Contacts of the helix formed by residues 7 - 37 (chain B) in PDB entry 2ZI0
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 PRO 7 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B GLU 4.4 3.4 - - - +
6B ILE* 1.3 95.5 - - + +
8B LEU* 1.3 63.8 + - - +
9B HIS* 3.5 31.4 - - + +
10B GLU* 3.4 30.4 + - + +
11B ILE* 3.6 8.1 + - - +
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Residues in contact with LEU 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE 3.7 0.8 + - - -
7B PRO* 1.3 72.7 - - - +
9B HIS* 1.3 63.6 + - - +
11B ILE* 3.1 31.1 + - + +
12B ILE* 3.0 36.6 + - + +
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Residues in contact with HIS 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO* 3.5 24.2 - - + +
8B LEU* 1.3 77.2 + - - +
10B GLU* 1.3 81.0 + - - +
12B ILE* 3.8 12.9 - - + +
13B ARG* 3.0 61.9 + - - +
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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 ILE* 4.5 11.4 - - + -
7B PRO* 3.5 34.7 - - + +
8B LEU 3.1 0.4 - - - -
9B HIS* 1.3 92.8 + - + +
11B ILE* 1.3 57.6 + - - +
13B ARG* 3.3 15.7 + - - +
14B LYS* 2.8 36.8 + - - +
17B ARG* 5.1 6.1 + - - -
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Residues in contact with ILE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 5.9 4.7 - - + -
6B ILE* 4.6 17.3 - - + +
7B PRO 3.8 12.3 - - - +
8B LEU* 3.1 32.0 + - + +
10B GLU* 1.3 76.7 - - - +
12B ILE* 1.3 66.4 + - + +
14B LYS* 3.3 6.3 + - - +
15B LEU* 3.0 40.8 + - + +
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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 LEU* 3.0 31.8 + - + +
9B HIS* 3.8 14.6 - - + +
10B GLU 3.3 0.2 - - - -
11B ILE* 1.3 79.1 - - + +
13B ARG* 1.3 56.1 + - - +
15B LEU* 3.4 7.4 + - + +
16B GLU* 2.9 45.7 + - + +
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Residues in contact with ARG 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B HIS* 3.0 57.4 + - - +
10B GLU* 3.5 17.2 + - - +
12B ILE* 1.3 73.4 - - - +
14B LYS* 1.3 67.1 + - - +
16B GLU* 3.1 16.4 + - - +
17B ARG* 2.8 42.4 + - + +
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Residues in contact with LYS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 5.2 6.7 - - - +
10B GLU 2.8 21.2 + - - +
11B ILE* 3.6 7.4 - - - +
13B ARG* 1.3 72.3 - - - +
15B LEU* 1.3 60.4 + - + +
17B ARG* 3.1 28.0 + - - +
18B MSE 2.9 55.0 + - + +
6D G 3.6 31.5 + - - -
7D C 3.5 29.4 + - - -
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 6.2 4.0 - - + -
15A LEU* 3.9 33.0 - - + -
18A MSE 4.7 2.7 - - + -
11B ILE* 3.0 36.5 + - + +
12B ILE* 3.7 7.2 - - + +
14B LYS* 1.3 76.5 - - + +
16B GLU* 1.3 58.1 + - - +
18B MSE 3.8 24.7 - - + +
19B ASN* 3.0 30.1 + - - +
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Residues in contact with GLU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 2.9 34.2 + - + +
13B ARG* 3.1 23.7 + - + +
15B LEU* 1.3 75.4 - - - +
17B ARG* 1.3 63.1 + - - +
19B ASN* 3.4 8.1 + - - +
20B GLN* 3.0 35.1 + - + +
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Residues in contact with ARG 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLU* 5.1 5.9 + - - -
13B ARG* 2.8 28.4 + - + +
14B LYS* 3.1 42.0 + - - +
16B GLU* 1.3 75.9 - - - +
18B MSE 1.3 63.2 + - + +
20B GLN* 3.1 18.9 + - + +
21B LYS* 3.2 24.4 + - + +
7D C 4.6 18.2 + - - -
