Contacts of the helix formed by residues 1 - 33 (chain B) in PDB entry 2BNI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 1 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B TYZ 1.3 78.7 - - + -
2B MET* 1.3 77.8 + - + +
4B GLN* 3.5 9.3 + - - +
5B ILE* 3.2 32.1 + - + +
29C LEU* 2.7 51.5 + - + +
30C LEU* 4.9 0.6 - - - +
32C GLU* 3.8 11.3 + - - +
33C ARG* 2.9 54.6 + - - +
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Residues in contact with MET 2 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ARG* 1.3 94.7 - - + +
3B LYS* 1.3 61.8 + - - +
5B ILE* 3.1 8.4 + - + +
6B GLU* 2.8 38.4 + - - +
30C LEU* 3.7 31.9 - - + -
33C ARG* 4.8 6.3 - - - +
30D LEU* 3.5 41.7 - - + +
32D GLU* 5.1 9.0 - - + +
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Residues in contact with LYS 3 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B TYZ 3.5 23.1 + - + +
1B ARG 3.5 0.4 - - - -
2B MET* 1.3 78.0 - - - +
4B GLN* 1.3 62.6 + - - +
6B GLU* 3.3 16.1 + - - +
7B ASP* 2.9 40.9 + - - +
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Residues in contact with GLN 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B TYZ 2.9 20.6 + - - +
1B ARG* 3.6 8.8 - - - +
2B MET 3.2 0.2 - - - -
3B LYS* 1.3 75.9 - - - +
5B ILE* 1.3 58.6 + - + +
7B ASP* 3.3 7.2 + - - +
8B LYS* 3.0 28.9 + - + +
25C ARG* 6.1 1.8 - - - +
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Residues in contact with ILE 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ARG* 3.2 22.5 + - + +
2B MET* 3.1 18.0 + - + +
4B GLN* 1.3 74.0 - - + +
6B GLU* 1.3 67.8 + - - +
8B LYS* 3.2 7.1 + - - +
9B LEU* 2.9 24.9 + - + +
26C ILE* 3.6 33.0 - - + -
29C LEU* 4.3 33.4 - - + -
30C LEU* 3.8 22.4 - - + -
30D LEU* 3.7 23.3 - - + -
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Residues in contact with GLU 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B MET* 2.8 30.8 + - - +
3B LYS* 3.7 12.8 + - - +
5B ILE* 1.3 75.4 - - - +
7B ASP* 1.3 67.1 + - - +
9B LEU* 3.2 8.6 + - - +
10B GLU* 3.0 22.3 + - - +
27D LYS* 4.1 28.3 - - + +
30D LEU* 3.0 40.0 - - + +
31D GLY* 3.3 16.9 - - - +
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Residues in contact with ASP 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LYS* 2.9 35.3 + - - +
4B GLN* 3.3 6.5 + - - +
5B ILE 3.2 0.2 - - - -
6B GLU* 1.3 79.8 - - - +
8B LYS* 1.4 58.8 + - - +
10B GLU* 3.2 9.7 + - - +
11B GLU* 3.0 25.3 + - - +
27D LYS* 6.1 0.7 - - - -
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Residues in contact with LYS 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLN* 3.0 18.3 + - + +
5B ILE* 3.6 5.8 - - - +
7B ASP* 1.4 74.3 - - - +
9B LEU* 1.3 59.9 + - - +
11B GLU* 2.7 39.1 + - + +
12B ILE* 2.9 42.2 + - + +
18C HIS* 6.0 1.2 + - - -
22C GLU* 3.6 30.8 - - - +
25C ARG* 6.2 2.2 - - - +
26C ILE* 3.9 22.4 - - + -
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Residues in contact with LEU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 4.9 3.6 - - + -
5B ILE* 2.9 18.9 + - + +
6B GLU* 3.6 8.3 - - - +
8B LYS* 1.3 75.6 - - - +
10B GLU* 1.3 58.1 + - - +
12B ILE* 3.2 4.9 + - + +
13B LEU* 2.8 35.2 + - - +
23C LEU* 4.1 15.9 - - + -
26C ILE* 4.2 19.3 - - + -
23D LEU* 4.0 32.6 - - + +
26D ILE* 3.8 17.9 - - + -
27D LYS* 4.0 20.4 - - + +
30D LEU* 3.7 29.4 - - + -
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Residues in contact with GLU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLU 3.0 12.2 + - - +
7B ASP* 3.2 12.5 + - - +
9B LEU* 1.3 72.7 - - - +
11B GLU* 1.3 66.0 + - - +
13B LEU* 3.2 19.1 - - - +
14B SER* 3.0 27.0 + - - -
27D LYS* 2.8 39.7 + - + +
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Residues in contact with GLU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ASP 3.0 13.1 + - - +
8B LYS* 2.7 44.2 + - + +
10B GLU* 1.3 76.2 - - - +
