Contacts of the helix formed by residues 37 - 66 (chain a) in PDB entry 3J9X
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 VAL 37 (chain a).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1847 T 3.9 22.2 - - - +
1857 A 3.9 4.7 - - - +
16Z LYS* 4.7 9.6 - - + -
19Z ALA* 3.7 18.6 - - + -
20Z LYS* 3.6 31.2 - - + -
33a ILE 3.0 20.2 + - - +
34a LEU* 3.5 15.9 - - + +
36a ASN* 1.3 75.9 - - - +
38a SER* 1.3 69.7 + - - +
39a PRO* 3.5 1.3 - - - -
40a VAL* 3.3 8.7 + - + +
41a ALA* 2.9 19.5 + - + +
21b PHE* 4.5 9.2 - - + -
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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
----------------------------------------------------------
34a LEU 2.6 23.8 + - - -
35a SER* 3.3 15.2 - - - -
37a VAL* 1.3 81.1 - - - +
39a PRO* 1.4 73.7 - - - +
41a ALA* 2.9 9.7 + - - +
42a GLN* 2.9 27.1 + - - +
21b PHE* 3.5 21.8 - - - -
22b ASN* 5.5 2.5 + - - -
25b SER* 4.7 4.9 + - - -
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Residues in contact with PRO 39 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35a SER 4.0 4.5 - - - +
36a ASN 3.6 12.8 - - - +
37a VAL 3.5 1.3 - - - -
38a SER* 1.4 96.7 - - - +
40a VAL* 1.3 68.8 + - + +
42a GLN* 3.5 19.5 - - + +
43a GLN* 3.1 21.5 + - - +
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Residues in contact with VAL 40 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1847 T 4.8 2.0 - - - +
12Z GLN* 5.0 2.0 - - - +
15Z ALA* 4.1 30.3 - - + +
16Z LYS* 3.9 32.3 - - + +
19Z ALA* 4.5 3.6 - - + -
36a ASN 4.3 13.5 - - - +
37a VAL* 3.5 13.2 - - + +
38a SER 3.0 0.6 - - - -
39a PRO* 1.3 78.7 - - + +
41a ALA* 1.3 67.3 + - - +
43a GLN* 3.1 9.6 + - + +
44a ASN* 3.1 31.4 + - - +
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Residues in contact with ALA 41 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1837 A 3.9 4.4 - - - +
1847 T 3.5 39.7 - - - +
37a VAL 2.9 17.9 + - - +
38a SER 3.4 3.6 - - - +
40a VAL* 1.3 76.8 - - - +
42a GLN* 1.3 57.5 + - - +
44a ASN* 3.1 3.1 + - - +
45a PHE* 2.8 30.8 + - - +
17b TRP* 4.2 15.0 - - + -
21b PHE* 4.5 9.2 - - + -
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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
----------------------------------------------------------
38a SER* 2.9 21.7 + - - +
39a PRO* 3.5 29.9 - - - +
41a ALA* 1.3 76.4 - - - +
43a GLN* 1.3 62.9 + - - +
45a PHE* 3.3 1.0 + - - +
46a GLN* 2.9 35.3 + - - +
14b TYR* 3.9 8.7 + - - +
17b TRP* 4.2 13.2 - - + -
18b GLN* 3.2 41.6 - - - +
21b PHE* 5.6 1.1 - - + -
22b ASN* 4.6 2.6 + - - -
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Residues in contact with GLN 43 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434 GLN* 3.1 41.9 - - - +
115 SER* 5.1 10.3 - - - -
125 GLN* 6.1 2.8 - - - +
12Z GLN* 5.3 7.2 - - + +
39a PRO 3.1 10.6 + - - +
40a VAL* 3.3 11.2 - - - +
42a GLN* 1.3 80.6 - - - +
44a ASN* 1.3 60.6 + - - +
46a GLN* 3.7 11.1 + - - +
47a THR* 2.6 60.3 + - - +
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Residues in contact with ASN 44 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1837 A 3.6 24.4 - - - +
1847 T 2.9 20.0 + - - -
8Z ARG* 3.7 24.6 - - - +
12Z GLN* 2.9 34.7 + - - +
16Z LYS* 5.5 3.4 - - - +
40a VAL* 3.1 21.5 + - - +
41a ALA 3.1 7.5 + - - +
43a GLN* 1.3 76.4 - - - +
45a PHE* 1.3 64.7 + - - +
47a THR* 3.4 4.8 + - - -
48a ASN* 3.1 25.0 + - - +
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Residues in contact with PHE 45 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1827 T 4.5 10.3 - - - -
