Contacts of the helix formed by residues 9 - 44 (chain A) in PDB entry 1ZXA
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 ALA 9 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LYS* 1.3 72.2 + - + +
11A ILE* 3.3 4.7 - - - +
12A LEU* 3.7 14.7 - - - +
13A MET* 2.9 34.4 + - + +
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Residues in contact with LYS 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 1.3 80.0 - - + +
11A ILE* 1.3 60.7 + - + +
13A MET* 3.8 4.7 - - - +
14A LEU* 2.8 32.2 + - - +
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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
----------------------------------------------------------
9A ALA 3.3 2.6 - - - +
10A LYS* 1.3 77.0 - - + +
12A LEU* 1.3 62.1 + - - +
14A LEU* 3.7 11.0 - - + +
15A LYS* 2.8 31.7 + - + +
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Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 3.3 18.1 + - - +
11A ILE* 1.3 79.5 - - - +
13A MET* 1.3 70.8 + - + +
15A LYS* 3.2 17.7 + - + +
16A GLU* 3.2 12.8 + - + +
12B LEU* 4.8 20.9 - - + -
15B LYS* 4.2 19.5 + - - +
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Residues in contact with MET 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 2.9 25.3 + - + +
10A LYS* 3.8 4.9 - - - +
12A LEU* 1.3 83.1 - - + +
14A LEU* 1.3 66.2 + - - +
16A GLU* 2.7 36.6 + - + +
17A GLU* 3.0 11.2 + - - +
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Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LYS 2.8 24.0 + - - +
11A ILE* 3.7 10.8 - - + +
13A MET* 1.3 72.5 - - - +
15A LYS* 1.3 63.5 + - - +
17A GLU* 3.2 22.6 + - + +
18A ARG* 2.9 25.0 + - + +
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Residues in contact with LYS 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 2.8 17.6 + - + +
12A LEU* 3.2 13.9 - - + +
13A MET 3.0 0.2 - - - -
14A LEU* 1.3 79.7 - - - +
16A GLU* 1.3 63.5 + - - +
18A ARG* 3.2 9.6 + - + +
19A ILE* 3.1 28.9 + - + +
12B LEU* 3.2 43.5 + - + +
15B LYS* 3.2 29.5 - - - +
16B GLU* 3.3 12.1 - - - +
19B ILE* 3.5 28.3 - - + -
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Residues in contact with GLU 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.2 9.7 + - + +
13A MET* 2.7 37.5 + - + +
15A LYS* 1.3 76.3 - - - +
17A GLU* 1.3 62.2 + - - +
19A ILE* 3.4 10.1 + - + +
20A LYS* 3.1 49.9 + - + +
15B LYS* 4.9 11.0 - - - +
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Residues in contact with GLU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A MET 3.0 9.8 + - - +
14A LEU* 3.6 25.6 - - + +
16A GLU* 1.3 76.2 - - - +
18A ARG* 1.3 64.9 - - - +
20A LYS* 4.8 5.8 - - - -
21A GLU* 2.7 60.3 + - + +
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Residues in contact with ARG 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 2.9 16.0 + - + +
15A LYS* 3.2 14.1 + - - +
17A GLU* 1.3 77.0 - - - +
19A ILE* 1.3 59.8 + - + +
21A GLU* 3.8 7.3 - - - +
22A LEU* 2.9 37.8 + - + +
25A ARG* 4.9 1.2 + - - -
19B ILE* 5.4 20.3 - - + +
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Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LYS* 3.1 18.5 + - + +
16A GLU* 3.7 8.1 - - + +
18A ARG* 1.3 74.1 - - + +
20A LYS* 1.3 74.3 + - + +
22A LEU* 2.6 22.0 + - + +
23A GLU* 2.8 13.7 + - + +
15B LYS* 4.2 26.2 - - + +
19B ILE* 3.9 36.3 - - + -
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Residues in contact with LYS 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 44.6 + - + +
17A GLU* 4.2 4.7 - - - +
19A ILE* 1.3 81.4 - - + +
21A GLU* 1.3 65.6 + - + +
23A GLU* 3.0 26.4 + - - +
24A LYS* 3.1 27.6 + - - +
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Residues in contact with GLU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU* 2.7 59.8 + - + +
18A ARG* 3.8 5.5 - - - +
19A ILE 2.9 1.4 + - - -