12B ILE* 1.3 64.2 + - + +
14B SER* 3.3 8.6 + - - -
15B LYS* 3.0 29.5 + - + +
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Residues in contact with ILE 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LYS* 2.9 36.6 + - + +
9B LEU* 3.2 6.7 + - - +
11B GLU* 1.3 76.4 - - + +
13B LEU* 1.3 52.7 + - - +
15B LYS* 3.3 6.7 + - - +
16B GLY* 2.8 33.0 + - - -
19C ILE* 3.7 34.2 - - + +
22C GLU* 4.0 26.7 - - + -
23C LEU* 3.9 22.4 - - + -
26C ILE* 4.2 7.9 - - + -
23D LEU* 3.8 21.7 - - + +
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU 2.8 19.4 + - - +
10B GLU* 3.2 32.8 - - - +
12B ILE* 1.3 76.4 - - - +
14B SER* 1.3 58.1 + - - +
16B GLY* 3.3 1.4 + - - -
17B HIS* 2.9 41.4 + - + +
20D CYS* 3.1 49.3 - - + +
23D LEU* 3.9 14.4 - - + +
24D ALA* 3.8 28.5 - - + +
27D LYS* 4.9 3.8 - - + -
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Residues in contact with SER 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLU* 3.0 12.6 + - - -
11B GLU* 3.5 11.9 - - - -
13B LEU* 1.3 79.0 - - - +
15B LYS* 1.3 57.8 + - - +
17B HIS* 3.2 9.5 + - - +
18B HIS* 2.9 28.0 + - - +
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Residues in contact with LYS 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLU* 3.0 30.9 + - + +
12B ILE* 3.6 5.6 - - - +
14B SER* 1.3 74.7 - - - +
16B GLY* 1.3 52.2 + - - +
18B HIS* 3.1 11.4 + - + +
19B ILE* 2.8 42.0 + - + +
19C ILE* 4.3 17.0 - - + -
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Residues in contact with GLY 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 2.8 20.2 + - - -
13B LEU 3.8 1.6 - - - -
15B LYS* 1.3 71.4 - - - +
17B HIS* 1.3 61.9 + - - +
19B ILE* 3.2 11.4 + - - +
20B CYS* 2.9 27.7 + - - -
19C ILE* 4.7 5.0 - - - +
20D CYS* 4.0 13.7 - - - -
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Residues in contact with HIS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 2.9 30.7 + - + +
14B SER* 3.2 10.3 + - - +
16B GLY* 1.3 74.7 - - - +
18B HIS* 1.3 56.4 + - - +
20B CYS* 3.3 5.0 + - - +
21B ASN* 2.9 41.4 + - - +
17D HIS* 4.3 22.6 + + + -
20D CYS* 3.4 31.9 - - + +
21D ASN* 5.3 4.9 + - - -
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Residues in contact with HIS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B SER 2.9 12.9 + - - +
15B LYS* 3.4 13.5 - - + +
17B HIS* 1.3 75.4 - - - +
19B ILE* 1.3 64.1 + - + +
21B ASN* 3.1 14.4 + - - +
22B GLU* 2.9 62.5 + - + +
8C LYS* 5.5 4.2 + - - -
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Residues in contact with ILE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 5.9 0.2 - - + -
15B LYS* 2.8 24.5 + - + +
16B GLY* 3.6 7.0 - - - +
18B HIS* 1.3 75.9 - - + +
20B CYS* 1.3 67.9 + - - +
22B GLU* 3.1 9.6 + - + +
23B LEU* 2.9 33.7 + - + +
12C ILE* 3.7 35.2 - - + +
15C LYS* 4.2 22.0 - - + -
16C GLY* 4.7 3.8 - - - +
19C ILE* 3.8 27.4 - - + -
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Residues in contact with CYS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLY 2.9 21.2 + - - -
17B HIS* 3.6 9.2 - - - +
19B ILE* 1.3 79.4 - - - +
21B ASN* 1.4 59.4 + - - +
23B LEU* 3.3 6.8 + - - +
24B ALA* 2.9 29.5 + - - +
13D LEU* 3.8 25.4 - - + +
16D GLY* 3.7 35.9 - - - -
17D HIS* 3.8 24.5 - - + +
20D CYS* 5.1 0.7 - - - -
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Residues in contact with ASN 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B HIS* 2.9 26.9 + - - +
18B HIS* 3.1 13.6 + - - +
20B CYS* 1.4 79.8 - - - +
22B GLU* 1.3 58.0 + - + +
24B ALA* 3.3 8.2 + - - +
25B ARG* 2.9 27.3 + - - +
17D HIS* 5.1 4.5 + - - -
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B HIS* 2.9 51.1 + - + +
19B ILE* 3.1 9.4 + - - +
21B ASN* 1.3 74.7 - - + +
23B LEU* 1.3 59.8 + - - +
25B ARG* 3.2 21.3 + - - +
26B ILE* 2.9 35.4 + - + +
8C LYS* 3.6 28.9 + - - +
12C ILE* 4.1 18.4 - - + -
