Contacts of the helix formed by residues 1 - 33 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 2.8 51.6 + - + +
30B LEU* 4.8 2.6 - - - +
32B GLU* 3.6 11.7 + - - -
33B ARG* 3.0 54.2 + - - +
0C TYZ 1.3 78.8 - - + +
2C MET* 1.3 65.7 + - - +
4C GLN* 3.6 9.6 + - - +
5C ILE* 3.3 37.9 + - + +
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Residues in contact with MET 2 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.6 44.2 - - + +
30B LEU* 3.7 31.9 - - + -
33B ARG* 5.4 8.7 - - - +
0C TYZ 3.4 0.2 - - - -
1C ARG* 1.3 78.6 - - - +
3C LYS* 1.3 60.4 + - - +
5C ILE* 3.1 8.4 + - - +
6C GLU* 2.9 40.3 + - - +
2D MET* 4.6 9.9 - - + -
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Residues in contact with LYS 3 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0C TYZ 3.4 24.5 + - + +
2C MET* 1.3 76.3 - - - +
4C GLN* 1.3 63.5 + - - +
6C GLU* 3.3 14.0 + - + +
7C ASP* 2.9 39.8 + - - +
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Residues in contact with GLN 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0C TYZ 2.9 19.0 + - - +
1C ARG* 3.7 8.7 - - - +
3C LYS* 1.3 78.8 - - - +
5C ILE* 1.3 59.4 + - + +
7C ASP* 3.5 7.1 + - + +
8C LYS* 2.9 28.9 + - + +
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Residues in contact with ILE 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.8 23.8 - - + -
26B ILE* 3.6 31.6 - - + +
29B LEU* 4.3 29.4 - - + -
30B LEU* 3.7 25.1 - - + -
1C ARG* 3.3 26.9 + - + +
2C MET* 3.1 14.3 + - - +
4C GLN* 1.3 75.7 - - + +
6C GLU* 1.3 60.6 + - - +
8C LYS* 3.1 7.0 + - - +
9C LEU* 2.8 30.8 + - + +
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Residues in contact with GLU 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS* 3.3 41.7 - - + +
30A LEU* 3.5 42.2 - - + +
2C MET* 2.9 31.7 + - - +
3C LYS* 3.7 10.6 + - + +
5C ILE* 1.3 75.9 - - - +
7C ASP* 1.3 63.1 + - - +
9C LEU* 3.2 6.5 + - - +
10C GLU 3.0 17.8 + - - -
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Residues in contact with ASP 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS* 5.3 3.3 - - - -
3C LYS* 2.9 34.1 + - - +
4C GLN* 3.9 6.4 - - - +
6C GLU* 1.3 78.4 - - - +
8C LYS* 1.3 62.0 + - - +
10C GLU* 3.2 9.3 + - - +
11C GLU* 3.1 21.7 + - - +
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Residues in contact with LYS 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B HIS* 5.5 3.8 + - - -
22B GLU* 3.6 32.1 + - - +
26B ILE* 4.0 22.0 - - + -
4C GLN* 2.9 19.5 + - + +
5C ILE* 3.1 6.3 + - - +
7C ASP* 1.3 72.5 - - - +
9C LEU* 1.3 66.1 + - - +
11C GLU* 2.8 39.4 + - - +
12C ILE* 2.9 36.3 + - + +
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Residues in contact with LEU 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.2 20.5 - - + +
26A ILE* 3.7 26.2 - - + -
27A LYS* 3.9 22.2 - - + +
30A LEU* 3.8 18.8 - - + -
23B LEU* 4.1 26.2 - - + -
26B ILE* 4.3 15.3 - - + -
5C ILE* 2.8 22.7 + - + +
6C GLU* 3.2 8.5 + - - +
8C LYS* 1.3 75.4 - - - +
10C GLU* 1.3 58.0 + - - +
12C ILE* 3.3 4.6 + - + +
13C LEU* 2.8 35.9 + - + +
9D LEU* 4.8 4.0 - - + -
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Residues in contact with GLU 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS* 3.6 38.0 + - - +
6C GLU 3.0 6.4 + - - +
7C ASP* 3.6 11.7 - - - +
8C LYS 3.2 0.4 - - - -
9C LEU* 1.3 75.4 - - - +
11C GLU* 1.3 63.2 + - - +
13C LEU* 3.5 20.6 + - - +
14C SER* 3.0 39.0 + - - +
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Residues in contact with GLU 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ASP 3.1 10.9 + - - +
8C LYS* 2.8 43.9 + - + +
10C GLU* 1.3 77.7 - - - +
12C ILE* 1.3 59.5 + - + +
14C SER* 3.3 7.9 + - - -
15C LYS* 2.9 37.8 + - + +
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Residues in contact with ILE 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.8 21.5 - - + -
19B ILE* 3.7 32.5 - - + +
22B GLU* 4.1 22.4 - - + -
23B LEU* 4.1 15.3 - - + -
26B ILE* 4.0 25.8 - - + -
8C LYS* 2.9 29.8 + - + +
9C LEU* 3.7 5.8 - - - +
11C GLU* 1.3 77.6 - - + +
13C LEU* 1.3 60.5 + - - +
15C LYS* 3.2 7.8 + - - +
16C GLY* 2.8 26.7 + - - -
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Residues in contact with LEU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A CYS* 3.9 17.8 - - - +
