Contacts of the helix formed by residues 18 - 44 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B PHE* 3.4 2.3 + - - +
17B LYS* 1.3 104.1 - - + +
19B ASP* 1.3 60.0 + - - +
20B ASP* 3.1 14.3 + - - +
21B GLN* 2.9 30.0 + - - +
22B LYS* 2.9 27.2 + - - +
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Residues in contact with ASP 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A THR* 4.8 2.9 - - - +
79A ALA* 6.1 1.3 - - - +
80A PHE* 3.9 6.1 - - - -
83A ARG* 3.1 35.6 + - - +
18B ASN* 1.3 71.2 - - - +
20B ASP* 1.3 63.0 + - - +
21B GLN 3.0 2.0 - - - -
22B LYS* 4.2 8.1 - - - +
23B SER* 2.4 66.9 + - - -
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Residues in contact with ASP 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LYS* 3.4 29.0 + - - +
49A LEU* 3.8 11.1 - - - +
50A ASP* 3.0 27.6 + - + +
83A ARG* 2.9 36.4 + - - -
18B ASN* 3.1 12.8 + - - +
19B ASP* 1.3 76.4 - - - +
21B GLN* 1.3 59.5 + - + +
24B ALA* 3.3 11.1 + - - +
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Residues in contact with GLN 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASP* 3.9 16.4 + - + +
53A GLN* 3.8 35.2 + - + +
15B ALA 4.4 1.0 - - - +
16B PHE* 3.7 12.8 - - + -
17B LYS* 2.9 47.1 + - - +
18B ASN* 2.9 21.0 + - - +
19B ASP 3.0 0.2 - - - -
20B ASP* 1.3 78.9 - - + +
22B LYS* 1.3 67.7 + - - +
23B SER 3.3 0.2 - - - -
24B ALA* 3.2 3.3 + - - +
25B TYR* 2.9 23.7 + - - +
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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
----------------------------------------------------------
68A LEU* 4.0 21.9 - - + +
72A GLU* 5.8 3.6 - - - +
75A GLN* 4.4 8.9 + - - -
76A THR* 3.6 28.7 + - + +
16B PHE* 3.9 34.3 - - + -
18B ASN 2.9 16.0 + - - +
19B ASP* 4.3 8.7 - - - +
21B GLN* 1.3 76.3 - - - +
23B SER* 1.3 57.6 + - - +
25B TYR* 3.3 3.6 + - - +
26B ALA* 2.9 27.2 + - - +
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Residues in contact with SER 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 4.0 4.7 - - - -
76A THR* 4.0 13.6 + - - +
77A LEU* 4.3 1.3 - - - +
80A PHE* 3.5 39.8 + - - +
19B ASP* 2.4 47.1 + - - -
22B LYS* 1.3 69.9 - - - +
24B ALA* 1.3 65.7 + - - +
26B ALA* 3.3 1.8 + - - +
27B LEU* 2.9 27.1 + - - +
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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
----------------------------------------------------------
49A LEU* 4.0 18.4 - - + +
50A ASP 3.3 30.3 - - - +
53A GLN* 4.0 0.9 - - + -
54A LEU* 3.5 19.2 - - + +
20B ASP 3.3 20.0 + - - +
21B GLN 3.2 4.6 + - - +
23B SER* 1.3 79.6 - - - +
25B TYR* 1.3 56.8 + - - +
27B LEU* 3.1 4.2 + - - +
28B GLY 2.8 25.6 + - - -
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Residues in contact with TYR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLN* 3.5 29.6 + - - +
56A ALA* 3.8 4.9 - - + -
57A GLY* 3.6 26.7 - - - -
60A ASP* 2.6 36.6 + - + +
66A SER* 3.8 11.4 - - - -
67A LYS* 2.8 52.0 + - + +
68A LEU* 3.9 13.0 - - + -
16B PHE* 3.5 20.9 - + + -
21B GLN 2.9 12.8 + - - +
22B LYS 3.6 7.6 - - - +
24B ALA* 1.3 76.6 - - - +
26B ALA* 1.3 58.9 + - - +
28B GLY* 3.2 1.4 + - - -
29B ALA* 2.8 29.0 + - + -
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 3.9 16.8 - - + -
73A ILE* 4.0 10.1 - - - +
76A THR* 3.6 24.0 - - + -
77A LEU* 3.7 15.9 - - + -
22B LYS 2.9 17.4 + - - +
23B SER 3.6 4.3 - - - +
25B TYR* 1.3 76.5 - - - +
27B LEU* 1.3 56.4 + - - +
