Contacts of the helix formed by residues 22 - 52 (chain D) in PDB entry 1ZLL
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 GLN 22 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ILE* 5.9 1.9 - - - +
20D MET* 2.7 29.7 + - - +
21D PRO* 1.3 79.1 + - - +
23D GLN* 1.3 73.5 + - - +
24D ALA 2.9 0.7 - - - -
25D ARG* 2.5 53.3 + - - +
26D GLN* 3.4 11.9 + - - +
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Residues in contact with GLN 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D PRO* 2.3 39.2 + - + +
22D GLN* 1.3 81.0 + - - +
24D ALA* 1.3 61.7 - - - +
26D GLN* 3.6 13.3 + - - +
27D LYS* 3.0 43.3 + - + +
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Residues in contact with ALA 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D MET* 4.9 5.4 - - + -
21D PRO* 3.8 28.7 + - + +
22D GLN 2.6 5.7 + - - -
23D GLN* 1.3 75.3 - - - +
25D ARG* 1.3 59.0 + - - +
27D LYS* 4.5 6.7 - - - +
28D LEU* 2.7 53.0 + - + +
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Residues in contact with ARG 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ILE* 5.1 13.1 - - - +
20D MET* 3.4 32.5 - - + +
22D GLN* 2.5 36.5 + - - +
24D ALA* 1.3 75.6 - - - +
26D GLN* 1.3 81.7 + - - +
28D LEU* 3.8 3.1 - - - +
29D GLN* 3.2 37.8 + - + +
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Residues in contact with GLN 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D GLN* 3.4 15.7 + - - +
23D GLN* 4.2 13.6 + - - +
24D ALA 3.4 0.2 - - - -
25D ARG* 1.3 101.7 + - - +
27D LYS* 1.3 65.4 + - + +
28D LEU 3.1 1.0 + - - -
29D GLN* 3.3 11.7 + - - +
30D ASN* 3.3 14.0 + - - +
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Residues in contact with LYS 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D GLN* 3.0 34.9 + - + +
24D ALA* 4.1 4.9 - - - +
26D GLN* 1.3 78.3 - - + +
28D LEU* 1.3 58.6 + - + +
30D ASN* 5.2 2.5 - - - -
31D LEU* 2.8 57.0 + - + +
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Residues in contact with LEU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D MET* 5.3 7.9 - - + -
24D ALA* 2.7 46.0 + - + +
25D ARG* 3.8 4.7 - - - +
27D LYS* 1.3 72.5 - - + +
29D GLN* 1.3 60.1 + - + +
31D LEU* 4.5 4.5 - - + -
32D PHE* 2.6 42.0 + - + +
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Residues in contact with GLN 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 6.0 2.2 - - - +
34C ASN* 3.6 29.1 + - - +
25D ARG* 3.2 28.4 + - + +
26D GLN* 3.3 4.2 + - - +
28D LEU* 1.3 78.4 - - + +
30D ASN* 1.3 63.5 + - - +
32D PHE* 3.7 4.6 - - - +
33D ILE* 3.2 31.5 + - + +
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Residues in contact with ASN 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D GLN 3.3 12.4 + - - +
27D LYS* 4.3 2.2 - - - +
28D LEU 3.3 0.2 - - - -
29D GLN* 1.3 76.9 - - - +
31D LEU* 1.3 62.1 + - + +
32D PHE 3.0 1.0 + - - -
33D ILE* 3.2 17.1 + - - +
34D ASN* 2.0 39.4 + - - +
29E GLN* 4.1 14.9 + - - +
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Residues in contact with LEU 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LYS* 2.8 55.5 + - + +
28D LEU* 4.3 4.9 - - + +
30D ASN* 1.3 75.4 - - + +
32D PHE* 1.3 59.9 + - - +
34D ASN* 1.9 42.7 - - - +
35D PHE* 2.9 12.1 + - - +
25E ARG* 5.2 12.6 - - - +
29E GLN* 5.8 3.4 - - - +
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Residues in contact with PHE 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ASN 5.3 0.2 - - - -
37C LEU* 4.8 8.3 - - + -
38C ILE* 3.7 44.4 - - + -
41C CYS* 5.1 4.9 - - + -
28D LEU* 2.6 31.9 + - + +
29D GLN* 3.7 4.9 - - - +
31D LEU* 1.3 72.5 - - - +
33D ILE* 1.3 73.2 + - + +
35D PHE* 2.6 27.7 + + + +
36D CYS* 2.7 44.6 + - - -
