Distributions of interacting atoms around amino acids

The page is made by Hung-Pin Peng

Advisor: Dr. An-Suei Yang


Contributions:
  1. Source code fo amino acid conformational clustering is made by Ching-Tai Chen (use Fuzzy C-Mean algorithm) and Ei-Wen Yang (Intra group RMSD-based method). Amino acid conformation data input is made by Ei-Wen Yang.
  2. Source code for creating density map is written by Hung-Pin Peng, Ei-Wen Yang, Ching-Tai Chen, Jun-Bo Chen and Dr. Keng-Chang Tsai.
  3. Non-interacting atomic pairs filter table for probe 1 ~ 30 is made by Dr. Keng-Chang Tsai.
  4. Protein atomistic non-covalent interacting database is made by Hung-Pin Peng.
  5. Database for constructing water density map is made by Jun-Bo Chen.
  6. Jeng-Yih Chang, Jhih-Wei Jian and Po-Chiang Hsu provided constructive suggestions in software development and bug reports.
  7. Supervised by Dr. An-Suei Yang.

(These pages use Jmol and take time to load data depend on network bandwidth)

Index by amino acid and conformation cluster type

Amino acidConformation cluster
A 6 1 2 3 4 5 6
C 6 1 2 3 4 5 6
D 6 1 2 3 4 5 6
E 7 1 2 3 4 5 6 7
F 7 1 2 3 4 5 6 7
G 6 1 2 3 4 5 6
H 10 1 2 3 4 5 6 7 8 9 10
I 7 1 2 3 4 5 6 7
K 13 1 2 3 4 5 6 7 8 9 10 11 12 13
L 7 1 2 3 4 5 6 7
M 10 1 2 3 4 5 6 7 8 9 10
N 8 1 2 3 4 5 6 7 8
P 4 1 2 3 4
Q 10 1 2 3 4 5 6 7 8 9 10
R 10 1 2 3 4 5 6 7 8 9 10
S 7 1 2 3 4 5 6 7
T 4 1 2 3 4
V 6 1 2 3 4 5 6
W 10 1 2 3 4 5 6 7 8 9 10
Y 8 1 2 3 4 5 6 7 8

Index By probe type

Probe
1 A C D E F G H I K L M N P Q R S T V W Y
2 A C D E F G H I K L M N P Q R S T V W Y
3 A C D E F G H I K L M N P Q R S T V W Y
4 A C D E F G H I K L M N P Q R S T V W Y
5 A C D E F G H I K L M N P Q R S T V W Y
6 A C D E F G H I K L M N P Q R S T V W Y
7 A C D E F G H I K L M N P Q R S T V W Y
8 A C D E F G H I K L M N P Q R S T V W Y
9 A C D E F G H I K L M N P Q R S T V W Y
10 A C D E F G H I K L M N P Q R S T V W Y
11 A C D E F G H I K L M N P Q R S T V W Y
12 A C D E F G H I K L M N P Q R S T V W Y
13 A C D E F G H I K L M N P Q R S T V W Y
14 A C D E F G H I K L M N P Q R S T V W Y
15 A C D E F G H I K L M N P Q R S T V W Y
16 A C D E F G H I K L M N P Q R S T V W Y
17 A C D E F G H I K L M N P Q R S T V W Y
18 A C D E F G H I K L M N P Q R S T V W Y
19 A C D E F G H I K L M N P Q R S T V W Y
20 A C D E F G H I K L M N P Q R S T V W Y
21 A C D E F G H I K L M N P Q R S T V W Y
22 A C D E F G H I K L M N P Q R S T V W Y
23 A C D E F G H I K L M N P Q R S T V W Y
24 A C D E F G H I K L M N P Q R S T V W Y
25 A C D E F G H I K L M N P Q R S T V W Y
26 A C D E F G H I K L M N P Q R S T V W Y
27 A C D E F G H I K L M N P Q R S T V W Y
28 A C D E F G H I K L M N P Q R S T V W Y
29 A C D E F G H I K L M N P Q R S T V W Y
30 A C D E F G H I K L M N P Q R S T V W Y
31 A C D E F G H I K L M N P Q R S T V W Y

Water distribution with pre-compiled density map (cutoff = 0.001)

31 A C D E F G H I K L M N P Q R S T V W Y

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