29B ALA* 3.3 5.5 + - - +
30B SER* 2.9 30.5 + - - -
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A MSE 4.8 19.8 - - + +
38A SER* 6.1 0.4 - - - -
39A LEU* 4.5 8.1 - - + -
42A GLN* 3.7 18.2 - - - +
49A LEU* 3.5 30.3 - - + -
54A LEU* 4.3 7.9 - - + -
77A LEU* 3.7 23.5 - - + +
80A PHE* 4.0 11.0 - - + -
23B SER 2.9 15.6 + - - +
24B ALA 3.4 4.7 - - - +
26B ALA* 1.3 75.8 - - - +
28B GLY* 1.3 62.5 + - - +
30B SER* 3.3 8.9 + - - -
31B LEU* 3.2 19.6 + - - +
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Residues in contact with GLY 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.4 30.6 - - - +
58A VAL* 3.3 21.2 - - - -
24B ALA 2.8 11.3 + - - -
25B TYR 3.6 2.0 - - - -
27B LEU* 1.3 74.7 - - - +
29B ALA* 1.3 59.5 + - - +
31B LEU* 2.9 6.1 + - - +
32B GLY 2.8 23.9 + - - -
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Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLY* 3.3 21.0 - - - +
61A ALA* 3.3 9.4 - - + +
66A SER* 3.9 15.5 - - - +
73A ILE* 3.4 27.5 - - + +
25B TYR* 2.8 22.9 + - + +
26B ALA* 3.7 3.1 - - - +
28B GLY* 1.3 71.8 - - - +
30B SER* 1.3 57.1 + - - +
32B GLY 3.2 0.3 + - - -
33B ARG* 2.8 29.8 + - - +
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Residues in contact with SER 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 4.4 9.4 - - - +
77A LEU* 4.0 21.4 - - - +
26B ALA 2.9 14.1 + - - -
27B LEU* 3.4 12.6 - - - -
28B GLY 3.1 0.2 - - - -
29B ALA* 1.3 79.1 - - - +
31B LEU* 1.3 59.8 + - - +
33B ARG* 3.5 7.3 + - - +
34B TYR* 3.1 22.5 + - - +
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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
----------------------------------------------------------
31A LEU* 4.1 39.5 - - + +
34A TYR* 5.8 1.6 - - + -
35A MSE 4.5 32.8 - - + -
54A LEU* 5.5 0.2 - - + -
58A VAL* 4.0 18.2 - - + -
27B LEU 3.2 11.1 + - - +
28B GLY* 2.9 10.1 + - - +
30B SER* 1.3 74.5 - - - +
32B GLY* 1.3 67.4 + - - +
34B TYR* 3.1 11.9 + - + +
35B MSE 3.0 37.1 + - + +
58B VAL* 4.2 18.8 - - + -
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Residues in contact with GLY 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A VAL* 3.8 21.5 - - - +
61A ALA* 4.1 6.7 - - - -
62A PHE* 3.8 9.2 - - - -
28B GLY 2.8 13.7 + - - -
29B ALA 3.2 3.1 + - - -
31B LEU* 1.3 77.3 - - - +
33B ARG* 1.3 61.7 + - - +
35B MSE 3.3 15.4 + - - +
36B GLU* 3.1 22.5 + - - +
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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
----------------------------------------------------------
61A ALA* 4.0 11.4 + - + +
64A ASP* 5.3 4.9 + - - +
66A SER* 6.2 2.0 - - - -
70A ASP* 2.4 43.3 + - - -
73A ILE* 5.7 4.9 - - + -
29B ALA 2.8 17.2 + - - +
30B SER* 3.6 8.3 - - - +
32B GLY* 1.3 76.0 - - - +
34B TYR* 1.3 58.3 + - - +
36B GLU* 3.3 18.8 + - - +
37B ASN* 2.9 52.7 + - - +
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Residues in contact with TYR 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 5.7 3.1 - - + -
31A LEU* 4.1 32.3 - - + +
30B SER 3.1 15.0 + - - +
31B LEU* 3.1 16.6 + - + +
33B ARG* 1.3 77.4 - - - +
35B MSE 1.3 60.4 + - - +
37B ASN* 3.3 10.5 + - + +
38B SER* 2.9 50.4 + - - -
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Residues in contact with MSE 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 4.0 23.3 - - + -
58A VAL* 3.8 16.2 - - + -
62A PHE* 3.7 26.0 - - + -
31B LEU* 3.0 37.8 + - + +
32B GLY* 3.6 7.2 - - - +