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Residues in contact with ILE 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ASN* 5.4 15.0 - - + +
37C LEU* 5.2 15.7 - - + -
29D GLN* 3.2 20.1 + - + +
30D ASN* 3.2 12.0 + - - +
32D PHE* 1.3 84.6 - - + +
34D ASN* 1.3 67.3 + - - +
36D CYS* 2.8 24.1 + - + +
37D LEU* 3.1 25.5 + - + +
33E ILE* 6.0 5.4 - - + -
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Residues in contact with ASN 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ASN* 2.0 47.7 + - - +
31D LEU* 1.9 41.1 - - - +
33D ILE* 1.3 79.4 - - - +
35D PHE* 1.3 65.1 + - - +
36D CYS 3.3 0.2 + - - -
37D LEU* 3.3 14.4 + - + +
38D ILE* 3.3 27.1 + - + +
29E GLN* 4.8 17.0 - - - +
32E PHE* 4.8 9.8 - - + -
33E ILE* 5.7 6.3 - - + -
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Residues in contact with PHE 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D LEU 3.2 10.5 - - - +
32D PHE* 2.6 31.0 + + + +
34D ASN* 1.3 79.2 + - - +
36D CYS* 1.3 55.3 + - - -
38D ILE* 3.4 16.6 + - + +
39D LEU* 2.8 52.2 + - + +
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Residues in contact with CYS 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 4.5 16.2 - - + -
41C CYS* 4.6 7.6 - - - -
32D PHE* 2.7 79.5 + - - -
33D ILE* 2.8 10.4 + - - +
35D PHE* 1.3 70.4 - - - +
37D LEU* 1.3 67.3 + - + +
39D LEU* 2.9 10.4 + - - +
40D ILE* 2.8 39.1 + - + +
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Residues in contact with LEU 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 5.1 9.0 - - + -
33D ILE* 3.1 23.0 + - + +
34D ASN* 3.6 12.1 - - - +
36D CYS* 1.3 78.4 - - + +
38D ILE* 1.3 57.6 + - - +
40D ILE* 3.4 12.9 + - + +
41D CYS* 2.5 36.5 + - - -
32E PHE* 4.7 1.8 - - + -
33E ILE* 4.1 27.8 - - + -
36E CYS* 4.0 37.0 - - + -
37E LEU* 5.6 7.9 - - + -
40E ILE* 5.0 12.6 - - + -
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Residues in contact with ILE 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ASN* 3.3 11.4 + - + +
35D PHE* 3.8 18.8 - - + +
36D CYS 3.2 0.6 - - - -
37D LEU* 1.3 79.7 - - - +
39D LEU* 1.3 64.0 + - - +
41D CYS* 3.3 8.5 + - + +
42D LEU* 3.1 39.9 + - + +
32E PHE* 3.5 37.2 - - + -
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Residues in contact with LEU 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C CYS* 4.4 25.6 - - + -
45C ILE* 5.3 9.0 - - + -
35D PHE* 2.8 41.8 + - + +
36D CYS* 2.9 9.8 + - - +
38D ILE* 1.3 79.4 - - - +
40D ILE* 1.3 64.2 + - + +
41D CYS 3.2 0.2 + - - -
42D LEU* 3.5 2.5 + - - -
43D LEU* 2.9 58.4 + - + +
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Residues in contact with ILE 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 4.8 10.8 - - + -
40C ILE* 5.3 9.0 - - + -
41C CYS* 4.4 20.4 - - - -
44C LEU* 3.9 26.2 - - + -
36D CYS* 2.8 38.4 + - + +
37D LEU* 3.9 11.0 - - + +
39D LEU* 1.3 76.7 - - + +
41D CYS* 1.3 65.3 + - - +
43D LEU* 3.2 9.7 - - + +
44D LEU* 3.0 34.1 + - + +
40E ILE* 4.8 14.6 - - + -
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Residues in contact with CYS 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 2.5 34.1 + - - -
38D ILE* 3.5 11.2 - - + +
39D LEU 3.1 0.2 - - - -
40D ILE* 1.3 72.4 - - - +
42D LEU* 1.3 68.5 + - + +
43D LEU 2.6 5.3 + - - -
44D LEU* 3.0 21.4 + - - +
45D ILE* 3.1 20.4 + - + +
32E PHE* 6.2 1.3 - - - -
36E CYS* 5.3 5.4 - - - -
39E LEU* 3.8 31.0 - - + -
40E ILE* 4.2 17.0 - - - -
43E LEU* 6.1 1.3 - - - -
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Residues in contact with LEU 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ILE* 3.1 29.9 + - + +
39D LEU* 4.1 4.3 - - - +
41D CYS* 1.3 80.4 - - + +