20A LYS* 1.3 74.7 - - + +
22A LEU* 1.3 65.7 + - - +
24A LYS* 2.9 25.2 + - + +
25A ARG* 3.1 44.9 + - - +
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 2.9 26.5 + - + +
19A ILE* 2.6 20.9 + - + +
21A GLU* 1.3 72.8 - - - +
23A GLU* 1.3 57.0 + - - +
25A ARG* 3.3 15.4 + - + +
26A LEU* 2.8 36.1 + - + +
19B ILE* 5.3 13.0 - - + -
22B LEU* 4.4 30.7 - - + -
26B LEU* 5.5 11.9 - - + -
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Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 2.8 12.5 + - + +
20A LYS* 3.0 20.3 + - - +
22A LEU* 1.3 81.2 - - - +
24A LYS* 1.3 59.3 + - + +
26A LEU* 3.7 10.0 - - + +
27A SER* 2.9 30.3 + - - -
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Residues in contact with LYS 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS* 3.1 23.5 + - - +
21A GLU* 2.9 16.4 + - + +
23A GLU* 1.3 80.9 + - + +
25A ARG* 1.3 62.4 + - + +
27A SER* 2.5 24.8 + - - -
28A GLU* 3.1 9.9 + - - +
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Residues in contact with ARG 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG 4.9 0.8 + - - -
21A GLU* 3.1 51.9 + - - +
22A LEU* 3.6 16.1 - - + +
24A LYS* 1.3 78.3 - - + +
26A LEU* 1.3 62.5 + - - +
28A GLU* 3.2 8.1 + - - +
29A LYS* 3.1 21.0 + - - +
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Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 2.8 25.4 + - + +
23A GLU* 3.7 9.6 - - + +
25A ARG* 1.3 77.9 - - - +
27A SER* 1.3 64.6 + - - +
29A LYS* 3.2 11.3 + - + +
30A GLU* 3.0 28.8 + - + +
22B LEU* 4.2 30.3 - - + -
25B ARG* 6.1 2.7 - - - +
26B LEU* 3.8 25.4 - - + -
29B LYS* 6.1 4.9 - - - -
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Residues in contact with SER 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 2.9 15.8 + - - -
24A LYS* 2.5 27.8 + - - -
26A LEU* 1.3 79.6 - - - +
28A GLU* 1.3 62.6 + - - +
30A GLU* 3.3 8.9 + - - +
31A GLU* 3.1 21.5 + - - +
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LYS 3.1 8.7 + - - +
25A ARG* 3.5 11.2 - - - +
27A SER* 1.3 85.6 + - - +
29A LYS* 1.3 62.9 + - - +
31A GLU* 3.2 24.7 + - - +
32A GLU* 3.1 21.0 + - - +
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Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG 3.1 12.3 + - - +
26A LEU* 3.2 17.2 + - + +
28A GLU* 1.3 78.0 - - - +
30A GLU* 1.3 63.7 + - - +
32A GLU* 2.9 24.5 + - + +
33A ILE* 3.0 25.2 + - + +
26B LEU* 6.1 4.3 - - + -
29B LYS* 5.9 2.2 - - + -
30B GLU* 6.1 1.2 - - - +
33B ILE* 3.3 33.5 - - + +
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Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 3.0 20.7 + - + +
27A SER* 3.6 11.2 - - - +
28A GLU 3.3 0.2 - - - -
29A LYS* 1.3 77.3 - - - +
31A GLU* 1.3 64.7 + - - +
33A ILE* 3.3 23.1 + - - +
34A GLN* 3.1 24.2 + - - +
25B ARG* 5.9 0.9 + - - -
29B LYS* 4.5 13.0 - - - -
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Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER 3.1 10.5 + - - +
28A GLU* 3.5 30.8 - - - +
29A LYS 3.2 0.2 - - - -
30A GLU* 1.3 79.9 - - - +
32A GLU* 1.3 62.3 + - - +
34A GLN* 3.3 16.5 + - - +
35A GLU* 3.0 22.5 + - + +
----------------------------------------------------------
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Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 3.1 11.8 + - - +
29A LYS* 2.9 22.0 + - + +
31A GLU* 1.3 74.7 - - - +
33A ILE* 1.3 70.0 + - + +
35A GLU* 2.9 36.0 + - - +
36A LEU* 2.9 24.8 + - + +
----------------------------------------------------------
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Residues in contact with ILE 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LYS* 3.0 21.1 + - + +
30A GLU* 3.7 24.7 - - - +
32A GLU* 1.3 76.4 - - + +
34A GLN* 1.3 58.1 + - - +
36A LEU* 3.5 6.6 + - - +
37A LYS* 3.0 32.1 + - + +
29B LYS* 3.8 33.9 - - + -
33B ILE* 4.2 26.0 - - + -
36B LEU* 6.0 6.0 - - + +
