Contacts of the helix formed by residues 7 - 36 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLU 3.4 9.4 - - - +
6A ILE* 1.3 91.3 - - + +
8A LEU* 1.3 66.3 + - - +
9A HIS* 3.8 25.1 - - + +
10A GLU* 3.0 37.8 + - + +
11A ILE* 3.4 5.2 + - - +
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Residues in contact with LEU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE 3.7 2.2 + - - -
7A PRO* 1.3 72.2 - - - +
9A HIS* 1.3 63.2 + - - +
11A ILE* 3.2 34.2 + - + +
12A ILE* 3.0 34.8 + - + +
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Residues in contact with HIS 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO* 3.8 22.0 - - + +
8A LEU* 1.3 78.2 + - - +
10A GLU* 1.3 97.1 + - - +
12A ILE* 3.1 14.9 + - + +
13A ARG* 2.8 57.5 + - - +
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Residues in contact with GLU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.4 13.0 - - + -
7A PRO* 3.0 30.9 + - + +
9A HIS* 1.3 100.2 + - + +
11A ILE* 1.3 65.6 + - - +
13A ARG* 3.2 20.7 + - - +
14A LYS* 3.0 25.2 + - - +
17A ARG* 4.0 19.1 + - - -
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Residues in contact with ILE 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.5 22.4 - - + +
7A PRO 3.4 7.4 + - - +
8A LEU* 3.2 37.4 + - + +
10A GLU* 1.3 76.5 - - - +
12A ILE* 1.3 63.2 + - + +
14A LYS* 3.4 5.5 + - - +
15A LEU* 3.1 35.8 + - + +
15B LEU* 6.2 3.4 - - + -
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Residues in contact with ILE 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.0 33.8 + - + +
9A HIS* 3.1 15.9 + - + +
11A ILE* 1.3 78.6 - - + +
13A ARG* 1.3 60.6 + - + +
15A LEU* 3.5 8.2 + - - +
16A GLU* 3.0 44.4 + - + +
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Residues in contact with ARG 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A HIS* 2.8 46.9 + - - +
10A GLU* 3.2 22.0 + - - +
12A ILE* 1.3 78.6 - - + +
14A LYS* 1.3 57.2 + - - +
16A GLU* 3.3 15.6 + - - +
17A ARG* 2.9 53.8 + - - +
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Residues in contact with LYS 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU 3.0 16.1 + - - +
11A ILE* 3.8 6.5 - - - +
12A ILE 3.2 0.2 - - - -
13A ARG* 1.3 74.7 - - - +
15A LEU* 1.3 69.1 + - + +
17A ARG* 3.2 17.7 + - + +
18A MSE 2.9 45.8 + - - +
22B LYS* 4.7 7.0 - - - +
6C G 4.0 28.5 + - - -
7C C 3.7 28.8 + - - +
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Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.1 28.0 + - + +
12A ILE* 3.8 6.7 - - - +
14A LYS* 1.3 81.6 - - + +
16A GLU* 1.3 55.2 + - - +
18A MSE 3.2 33.1 + - + +
19A ASN* 2.8 31.1 + - - +
11B ILE* 5.9 4.3 - - + -
15B LEU* 3.9 29.2 - - + -
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Residues in contact with GLU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 3.0 33.3 + - + +
13A ARG* 3.5 18.7 - - - +
15A LEU* 1.3 73.6 - - - +
17A ARG* 1.3 65.1 + - - +
19A ASN* 3.5 7.6 + - + +
20A GLN* 3.1 34.3 + - - +
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Residues in contact with ARG 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU* 4.0 13.7 + - - -
13A ARG* 2.9 46.9 + - - +
14A LYS* 3.5 16.6 - - + +
16A GLU* 1.3 72.9 - - - +