8D A 5.0 12.1 - - - -
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Residues in contact with MSE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A MSE 3.4 35.2 - - + -
22A LYS* 3.4 35.2 - - - +
14B LYS* 2.9 39.4 + - + +
15B LEU* 3.8 21.5 - - + +
17B ARG* 1.3 76.3 - - + +
19B ASN* 1.3 58.1 + - - +
21B LYS* 3.5 9.5 + - - +
22B LYS* 3.1 40.2 + - + +
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Residues in contact with ASN 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU 3.0 18.3 + - - +
16B GLU* 3.7 7.4 + - - +
18B MSE 1.3 75.6 - - - +
20B GLN* 1.3 67.9 + - - +
22B LYS* 3.4 12.6 + - - +
23B GLN* 3.1 48.1 + - - +
5C A 4.8 5.7 + - - +
6C G 5.4 3.6 + - - -
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Residues in contact with GLN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLU* 3.0 29.0 + - - +
17B ARG* 3.1 9.1 + - - +
19B ASN* 1.3 80.5 - - - +
21B LYS* 1.3 62.9 + - + +
23B GLN* 3.4 21.0 + - - +
24B ALA* 2.8 28.5 + - - +
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Residues in contact with LYS 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ARG* 3.2 21.9 + - + +
18B MSE 3.7 10.1 - - - +
20B GLN* 1.3 77.8 - - - +
22B LYS* 1.3 60.6 + - + +
24B ALA* 3.5 9.2 + - + +
25B GLN* 3.1 43.7 + - - +
8D A 4.1 29.0 + - - +
9D U 3.1 32.8 + - - +
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Residues in contact with LYS 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LYS* 4.7 9.5 - - - +
18A MSE 3.9 32.2 - - - +
18B MSE 3.1 29.7 + - - +
19B ASN* 3.7 15.5 - - - +
20B GLN 3.3 0.2 - - - -
21B LYS* 1.3 77.8 - - - +
23B GLN* 1.3 62.2 + - + +
25B GLN* 3.2 15.3 + - - +
26B ARG* 3.1 25.0 + - - +
6C G 4.9 18.9 + - - +
7C C 4.7 9.5 + - - -
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Residues in contact with GLN 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ASN* 3.1 28.1 + - - +
20B GLN* 3.6 28.9 + - - +
22B LYS* 1.3 72.8 - - + +
24B ALA* 1.3 65.4 + - - +
26B ARG* 3.5 7.9 + - - +
27B LYS* 3.1 23.6 + - - +
4C C 4.6 4.0 + - - -
5C A 3.1 37.6 + - - +
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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 GLN 2.8 16.9 + - - +
21B LYS* 3.6 13.2 - - + +
22B LYS 3.2 0.2 - - - -
23B GLN* 1.3 77.1 - - - +
25B GLN* 1.3 59.6 + - - +
27B LYS* 3.4 8.1 + - - +
28B ARG* 3.0 47.2 + - - +
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Residues in contact with GLN 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LYS* 3.1 25.4 + - - +
22B LYS* 3.2 16.4 + - - +
24B ALA* 1.3 74.5 - - - +
26B ARG* 1.3 65.3 + - - +
28B ARG* 3.3 25.0 + - - +
29B HIS* 2.8 26.5 + - - +
10D U 3.0 25.5 + - + +
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Residues in contact with ARG 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LYS 3.1 16.6 + - - +
23B GLN* 3.8 10.0 - - - +
24B ALA 3.5 0.2 - - - -
25B GLN* 1.3 75.7 - - - +
27B LYS* 1.3 53.9 + - - +
29B HIS* 3.8 4.4 - - - +
30B LYS* 2.5 41.1 + - + +
4C C 5.9 2.5 - - - -
5C A 3.3 49.6 + - - +
6C G 2.4 77.1 + - - -
7C C 4.8 5.0 - - - +
14D C 5.0 1.0 - - - +
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Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLN 3.1 15.1 + - - +
24B ALA* 3.6 7.2 - - - +
25B GLN 3.2 0.2 - - - -
26B ARG* 1.3 79.6 - - - +
28B ARG* 1.3 67.5 + - + +
30B LYS* 3.7 17.2 - - - +
31B LEU* 2.9 57.5 + - + +