23A LEU* 4.1 22.4 - - + +
24A ALA* 3.8 35.0 - - + +
27A LYS* 4.9 3.1 - - + -
9C LEU 2.8 28.8 + - - +
10C GLU* 3.7 30.1 - - - +
12C ILE* 1.3 75.4 - - - +
14C SER* 1.3 59.2 + - - +
16C GLY* 3.7 0.8 - - - +
17C HIS* 2.9 51.7 + - + +
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Residues in contact with SER 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLU* 3.0 30.7 + - - +
11C GLU* 3.5 7.9 - - - -
13C LEU* 1.3 77.2 - - - +
15C LYS* 1.3 61.2 + - - +
17C HIS* 3.2 8.5 + - - +
18C HIS* 2.9 22.5 + - - +
----------------------------------------------------------
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Residues in contact with LYS 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 4.2 17.3 - - + -
11C GLU* 2.9 28.5 + - + +
12C ILE* 3.6 9.4 - - - +
14C SER* 1.3 74.1 - - - +
16C GLY* 1.3 57.1 + - - +
18C HIS* 3.1 10.7 + - + +
19C ILE* 2.8 37.1 + - + +
----------------------------------------------------------
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Residues in contact with GLY 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A CYS* 3.9 13.5 - - - -
19B ILE* 4.7 4.2 - - - +
12C ILE* 2.8 16.3 + - - -
13C LEU* 3.7 2.5 - - - -
15C LYS* 1.3 76.7 - - - +
17C HIS* 1.3 56.9 + - - +
19C ILE* 3.4 11.3 + - - +
20C CYS* 2.9 34.1 + - - -
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Residues in contact with HIS 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A HIS* 4.5 22.1 - + + -
20A CYS* 3.4 30.4 - - + +
13C LEU* 2.9 39.8 + - + +
14C SER* 3.7 6.3 - - - +
16C GLY* 1.3 75.3 - - - +
18C HIS* 1.3 56.3 + - - +
20C CYS* 3.2 5.6 + - - +
21C ASN* 2.9 40.6 + - - +
----------------------------------------------------------
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Residues in contact with HIS 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LYS* 6.0 1.2 + - - -
14C SER 2.9 13.3 + - - +
15C LYS* 3.1 13.2 + - + +
17C HIS* 1.3 74.9 - - - +
19C ILE* 1.3 62.8 + - + +
21C ASN* 3.1 14.5 + - - +
22C GLU* 2.9 57.5 + - + +
----------------------------------------------------------
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Residues in contact with ILE 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 3.7 32.5 - - + -
15B LYS* 4.3 20.4 - - + -
16B GLY* 4.7 7.2 - - - +
19B ILE* 3.8 26.5 - - + -
15C LYS* 2.8 24.8 + - + +
16C GLY* 3.6 7.4 - - - +
18C HIS* 1.3 78.2 - - + +
20C CYS* 1.3 67.0 + - - +
22C GLU* 3.1 9.2 + - - +
23C LEU* 2.9 33.5 + - + +
----------------------------------------------------------
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Residues in contact with CYS 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE 5.2 0.2 - - - -
13A LEU* 3.2 25.5 - - + +
16A GLY* 3.8 36.3 - - - -
17A HIS* 3.8 27.1 - - + +
20A CYS* 5.1 0.7 - - - -
16C GLY 2.9 20.3 + - - -
17C HIS* 3.6 9.0 - - - +
19C ILE* 1.3 79.4 - - - +
21C ASN* 1.3 60.4 + - - +
23C LEU* 3.2 4.1 + - - -
24C ALA* 2.9 27.8 + - - +
----------------------------------------------------------
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Residues in contact with ASN 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A HIS* 5.2 4.3 + - - -
17C HIS* 2.9 27.2 + - - +
18C HIS* 3.1 14.5 + - - +
20C CYS* 1.3 78.3 - - - +
22C GLU* 1.3 56.4 + - - +
24C ALA* 3.3 8.7 + - - +
25C ARG* 3.0 27.2 + - - +
----------------------------------------------------------
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Residues in contact with GLU 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LYS* 3.6 30.1 - - - +
12B ILE* 4.0 18.6 - - + -
18C HIS* 2.9 45.7 + - + +
19C ILE* 3.1 8.7 + - - +
21C ASN* 1.3 76.6 - - - +
23C LEU* 1.3 56.6 + - - +
25C ARG* 3.1 25.3 + - - +
26C ILE* 2.9 34.5 + - + +
----------------------------------------------------------
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Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 4.1 17.0 - - + +
12A ILE* 3.7 30.5 - - + -
13A LEU* 3.8 17.7 - - + +
9B LEU* 4.1 7.9 - - + -
12B ILE* 3.9 21.3 - - + -
19C ILE* 2.9 32.2 + - + +
20C CYS* 3.6 8.7 - - - +
22C GLU* 1.3 74.1 - - - +
24C ALA* 1.3 58.9 + - - +
26C ILE* 3.3 6.1 + - + +