1837 A 3.5 28.0 - - - -
1688 T 5.3 6.5 - - - -
41a ALA 2.8 16.3 + - - +
42a GLN 3.7 3.6 - - - +
44a ASN* 1.3 76.7 - - - +
46a GLN* 1.3 59.1 + - - +
49a VAL* 2.9 69.1 + - + +
10b TYR* 5.1 0.9 - + - -
13b ARG* 4.4 6.1 - - + -
14b TYR* 3.5 43.5 - + + -
17b TRP* 3.5 56.8 - + + -
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Residues in contact with GLN 46 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115 SER* 2.8 29.8 + - - +
145 TYR* 6.2 2.2 - - - -
42a GLN* 2.9 27.6 + - - +
43a GLN* 3.8 12.7 + - - +
45a PHE* 1.3 79.3 - - - +
47a THR* 1.3 63.6 + - - +
50a PRO* 3.1 22.3 - - - +
10b TYR* 5.2 9.1 + - + +
14b TYR* 3.4 48.5 + - + -
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Residues in contact with THR 47 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95 SER* 5.5 11.5 - - - +
115 SER* 4.1 6.6 - - - -
12Z GLN* 4.9 12.7 + - - +
43a GLN* 2.6 47.0 + - - +
44a ASN* 3.7 6.3 - - - -
46a GLN* 1.3 80.4 - - - +
48a ASN* 1.3 72.1 + - - +
50a PRO* 4.3 2.4 - - - +
51a LYS* 3.4 24.4 - - - +
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Residues in contact with ASN 48 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1827 T 3.8 18.3 + - - +
1837 A 3.0 20.2 + - - -
7Z SER* 4.5 8.3 + - - -
8Z ARG* 3.8 13.5 - - - +
12Z GLN* 5.5 3.6 - - - +
44a ASN* 3.1 10.3 + - - +
47a THR* 1.3 86.3 - - - +
49a VAL* 1.3 66.4 + - - +
50a PRO* 3.4 1.3 - - - -
51a LYS* 2.9 49.7 + - + +
52a PHE* 3.4 11.9 - - + -
88a ASN* 4.9 5.4 + - - -
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Residues in contact with VAL 49 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1827 T 3.6 32.1 - - + +
45a PHE* 2.9 58.8 + - + +
48a ASN* 1.3 74.4 - - - +
50a PRO* 1.3 63.4 - - + +
51a LYS 3.0 0.2 - - - -
52a PHE* 2.9 26.8 + - + +
53a THR* 3.0 12.5 + - - +
10b TYR* 4.6 6.5 - - + -
13b ARG* 3.8 29.4 - - + +
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Residues in contact with PRO 50 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105 TYR* 4.9 13.2 - - + -
115 SER* 4.8 2.7 - - - +
506 PRO* 5.8 1.6 - - + -
546 SER* 5.3 1.0 - - - -
45a PHE 3.8 1.1 - - - +
46a GLN 3.1 26.9 - - - +
47a THR 4.2 2.5 - - - +
48a ASN 3.4 2.5 - - - -
49a VAL* 1.3 95.4 - - + +
51a LYS* 1.3 61.0 + - + +
53a THR* 3.7 1.8 - - - +
54a SER* 3.2 23.9 + - - -
10b TYR* 3.7 48.9 - - + -
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Residues in contact with LYS 51 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95 SER* 6.0 5.6 - - - -
576 GLU* 4.2 27.1 - - - +
47a THR* 3.4 23.8 + - - +
48a ASN* 2.9 35.5 + - - +
49a VAL 3.0 0.4 - - - -
50a PRO* 1.3 79.5 - - + +
52a PHE* 1.3 64.4 + - + +
54a SER* 2.9 18.8 + - - -
55a VAL* 3.3 13.5 - - - +
84a ALA* 5.5 0.4 - - - +
88a ASN* 3.9 27.4 + - - +
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Residues in contact with PHE 52 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1817 A 3.7 16.4 - - + +
1827 T 3.4 39.0 - - - +
48a ASN* 3.4 20.0 - - + -
49a VAL* 2.9 8.3 + - + +
51a LYS* 1.3 76.8 - - + +
53a THR* 1.3 67.1 + - - +
54a SER 3.2 1.3 - - - -
55a VAL* 3.1 6.7 + - + +
56a ASN* 2.9 27.9 + - - +
81a LEU* 3.7 30.6 - - + +
84a ALA* 3.6 25.6 - - + -
85a ARG* 3.6 14.1 - - - -
88a ASN* 3.3 31.4 - - - -
13b ARG* 4.5 5.8 - - - +
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Residues in contact with THR 53 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49a VAL* 3.0 7.6 + - - +
50a PRO 3.4 5.8 + - - -
52a PHE* 1.3 77.6 - - - +
54a SER* 1.3 63.6 + - - +
56a ASN* 3.1 9.5 + - + +
57a GLU* 3.0 23.3 + - + +
8b ARG 4.7 4.7 - - - +