----------------------------------------------------------
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Residues in contact with GLN 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 3.1 13.4 + - + +
31A GLU* 3.5 21.1 + - + +
32A GLU 3.0 0.6 - - - -
33A ILE* 1.3 79.1 - - - +
35A GLU* 1.3 63.2 + - - +
37A LYS* 3.3 9.7 + - + +
38A ARG* 2.9 24.7 + - + +
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Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLU* 3.0 12.7 + - + +
32A GLU* 2.9 29.8 + - - +
34A GLN* 1.3 76.4 - - - +
36A LEU* 1.3 63.8 + - - +
38A ARG* 3.3 11.8 + - + +
39A LYS* 3.1 20.1 + - - +
----------------------------------------------------------
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLU* 2.9 26.4 + - + +
33A ILE* 3.9 6.5 - - - +
35A GLU* 1.3 78.6 - - - +
37A LYS* 1.3 63.9 + - - +
39A LYS* 3.1 17.4 + - + +
40A LEU* 3.2 31.0 + - + +
36B LEU* 4.5 21.1 - - + -
37B LYS* 5.8 9.6 - - - +
40B LEU* 4.8 11.2 - - + -
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Residues in contact with LYS 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 3.0 22.8 + - + +
34A GLN* 3.6 9.6 - - + +
36A LEU* 1.3 78.4 - - - +
38A ARG* 1.3 57.9 + - - +
40A LEU* 3.3 6.8 + - + +
41A HIS* 2.8 40.0 + - + +
36B LEU* 5.5 7.1 - - + +
----------------------------------------------------------
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Residues in contact with ARG 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLN* 2.9 15.4 + - + +
35A GLU* 3.5 14.1 - - - +
36A LEU 3.2 0.4 - - - -
37A LYS* 1.3 76.2 - - - +
39A LYS* 1.3 64.3 + - - +
41A HIS* 3.4 11.5 - - + +
42A LYS* 2.9 52.5 + - + +
----------------------------------------------------------
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Residues in contact with LYS 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU 3.1 11.3 + - - +
36A LEU* 3.1 17.8 + - + +
38A ARG* 1.3 77.9 - - - +
40A LEU* 1.3 71.5 + - + +
42A LYS* 3.4 21.3 + - - +
43A CYS* 2.9 38.7 + - - -
----------------------------------------------------------
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.2 34.3 + - + +
37A LYS* 3.9 8.3 - - + +
39A LYS* 1.3 85.7 - - + +
41A HIS* 1.3 63.1 + - - +
43A CYS* 3.3 14.4 + - + +
44A GLN* 3.2 32.6 + - + +
36B LEU* 5.0 15.7 - - + -
39B LYS* 6.0 4.0 - - - +
40B LEU* 4.0 32.8 - - + -
43B CYS* 5.7 3.8 - - - -
----------------------------------------------------------
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Residues in contact with HIS 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LYS* 2.8 29.9 + - + +
38A ARG* 3.2 15.2 + - + +
40A LEU* 1.3 80.0 - - - +
42A LYS* 1.3 71.5 + - + +
44A GLN* 3.4 20.6 + - - +
----------------------------------------------------------
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Residues in contact with LYS 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ARG* 2.9 52.4 + - + +
39A LYS* 3.9 23.5 + - - +
41A HIS* 1.3 80.5 - - + +
43A CYS* 1.3 70.7 + - - +
44A GLN 3.1 5.9 + - - -
----------------------------------------------------------
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Residues in contact with CYS 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS* 2.9 42.1 + - - -
40A LEU* 3.5 20.4 - - + +
41A HIS 3.3 0.2 - - - -
42A LYS* 1.3 81.1 - - - +
44A GLN* 1.3 64.2 + - + +
----------------------------------------------------------
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Residues in contact with GLN 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 3.2 19.6 + - + +
41A HIS* 3.8 16.4 + - - +
42A LYS 3.2 8.6 - - - -
43A CYS* 1.3 84.3 - - + +
39B LYS* 5.2 8.0 + - - -
----------------------------------------------------------
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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