Contacts of the helix formed by residues 18 - 44 (chain A) in PDB entry 1Q6H
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 ASN 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A PHE 3.4 1.4 - - - -
17A LYS* 1.3 85.6 + - - +
19A ASP* 1.3 61.2 + - - +
20A ASP* 3.2 11.5 + - - +
21A GLN* 2.8 53.3 + - - +
22A LYS* 2.8 28.9 + - - +
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Residues in contact with ASP 19 (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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18A ASN* 1.3 76.9 - - - +
20A ASP* 1.3 57.2 + - - +
22A LYS* 4.2 6.0 - - - +
23A SER* 2.7 61.8 + - - -
76B THR* 4.7 5.7 - - - +
79B ALA* 5.7 3.6 - - - +
80B PHE* 4.3 4.2 + - - -
83B ARG* 2.9 34.9 + - - +
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Residues in contact with ASP 20 (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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18A ASN* 3.2 10.3 + - - +
19A ASP* 1.3 78.2 - - - +
21A GLN* 1.3 60.8 + - - +
24A ALA* 3.2 12.1 + - - +
47B ILE* 4.7 0.5 - - - +
48B LYS* 3.6 28.2 + - - +
49B LEU* 3.8 10.7 - - - +
50B ASP* 3.2 26.7 + - + +
83B ARG* 3.2 35.5 + - - -
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Residues in contact with GLN 21 (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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15A ALA 4.0 2.3 - - - +
16A PHE* 3.8 12.1 - - + -
17A LYS* 2.9 44.1 + - - +
18A ASN* 2.8 26.3 + - - +
20A ASP* 1.3 77.7 - - + +
22A LYS* 1.3 59.9 + - - +
24A ALA 3.4 0.7 + - - -
25A TYR* 3.0 28.9 + - - +
50B ASP* 3.6 26.7 + - + +
53B GLN* 3.6 24.4 + - + +
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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
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16A PHE* 3.9 32.1 - - + +
18A ASN 2.8 19.5 + - - +
19A ASP* 4.1 6.5 - - - +
21A GLN* 1.3 70.7 - - - +
23A SER* 1.3 61.5 + - - +
25A TYR* 3.3 3.4 + - - +
26A ALA* 2.9 28.1 + - - +
68B LEU* 4.2 23.6 - - + +
72B GLU* 4.6 13.7 + - - +
76B THR* 3.7 27.4 + - + +
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Residues in contact with SER 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 ASP* 2.7 47.3 + - - -
22A LYS* 1.3 74.6 - - - +
24A ALA* 1.3 59.9 + - - +
26A ALA* 3.8 1.3 - - - +
27A LEU* 2.9 26.2 + - - +
49B LEU* 4.3 3.8 - - - -
76B THR* 3.7 15.6 + - - +
77B LEU* 4.4 2.3 - - - +
80B PHE* 3.6 41.1 - - - +
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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 ASP 3.2 22.8 + - - +
21A GLN 3.4 4.0 + - - +
22A LYS 3.2 0.4 - - - -
23A SER* 1.3 76.7 - - - +
25A TYR* 1.3 58.6 + - - +
27A LEU* 3.3 2.2 + - - +
28A GLY 2.9 24.4 + - - -
49B LEU* 4.0 19.4 - - + +
50B ASP 3.3 27.8 - - - +
53B GLN* 4.0 0.2 - - + -
54B LEU* 3.4 21.2 - - + +
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Residues in contact with TYR 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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16A PHE* 3.5 28.3 - + + -
21A GLN 3.0 17.0 + - - +
22A LYS 3.7 3.8 - - - +
24A ALA* 1.3 78.2 - - - +
26A ALA* 1.3 59.2 + - - +
28A GLY* 3.2 1.7 + - - -
29A ALA* 2.8 28.8 + - + +
53B GLN* 3.4 28.7 + - - +
56B ALA* 3.8 5.4 - - + -
57B GLY* 3.5 28.4 - - - -
60B ASP* 2.6 37.7 + - + +
66B SER* 3.5 11.9 - - - -
67B LYS* 2.9 39.7 + - + +
68B LEU* 3.8 14.6 - - + -
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Residues in contact with ALA 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 2.9 16.5 + - - +
23A SER 3.8 1.1 - - - +
25A TYR* 1.3 77.9 - - - +
27A LEU* 1.3 57.5 - - - +
29A ALA* 3.2 5.6 + - - +
30A SER* 2.8 31.2 + - - -
68B LEU* 4.2 15.0 - - + +
73B ILE* 4.0 13.4 - - - +