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 5.7 0.4 - - + -
23A LEU* 3.9 28.9 - - + -
19B ILE* 2.9 36.8 + - + +
20B CYS* 3.7 8.7 - - - +
22B GLU* 1.3 72.1 - - - +
24B ALA* 1.3 60.2 + - - +
26B ILE* 3.3 6.4 + - + +
27B LYS* 2.9 29.3 + - - +
9C LEU* 4.1 14.4 - - + -
12C ILE* 4.1 14.6 - - + -
9D LEU* 4.0 19.4 - - + +
12D ILE* 3.8 28.3 - - + -
13D LEU* 4.2 14.8 - - + +
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B CYS 2.9 14.3 + - - +
21B ASN* 3.5 11.4 - - - +
23B LEU* 1.3 74.6 - - - +
25B ARG* 1.3 64.1 + - - +
27B LYS* 3.3 6.1 + - - +
28B LYS* 3.0 22.7 + - - +
13D LEU* 3.7 23.1 - - + +
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Residues in contact with ARG 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASN 2.9 14.2 + - - +
22B GLU* 3.2 25.1 + - - +
24B ALA* 1.3 76.7 - - - +
26B ILE* 1.4 58.6 + - + +
28B LYS* 3.1 8.9 + - + +
29B LEU* 3.0 47.5 + - + +
----------------------------------------------------------
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Residues in contact with ILE 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLU* 2.9 23.2 + - + +
23B LEU* 3.6 7.0 - - - +
25B ARG* 1.4 72.0 - - + +
27B LYS* 1.3 66.3 + - - +
29B LEU* 3.3 11.0 + - + +
30B LEU* 2.9 35.7 + - + +
5C ILE* 3.6 34.5 - - + +
8C LYS* 4.0 22.4 - - + -
9C LEU* 4.3 20.2 - - + -
12C ILE* 4.0 25.1 - - + -
9D LEU* 4.3 7.9 - - + -
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Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU 2.9 17.6 + - - +
24B ALA* 3.5 7.9 - - - +
25B ARG 3.3 0.2 - - - -
26B ILE* 1.3 76.1 - - - +
28B LYS* 1.3 63.5 + - - +
31B GLY* 3.2 5.4 + - - -
6D GLU* 2.8 73.6 - - - +
7D ASP* 5.3 3.7 + - - -
9D LEU* 3.9 13.5 - - + -
10D GLU* 2.9 45.5 + - + +
13D LEU* 4.8 3.4 - - + -
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Residues in contact with LYS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA 3.0 14.0 + - - +
25B ARG* 3.1 11.2 + - - +
27B LYS* 1.3 77.8 - - - +
29B LEU* 1.3 68.3 + - + +
31B GLY* 3.1 12.5 + - - -
32B GLU* 2.6 44.5 + - + +
----------------------------------------------------------
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 3.0 35.3 + - + +
26B ILE* 3.8 9.9 - - + +
28B LYS* 1.3 80.2 - - + +
30B LEU* 1.3 62.1 + - - +
32B GLU* 3.1 29.4 + - - +
33B ARG 3.7 0.9 - - - +
1C ARG* 2.8 39.0 + - + +
5C ILE* 4.3 22.4 - - + -
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 5.4 0.4 - - + -
30A LEU* 4.0 20.4 - - + -
26B ILE* 2.9 39.2 + - + +
28B LYS 3.3 0.2 - - - -
29B LEU* 1.3 76.1 - - - +
31B GLY* 1.4 59.7 + - - +
33B ARG 3.9 11.8 + - - +
1C ARG* 5.2 1.6 - - - +
2C MET* 3.7 36.3 - - + -
5C ILE* 3.7 14.4 - - + -
2D MET* 4.0 31.3 - - + +
5D ILE* 4.1 11.9 - - + -
6D GLU* 3.7 13.7 - - - -
9D LEU* 4.0 16.6 - - + -
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Residues in contact with GLY 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LYS 3.2 8.9 + - - -
28B LYS 3.1 10.3 + - - -
30B LEU* 1.4 78.9 - - - +
32B GLU* 1.3 60.6 + - - +
33B ARG 3.7 0.2 - - - -
2D MET* 5.8 0.9 - - - -
6D GLU* 3.7 10.5 - - - -
----------------------------------------------------------
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Residues in contact with GLU 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LYS* 2.6 51.0 + - + +
29B LEU* 3.1 18.5 + - - +
31B GLY* 1.3 79.1 - - - +
33B ARG* 1.3 95.1 + - - +
1C ARG* 3.6 11.2 + - - +
----------------------------------------------------------
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Residues in contact with ARG 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU 3.7 4.0 + - - +
30B LEU* 3.9 11.0 - - - +
31B GLY 3.7 1.2 - - - -
32B GLU* 1.3 110.3 + - - +
1C ARG* 3.0 51.0 + - - +
2C MET* 5.4 7.8 - - - +
----------------------------------------------------------
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il