18A MSE 1.3 62.4 + - + +
20A GLN* 3.4 16.8 - - - +
21A LYS* 3.2 29.7 + - - +
7C C 5.6 9.2 - - - +
8C A 5.2 11.4 - - - +
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Residues in contact with MSE 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LYS* 2.9 32.9 + - + +
15A LEU* 3.3 34.3 - - + +
17A ARG* 1.3 74.5 - - + +
19A ASN* 1.3 66.2 + - - +
21A LYS* 3.1 17.9 + - - +
22A LYS* 3.1 20.0 + - - +
15B LEU* 4.7 2.7 - - + -
18B MSE 3.4 41.1 - - + -
22B LYS* 3.9 27.8 - - - +
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Residues in contact with ASN 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU 2.8 19.9 + - - +
16A GLU* 3.9 8.2 - - + +
18A MSE 1.3 71.3 - - - +
20A GLN* 1.3 62.4 + - - +
22A LYS* 3.1 14.7 + - - +
23A GLN* 3.0 41.8 + - - +
5D A 4.5 11.3 + - - +
6D G 5.2 6.8 + - - -
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Residues in contact with GLN 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLU* 3.1 23.2 + - - +
17A ARG* 3.4 23.2 - - - +
19A ASN* 1.3 74.7 - - - +
21A LYS* 1.3 66.4 + - + +
23A GLN* 3.4 15.0 + - - +
24A ALA* 3.0 23.2 + - - +
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Residues in contact with LYS 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG* 3.2 17.0 + - - +
18A MSE 3.1 11.4 + - - +
20A GLN* 1.3 83.3 - - + +
22A LYS* 1.3 57.9 + - + +
24A ALA* 3.1 10.5 + - + +
25A GLN* 2.9 37.9 + - - +
28A ARG* 4.6 5.4 + - - +
8C A 3.9 31.9 + - - +
9C U 2.5 37.0 + - - +
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Residues in contact with LYS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A MSE 3.1 18.3 + - - +
19A ASN* 3.1 15.5 + - - +
21A LYS* 1.3 75.5 - - + +
23A GLN* 1.3 58.5 + - + +
25A GLN* 3.4 15.2 + - - +
26A ARG* 3.0 38.1 + - - +
14B LYS* 5.2 6.6 - - - +
18B MSE 3.4 37.0 - - - +
6D G 4.9 16.6 + - - +
7D C 4.7 12.1 + - - -
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Residues in contact with GLN 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ASN* 3.0 33.1 + - - +
20A GLN* 3.8 14.9 - - - +
22A LYS* 1.3 76.8 - - + +
24A ALA* 1.3 58.3 + - - +
26A ARG* 3.5 11.1 + - - +
27A LYS* 3.0 30.3 + - - +
4D C 4.4 10.7 + - - -
5D A 3.2 36.7 + - - +
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLN 3.0 16.8 + - - +
21A LYS* 3.1 11.9 + - + +
23A GLN* 1.3 75.3 - - - +
25A GLN* 1.3 58.9 + - - +
27A LYS* 3.3 8.8 + - - +
28A ARG* 2.9 50.1 + - - +
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Residues in contact with GLN 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 2.9 23.4 + - + +
22A LYS* 3.6 19.1 - - - +
24A ALA* 1.3 76.5 - - - +
26A ARG* 1.3 63.2 + - - +
28A ARG* 3.1 31.5 + - - +
29A HIS* 2.9 24.8 + - - +
10C U 2.8 27.6 + - + +
11C A 5.0 10.5 + - - +
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Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LYS* 3.0 30.1 + - - +
23A GLN* 3.9 12.1 - - - +
24A ALA 3.3 0.2 - - - -
25A GLN* 1.3 76.5 - - - +
27A LYS* 1.3 57.5 + - - +
29A HIS* 3.2 6.3 + - - +
30A LYS* 2.8 39.5 + - + +
4D C 5.4 6.5 - - - +
5D A 3.3 55.1 + - - +
6D G 3.0 55.6 + - - -
7D C 5.4 2.8 - - - +
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Residues in contact with LYS 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLN 3.0 18.4 + - - +