27C LYS* 2.9 28.9 + - - +
19D ILE* 5.7 0.2 - - + -
23D LEU* 3.8 28.3 - - + -
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Residues in contact with ALA 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.6 21.9 - - + +
20C CYS 2.9 16.7 + - - +
21C ASN* 3.6 8.5 - - - +
23C LEU* 1.3 74.8 - - - +
25C ARG* 1.3 63.2 + - - +
27C LYS* 3.3 5.4 + - - +
28C LYS* 3.0 23.4 + - - +
----------------------------------------------------------
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Residues in contact with ARG 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLN* 6.1 2.0 - - - +
8B LYS* 6.2 2.2 - - - +
21C ASN 3.0 13.8 + - - +
22C GLU* 3.1 27.0 + - - +
24C ALA* 1.3 77.0 - - - +
26C ILE* 1.3 64.2 + - - +
28C LYS* 3.2 9.2 + - + +
29C LEU* 3.0 66.2 + - + +
----------------------------------------------------------
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Residues in contact with ILE 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 4.3 7.9 - - + -
5B ILE* 3.6 33.4 - - + -
8B LYS* 3.9 32.1 - - + -
9B LEU* 4.2 22.2 - - + -
12B ILE* 4.2 14.6 - - + -
22C GLU* 2.9 17.5 + - - +
23C LEU* 3.6 9.4 - - + +
25C ARG* 1.3 82.8 - - - +
27C LYS* 1.3 64.7 + - - +
29C LEU* 3.3 7.5 + - - +
30C LEU* 2.9 35.2 + - + +
----------------------------------------------------------
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Residues in contact with LYS 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLU* 3.2 52.1 + - + +
7A ASP* 5.2 3.0 + - - +
9A LEU* 4.0 16.1 - - + +
10A GLU* 3.4 38.3 + - + +
13A LEU* 4.6 3.8 - - + -
23C LEU 2.9 16.5 + - - +
24C ALA* 3.5 7.0 - - - +
25C ARG 3.3 0.2 - - - -
26C ILE* 1.3 76.8 - - - +
28C LYS* 1.3 63.1 + - - +
30C LEU* 3.4 3.8 + - - +
31C GLY* 3.2 18.2 + - - -
----------------------------------------------------------
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Residues in contact with LYS 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ALA 3.0 14.0 + - - +
25C ARG* 3.2 11.9 + - + +
27C LYS* 1.3 77.1 - - - +
29C LEU* 1.3 68.8 + - + +
31C GLY* 3.1 12.0 + - - -
32C GLU* 3.4 38.4 + - + +
----------------------------------------------------------
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Residues in contact with LEU 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ARG* 2.7 42.8 + - + +
5B ILE* 4.3 23.1 - - + -
25C ARG* 3.0 59.8 + - + +
26C ILE* 3.3 6.5 + - - +
28C LYS* 1.3 82.1 - - + +
30C LEU* 1.3 62.9 + - - +
32C GLU* 3.2 26.1 + - - +
33C ARG 3.7 0.7 - - - +
----------------------------------------------------------
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A MET* 4.0 25.6 - - + +
5A ILE* 4.1 12.8 - - + -
6A GLU* 3.2 12.5 - - + +
9A LEU* 4.0 16.8 - - + -
1B ARG* 5.2 0.2 - - - +
2B MET* 3.7 34.8 - - + -
5B ILE* 3.8 13.7 - - + -
9B LEU* 5.9 0.2 - - + -
26C ILE* 2.9 39.3 + - + +
27C LYS* 3.9 4.9 - - - +
28C LYS 3.2 0.4 - - - -
29C LEU* 1.3 75.6 - - - +
31C GLY* 1.4 59.6 + - - +
32C GLU 3.4 0.6 + - - -
33C ARG 3.9 12.5 + - - +
26D ILE* 5.4 0.7 - - + -
30D LEU* 4.0 24.5 - - + -
----------------------------------------------------------
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Residues in contact with GLY 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLU* 3.1 19.0 + - - -
27C LYS 3.2 8.0 + - - -
28C LYS 3.1 10.0 + - - -
30C LEU* 1.4 77.6 - - - +
32C GLU* 1.3 62.1 + - - +
----------------------------------------------------------
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Residues in contact with GLU 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ARG* 3.8 7.3 + - - +
28C LYS* 3.4 34.4 - - + +
29C LEU* 3.2 26.9 + - - +
31C GLY* 1.3 80.5 - - - +
33C ARG* 1.3 82.3 + - - +
----------------------------------------------------------
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Residues in contact with ARG 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ARG* 2.9 52.9 + - - +
2B MET* 4.8 7.1 - - - +
29C LEU 3.7 4.0 + - - +
30C LEU* 3.9 10.8 + - - +
31C GLY 3.7 1.0 - - - -
32C GLU* 1.3 97.7 + - - +
----------------------------------------------------------
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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