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Residues in contact with ARG 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 39.2 + - - +
25B GLN* 3.5 29.0 - - - +
26B ARG 3.3 0.2 - - - -
27B LYS* 1.3 79.7 - - + +
29B HIS* 1.3 59.7 + - - +
31B LEU* 4.0 5.4 - - + +
32B ASN* 3.0 34.4 + - - +
10D U 3.5 60.0 + - - -
11D A 2.8 40.9 + - - +
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Residues in contact with HIS 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLN 2.8 21.5 + - - +
26B ARG* 3.8 4.7 - - - +
28B ARG* 1.3 71.3 - - - +
30B LYS* 1.3 66.1 + - - +
32B ASN* 3.3 1.4 + - - +
33B ARG* 2.9 40.8 + - + +
11D A 5.3 0.6 + - - -
12D U 3.2 58.0 + + + +
13D G 3.0 59.6 + + - -
14D C 5.3 3.4 + - - -
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Residues in contact with LYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ARG* 2.5 25.4 + - + +
27B LYS* 3.7 15.9 - - - +
29B HIS* 1.3 72.6 - - - +
31B LEU* 1.3 85.9 + - - +
33B ARG* 3.1 16.0 + - - +
34B LYS* 3.0 35.7 + - + +
3C A 4.2 28.8 + - - +
4C C 5.1 10.5 + - + +
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LYS* 2.9 47.1 + - + +
28B ARG* 4.0 4.3 - - + +
30B LYS* 1.3 96.8 - - - +
32B ASN* 1.3 68.2 + - - +
34B LYS* 3.0 20.3 + - + +
35B GLU* 3.0 32.4 + - - +
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Residues in contact with ASN 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG 3.0 25.0 + - - +
29B HIS 3.3 2.4 + - - +
31B LEU* 1.3 78.2 - - - +
33B ARG* 1.3 61.8 + - - +
35B GLU* 3.4 26.2 + - - +
36B ARG* 3.4 21.1 + - - +
11D A 3.1 35.1 + - - -
12D U 2.8 38.7 + - - +
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Residues in contact with ARG 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B HIS* 2.9 34.2 + - + +
30B LYS* 3.4 12.1 - - - +
32B ASN* 1.3 76.7 - - - +
34B LYS* 1.3 63.3 + - - +
36B ARG* 3.2 16.7 + - - +
37B GLY 3.0 4.2 + - - -
38B HIS* 2.9 52.2 + - + +
40B SER* 3.6 6.5 - - - +
43B GLU* 2.9 37.9 + - - -
13D G 3.3 31.3 + - - -
14D C 2.5 48.9 + - - +
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Residues in contact with LYS 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LYS* 3.0 35.7 + - + +
31B LEU* 3.0 22.1 + - + +
33B ARG* 1.3 76.3 - - - +
35B GLU* 1.3 65.4 + - + +
37B GLY* 2.9 14.7 + - - +
38B HIS 5.5 0.4 - - - -
2C G 2.6 43.4 + - - +
3C A 5.3 2.5 + - - -
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Residues in contact with GLU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.0 21.8 + - - +
32B ASN* 3.7 20.2 - - - +
33B ARG 3.3 0.4 - - - -
34B LYS* 1.3 78.6 - - + +
36B ARG* 1.3 64.1 + - + +
37B GLY 3.3 0.3 + - - -
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Residues in contact with ARG 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASN* 3.4 11.0 + - - +
33B ARG* 3.2 26.1 + - - +
35B GLU* 1.3 78.8 - - + +
37B GLY* 1.3 62.1 + - - +
38B HIS* 3.4 16.3 + - + +
12D U 2.7 35.1 + - - -
13D G 2.9 39.0 + - - -
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Residues in contact with GLY 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG 3.0 0.6 + - - -
34B LYS* 2.9 17.6 + - - -
35B GLU 3.1 1.4 + - - -
36B ARG* 1.3 79.5 - - - +
38B HIS* 1.3 59.9 + - - +
39B LYS* 3.8 9.1 + - - +
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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