model (the model with the highest A3D score, -0.6574 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015