24A ALA* 3.6 7.6 - - - +
26A ARG* 1.3 78.4 - - - +
28A ARG* 1.3 63.8 - - + +
30A LYS* 3.6 12.6 - - - +
31A LEU* 3.1 55.5 + - + +
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Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 4.6 5.3 + - - +
24A ALA* 2.9 24.6 + - - +
25A GLN* 3.1 53.3 + - - +
27A LYS* 1.3 79.9 - - + +
29A HIS* 1.3 56.2 + - - +
31A LEU* 4.1 5.7 - - - +
32A ASN* 3.0 35.9 + - - +
9C U 5.5 3.2 + - - -
10C U 3.3 60.7 + - - -
11C A 3.1 38.5 + - - +
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Residues in contact with HIS 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLN 2.9 15.2 + - - +
26A ARG* 3.8 6.5 - - - +
28A ARG* 1.3 74.6 - - - +
30A LYS* 1.3 67.7 + - - +
32A ASN* 3.4 1.3 + - - +
33A ARG* 3.0 45.4 + - + +
11C A 5.6 1.3 - - - +
12C U 3.0 61.1 + + + +
13C G 2.8 57.5 + + - -
14C C 5.4 2.8 + - - -
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Residues in contact with LYS 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ARG* 2.8 26.3 + - + +
27A LYS* 3.6 14.4 - - - +
29A HIS* 1.3 77.7 - - - +
31A LEU* 1.3 71.3 + - - +
33A ARG* 3.2 11.9 + - - +
34A LYS* 3.0 29.3 + - + +
43A GLU* 5.8 4.0 - - - +
2D G 5.3 3.4 - - - -
3D A 2.8 32.2 + - - +
4D C 5.4 13.7 - - + +
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LYS* 3.1 46.2 + - + +
28A ARG* 4.2 4.9 - - - +
30A LYS* 1.3 93.0 - - + +
32A ASN* 1.3 68.4 + - - +
34A LYS* 3.7 18.2 - - + +
35A GLU* 3.1 25.8 + - - +
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Residues in contact with ASN 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG 3.0 19.6 + - - +
29A HIS 3.5 5.6 - - - +
31A LEU* 1.3 76.0 - - - +
33A ARG* 1.3 62.5 - - - +
35A GLU* 3.3 17.3 + - - +
36A ARG* 3.2 27.1 + - - +
11C A 3.0 34.6 + - - -
12C U 2.8 38.2 + - - +
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Residues in contact with ARG 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A HIS* 3.0 39.1 + - + +
30A LYS* 3.2 8.9 + - - +
32A ASN* 1.3 72.5 - - - +
34A LYS* 1.3 55.4 + - - +
36A ARG* 2.9 19.1 + - - +
37A GLY 2.8 30.0 + - - -
38A HIS* 2.9 42.8 + - + +
43A GLU* 2.8 38.0 + - - -
13C G 3.1 27.4 + - - +
14C C 2.3 51.7 + - - -
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Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LYS* 3.0 18.2 + - + +
31A LEU* 3.7 19.3 - - + +
33A ARG* 1.3 74.7 - - - +
35A GLU* 1.3 58.6 + - - +
37A GLY* 3.0 19.0 + - - +
38A HIS 4.5 2.4 + - - -
2D G 2.8 31.9 + - - +
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Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU 3.1 17.3 + - - +
32A ASN* 3.5 16.3 - - - +
33A ARG 3.1 0.2 - - - -
34A LYS* 1.3 82.6 - - - +
36A ARG* 1.3 63.0 + - + +
37A GLY 3.2 0.4 + - - -
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Residues in contact with ARG 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASN* 3.2 9.6 + - - +
33A ARG* 2.9 25.6 + - - +
35A GLU* 1.3 81.1 - - + +
37A GLY* 1.3 61.7 + - - +
38A HIS* 3.3 25.8 + - + +
12C U 2.6 37.0 + - - -
13C G 2.9 40.2 + - - -
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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