76B THR* 3.7 22.2 - - + -
77B LEU* 3.7 18.3 - - + +
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Residues in contact with LEU 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 SER 2.9 16.7 + - - +
24A ALA* 3.5 6.3 - - - +
25A TYR 3.2 0.2 - - - -
26A ALA* 1.3 77.3 - - - +
28A GLY* 1.3 63.0 + - - +
30A SER* 3.3 3.6 + - - -
31A LEU* 3.0 52.7 + - + +
34B TYR* 5.7 3.8 - - + -
38B SER* 5.9 5.6 - - - +
42B GLN* 4.4 7.2 - - - +
49B LEU* 4.3 12.1 - - + -
54B LEU* 4.0 10.3 - - + -
77B LEU* 3.6 15.6 - - + +
80B PHE* 3.8 33.0 - - + -
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Residues in contact with GLY 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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24A ALA 2.9 11.7 + - - -
25A TYR 3.7 1.8 - - - -
27A LEU* 1.3 75.8 - - - +
29A ALA* 1.3 57.8 + - - +
31A LEU* 3.1 3.0 + - - -
32A GLY 2.7 26.2 + - - -
54B LEU* 3.4 30.2 - - - +
58B VAL* 3.4 24.2 - - - +
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Residues in contact with ALA 29 (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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25A TYR* 2.8 21.2 + - + +
26A ALA* 3.7 5.2 - - - +
28A GLY* 1.3 72.3 - - - +
30A SER* 1.3 67.3 + - - +
33A ARG* 2.9 23.6 + - - +
57B GLY* 3.4 18.7 - - - +
61B ALA* 3.3 11.6 - - + +
66B SER* 4.1 12.1 - - - +
73B ILE* 3.9 25.7 - - + +
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Residues in contact with SER 30 (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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26A ALA 2.8 17.2 + - - -
27A LEU* 3.6 4.9 - - - -
29A ALA* 1.3 77.3 - - - +
31A LEU* 1.3 59.8 + - - +
33A ARG* 3.2 6.4 + - - +
34A TYR* 3.0 28.5 + - - +
73B ILE* 4.3 11.1 - - - +
77B LEU* 3.7 25.7 - - - +
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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 LEU* 3.0 41.7 + - + +
28A GLY* 3.5 9.6 - - - +
30A SER* 1.3 76.5 - - - +
32A GLY* 1.3 65.3 + - - +
34A TYR* 3.3 17.4 + - + +
35A MSE 3.0 22.7 + - - +
31B LEU* 4.1 23.3 - - + +
34B TYR* 4.1 24.0 - - + +
35B MSE 4.0 28.0 - - + -
54B LEU* 4.9 1.1 - - + -
58B VAL* 4.5 4.3 - - + -
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Residues in contact with GLY 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 GLY 2.7 19.7 + - - -
29A ALA 3.9 1.8 - - - -
31A LEU* 1.3 72.5 - - - +
33A ARG* 1.3 57.1 + - - +
35A MSE 3.3 7.9 + - - +
36A GLU* 2.8 29.3 + - - +
31B LEU* 5.4 0.2 - - - -
58B VAL* 4.0 20.1 - - - +
61B ALA* 3.9 14.1 - - - -
62B PHE* 3.8 7.9 - - - -
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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 ALA 2.9 17.9 + - - +
30A SER* 3.5 6.3 - - - +
32A GLY* 1.3 74.0 - - - +
34A TYR* 1.3 61.7 + - - +
36A GLU* 3.2 21.6 + - - +
37A ASN* 2.8 52.2 + - - +
61B ALA* 3.8 7.1 - - + +
70B ASP* 2.6 39.0 + - - -
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Residues in contact with TYR 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 SER 3.0 13.0 + - - +
31A LEU* 3.3 20.6 - - + +
33A ARG* 1.3 78.7 - - - +
35A MSE 1.3 84.8 + - + +
37A ASN* 3.5 7.8 + - + +
38A SER* 2.9 42.5 + - - -
31B LEU* 5.8 1.6 - - + -
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Residues in contact with MSE 35 (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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31A LEU 3.0 11.0 + - - +
32A GLY* 3.4 11.0 - - - +
34A TYR* 1.3 100.2 - - + +
36A GLU* 1.3 66.8 + - - +
38A SER* 3.1 11.6 + - - -
39A LEU* 3.0 32.4 + - - +
54A LEU* 3.8 42.4 - - + -
27B LEU* 4.8 24.5 - - + +
31B LEU* 4.5 30.5 - - + -
58B VAL* 6.3 0.2 - - + -
62B PHE* 4.1 10.1 - - + -