43D LEU* 1.3 69.5 + - + +
45D ILE* 3.6 17.9 + - + +
46D CYS* 3.1 29.3 + - - -
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C CYS* 5.4 1.6 - - - +
44C LEU* 4.7 18.2 - - + -
45C ILE* 4.6 18.2 - - + -
48C ILE* 4.3 18.2 - - + -
39D LEU* 2.9 52.9 + - + +
40D ILE* 3.2 15.5 - - + +
41D CYS 2.6 5.1 + - - -
42D LEU* 1.3 78.2 - - + +
44D LEU* 1.3 69.9 + - + +
46D CYS* 2.7 28.4 + - - +
47D ILE* 3.2 10.7 + - + +
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Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 4.6 22.0 - - + -
40D ILE* 3.3 30.5 - - + +
41D CYS* 3.0 9.1 + - - +
43D LEU* 1.3 78.9 - - + +
45D ILE* 1.3 62.5 + - - +
47D ILE* 3.4 14.9 + - + +
48D ILE* 3.0 27.3 + - - +
40E ILE* 4.4 21.8 - - + +
43E LEU* 4.4 26.7 - - + -
44E LEU* 4.2 22.4 - - + -
47E ILE* 4.2 16.2 - - + +
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Residues in contact with ILE 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D CYS* 3.1 19.9 + - + +
42D LEU* 3.6 21.5 - - + +
43D LEU 2.8 0.6 + - - -
44D LEU* 1.3 76.8 - - - +
46D CYS* 1.3 64.8 + - - +
48D ILE* 3.1 11.5 + - + +
49D VAL* 2.9 37.6 + - + +
39E LEU* 6.1 2.5 - - + -
43E LEU* 4.6 17.7 - - + -
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Residues in contact with CYS 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ILE* 5.1 8.5 - - + -
42D LEU* 3.1 22.1 + - - -
43D LEU* 2.7 20.4 + - - +
45D ILE* 1.3 74.5 - - - +
47D ILE* 1.3 68.6 + - + +
49D VAL* 2.9 19.9 + - - +
50D MET* 3.1 18.4 + - + +
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Residues in contact with ILE 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 4.4 20.4 - - + -
47C ILE* 6.2 2.5 - - + -
48C ILE* 3.8 32.3 - - + -
51C LEU* 3.9 29.2 - - + -
43D LEU* 3.2 13.9 - - + +
44D LEU* 3.6 20.0 - - + +
46D CYS* 1.3 73.8 - - - +
48D ILE* 1.3 65.0 + - + +
50D MET* 2.9 21.7 + - + +
51D LEU* 3.1 21.1 + - + +
47E ILE* 5.8 8.3 - - + -
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Residues in contact with ILE 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D LEU 3.0 18.1 + - - +
45D ILE* 3.4 10.1 - - + +
46D CYS 3.1 0.2 - - - -
47D ILE* 1.3 76.4 - - - +
49D VAL* 1.3 68.0 + - + +
50D MET 2.8 1.4 + - - -
51D LEU* 2.8 21.1 + - + +
52D LEU* 3.2 26.5 + - + +
43E LEU* 3.6 31.0 - - + -
46E CYS* 4.7 6.3 - - + -
47E ILE* 3.8 39.0 - - + +
50E MET* 5.9 4.9 - - + -
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Residues in contact with VAL 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ILE* 2.9 32.9 + - + +
46D CYS* 3.4 10.3 - - - +
48D ILE* 1.3 79.0 - - + +
50D MET* 1.3 62.5 + - + +
52D LEU* 3.7 31.0 - - + +
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Residues in contact with MET 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ILE* 5.8 3.1 - - - -
51C LEU* 5.3 10.1 - - + +
52C LEU* 3.8 35.2 - - + -
46D CYS* 3.3 18.4 - - + +
47D ILE* 3.2 12.6 - - + +
48D ILE 2.8 1.8 + - - -
49D VAL* 1.3 81.0 - - + +
51D LEU* 1.3 68.8 + - + +
52D LEU 3.4 3.3 + - - -
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Residues in contact with LEU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 4.6 19.1 - - + -
47D ILE* 3.5 19.7 - - + +
48D ILE* 2.8 14.5 + - + +
50D MET* 1.3 76.7 - - + +
52D LEU* 1.3 70.8 + - + +
47E ILE* 4.6 15.3 - - + -
50E MET* 5.5 15.4 - - + +
51E LEU* 3.8 29.4 - - + -
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Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ILE* 3.2 29.1 + - + +
49D VAL* 3.7 31.0 - - + +
50D MET 3.2 4.6 - - - -
51D LEU* 1.3 85.7 - - + +
50E MET* 4.6 26.7 - - + -
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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