33B ARG 3.3 0.2 - - - -
34B TYR* 1.3 79.1 - - + +
36B GLU* 1.3 55.3 + - - +
38B SER* 3.0 8.0 + - - -
39B LEU* 2.9 31.4 + - - +
54B LEU* 3.7 32.2 - - + +
55B ILE* 4.1 17.3 - - + -
58B VAL* 4.0 20.0 - - + -
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Residues in contact with GLU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ALA 4.1 5.0 - - - +
62A PHE* 4.1 19.0 - - + +
64A ASP* 2.7 40.0 - - - +
32B GLY 3.1 13.0 + - - +
33B ARG* 3.6 20.9 + - - +
35B MSE 1.3 76.3 - - - +
37B ASN* 1.3 64.4 + - - +
39B LEU* 3.2 15.9 + - + +
40B LYS* 3.0 47.2 + - + +
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Residues in contact with ASN 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG* 2.9 45.1 + - - +
34B TYR* 3.6 9.2 - - + +
36B GLU* 1.3 78.8 - - - +
38B SER* 1.3 60.6 + - - +
40B LYS* 3.3 27.8 + - - +
41B GLU* 3.2 27.2 + - + +
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Residues in contact with SER 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 5.9 5.8 - - - +
34B TYR* 2.9 39.9 + - - -
35B MSE 3.0 11.4 + - - -
37B ASN* 1.3 72.7 - - - +
39B LEU* 1.3 66.5 + - - +
41B GLU* 3.2 9.1 + - - +
42B GLN* 3.1 38.1 + - - +
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PHE* 3.7 33.7 - - + -
35B MSE 2.9 15.5 + - - +
36B GLU* 3.5 14.4 - - + +
38B SER* 1.3 75.8 - - - +
40B LYS* 1.3 57.6 + - + +
42B GLN* 3.1 21.8 + - - +
43B GLU* 2.9 44.3 + - - +
49B LEU* 4.0 24.5 - - + +
51B LYS* 3.9 30.7 - - + +
54B LEU* 4.2 14.4 - - + -
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Residues in contact with LYS 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG* 6.2 0.2 - - - +
36B GLU* 3.0 38.9 + - + +
37B ASN* 3.4 27.7 + - - +
39B LEU* 1.3 78.9 - - + +
41B GLU* 1.3 69.8 + - - +
43B GLU* 3.4 23.1 + - - +
44B LYS* 3.4 16.5 + - - +
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Residues in contact with GLU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASN 3.2 13.9 + - - +
38B SER* 3.2 9.5 + - - +
40B LYS* 1.3 83.7 - - - +
42B GLN* 1.3 63.7 + - + +
44B LYS* 2.7 56.3 + - + +
45B LEU* 3.7 11.3 - - - +
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Residues in contact with GLN 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 4.4 7.9 - - - +
38B SER* 3.1 27.5 + - - +
39B LEU* 3.5 22.8 - - - +
41B GLU* 1.3 75.4 - - + +
43B GLU* 1.3 60.0 + - - +
45B LEU* 2.9 25.7 + - - +
47B ILE* 2.9 36.1 + - + +
49B LEU* 3.4 29.5 - - - +
80B PHE* 3.7 31.2 - - + -
84B VAL* 4.9 10.5 - - + +
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Residues in contact with GLU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 2.9 35.6 + - + +
40B LYS* 3.8 15.9 - - - +
41B GLU 3.3 0.4 - - - -
42B GLN* 1.3 72.5 - - - +
44B LYS* 1.3 65.0 + - - +
45B LEU 2.9 2.0 - - - -
46B GLY* 2.9 15.6 + - - +
47B ILE 3.7 12.3 - - - +
48B LYS* 4.2 19.2 - - + +
51B LYS* 4.4 17.0 + - - -
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Residues in contact with LYS 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LYS 3.5 9.6 - - - +
41B GLU* 2.7 52.5 + - + +
42B GLN 3.2 0.2 - - - -
43B GLU* 1.3 77.4 - - - +
45B LEU* 1.3 64.8 + - + +
46B GLY 3.4 0.6 + - - -
91B LYS* 3.7 25.8 - - - +
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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
------------------------------------------------------------
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