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Residues in contact with GLU 36 (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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32A GLY 2.8 17.1 + - - +
33A ARG* 3.6 22.9 - - - +
35A MSE 1.3 79.1 - - - +
37A ASN* 1.3 63.8 + - - +
39A LEU* 3.2 4.5 + - - +
40A LYS* 2.9 54.9 + - - +
51A LYS* 4.4 13.9 + - - +
61B ALA 4.1 9.6 - - - +
62B PHE* 3.9 20.6 - - + +
64B ASP* 2.2 40.3 - - - +
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Residues in contact with ASN 37 (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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33A ARG* 2.8 54.3 + - - +
34A TYR* 3.8 7.4 + - + +
36A GLU* 1.3 84.2 + - - +
38A SER* 1.3 60.5 - - - +
40A LYS* 3.2 20.2 + - - +
41A GLU* 3.1 27.6 + - + +
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Residues in contact with SER 38 (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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34A TYR* 2.9 36.6 + - - -
35A MSE 3.1 18.5 + - - -
37A ASN* 1.3 75.9 - - - +
39A LEU* 1.3 62.7 + - - +
41A GLU* 3.2 10.5 + - - +
42A GLN* 3.1 35.0 + - - +
27B LEU* 6.1 0.4 - - - -
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Residues in contact with LEU 39 (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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35A MSE 3.0 23.4 + - - +
36A GLU* 3.7 7.6 - - - +
38A SER* 1.3 74.0 - - - +
40A LYS* 1.3 59.9 + - - +
42A GLN* 3.2 30.1 + - - +
43A GLU* 2.8 31.1 + - - +
47A ILE 4.4 1.4 - - - +
49A LEU* 4.1 24.0 - - + +
51A LYS* 3.9 29.4 - - + +
54A LEU* 3.8 24.9 - - + -
27B LEU* 4.5 0.9 - - + -
62B PHE* 3.9 24.9 - - + -
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Residues in contact with LYS 40 (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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36A GLU* 2.9 49.5 + - - +
37A ASN* 3.2 22.4 + - - +
39A LEU* 1.3 75.0 - - - +
41A GLU* 1.3 67.6 + - - +
43A GLU* 3.2 28.7 + - - +
44A LYS* 3.3 19.5 + - - +
51A LYS* 4.7 8.6 - - - +
64B ASP* 5.4 0.6 + - - -
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Residues in contact with GLU 41 (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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37A ASN* 3.1 15.7 + - + +
38A SER* 3.2 9.2 + - - +
40A LYS* 1.3 77.5 - - - +
42A GLN* 1.3 66.4 + - + +
44A LYS* 3.2 48.4 + - - +
45A LEU* 3.6 13.6 - - + +
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Residues in contact with GLN 42 (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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38A SER* 3.1 25.8 + - - +
39A LEU* 3.5 21.0 - - - +
41A GLU* 1.3 77.5 - - + +
43A GLU* 1.3 57.4 + - - +
45A LEU* 2.8 30.3 + - - +
47A ILE* 3.1 32.5 + - + +
49A LEU* 3.3 24.3 - - - +
80A PHE* 3.4 33.1 - - + -
84A VAL* 4.7 11.0 - - + -
27B LEU* 3.7 15.0 - - - +
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Residues in contact with GLU 43 (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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39A LEU 2.8 12.9 + - - +
40A LYS* 3.2 26.1 + - - +
42A GLN* 1.3 77.5 - - - +
44A LYS* 1.3 60.4 + - + +
46A GLY* 3.0 14.6 + - - -
47A ILE 3.3 12.3 + - - +
48A LYS* 3.7 36.3 + - + +
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Residues in contact with LYS 44 (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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40A LYS* 3.3 15.0 + - - +
41A GLU* 3.2 41.7 + - - +
42A GLN 3.1 1.0 - - - -
43A GLU* 1.3 76.8 - - + +
45A LEU* 1.3 63.9 + - + +
46A GLY 3.4 0.2 - - - -
91A LYS* 3.4 26.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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