9b SER* 4.2 7.0 - - - -
10b TYR* 3.1 46.0 - - + +
13b ARG* 2.7 30.1 + - - +
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Residues in contact with SER 54 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546 SER* 3.3 36.6 - - - -
576 GLU* 5.7 0.5 + - - -
586 ASN* 5.5 4.4 + - - -
50a PRO 3.2 9.6 + - - -
51a LYS* 2.9 21.8 + - - -
53a THR* 1.3 79.0 - - - +
55a VAL* 1.3 58.2 + - - +
57a GLU* 3.4 6.9 + - - +
58a ASN* 3.0 39.4 + - - -
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Residues in contact with VAL 55 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51a LYS 3.3 17.9 - - - +
52a PHE* 3.1 10.5 + - - +
53a THR 3.1 0.6 - - - -
54a SER* 1.3 77.3 + - - +
56a ASN* 1.3 60.7 + - - +
58a ASN* 3.3 2.9 + - - +
59a VAL* 2.8 51.8 + - + +
77a GLN* 5.2 1.1 - - - +
80a GLY 4.1 13.2 - - - +
81a LEU* 4.3 10.5 - - + +
84a ALA* 4.0 20.9 - - + -
125a ILE* 3.9 27.1 - - + -
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Residues in contact with ASN 56 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1698 A 4.8 4.6 + - - +
1708 T 4.1 35.4 + - - +
52a PHE* 2.9 17.4 + - - +
53a THR* 3.1 9.3 + - + +
55a VAL* 1.3 76.0 - - - +
57a GLU* 1.3 58.0 + - - +
60a SER* 2.9 30.7 + - - -
77a GLN* 3.1 21.2 + - - +
81a LEU* 3.3 30.6 - - - +
13b ARG* 4.0 21.6 - - - +
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Residues in contact with GLU 57 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53a THR* 3.0 13.8 + - + +
54a SER* 3.5 11.9 - - - +
56a ASN* 1.3 74.5 - - - +
58a ASN* 1.3 74.5 + - - +
60a SER* 3.2 8.2 + - - -
61a ALA* 3.0 23.6 + - + +
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Residues in contact with ASN 58 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546 SER* 5.3 4.8 + - - -
586 ASN* 4.2 20.4 - - - +
1246 ILE* 4.7 9.4 + - - +
1256 ILE* 4.8 9.5 - - - +
54a SER* 3.0 22.0 + - - +
55a VAL* 4.1 3.1 - - - +
57a GLU* 1.3 88.6 - - - +
59a VAL* 1.3 63.5 + - + +
61a ALA* 3.2 10.1 + - - +
62a VAL* 3.2 24.9 + - - +
124a ILE* 3.7 24.2 - - + +
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Residues in contact with VAL 59 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55a VAL* 2.8 36.8 + - + +
58a ASN* 1.3 73.4 - - + +
60a SER* 1.3 66.3 + - - +
62a VAL* 3.1 9.0 + - - +
63a LEU* 2.9 33.6 + - + +
76a TYR 4.3 1.6 - - - +
77a GLN* 3.3 32.5 - - - +
80a GLY* 4.7 2.2 - - - -
121a VAL* 4.0 38.1 - - + +
124a ILE* 5.5 3.4 - - + -
125a ILE* 4.4 7.4 - - + -
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Residues in contact with SER 60 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1708 T 4.9 0.4 - - - -
1718 A 3.4 9.6 + - - -
56a ASN 2.9 21.8 + - - -
57a GLU* 3.4 10.3 - - - -
58a ASN 3.2 0.2 - - - -
59a VAL* 1.3 76.8 - - - +
61a ALA* 1.3 62.6 + - - +
63a LEU* 3.1 2.8 + - - -
64a THR* 3.0 12.9 + - - -
73a ARG* 2.7 41.2 + - - +
77a GLN* 3.4 12.9 - - - +
89c ARG 4.7 2.8 + - - -
90c ILE 4.7 3.6 + - - -
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Residues in contact with ALA 61 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1256 ILE 6.1 0.9 - - - +
1266 THR 5.7 3.6 - - - +
57a GLU* 3.0 16.0 + - + +
58a ASN* 3.4 13.0 - - - +
60a SER* 1.3 75.4 - - - +
62a VAL* 1.3 64.1 + - + +
64a THR* 3.2 7.8 + - - -
65a GLN* 3.1 31.7 + - - +
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Residues in contact with VAL 62 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1266 THR 5.4 5.6 - - - +
1276 GLY* 5.7 0.4 - - - -
58a ASN 3.2 13.2 + - - +
59a VAL* 3.1 12.3 + - + +
61a ALA* 1.3 77.6 - - + +
63a LEU* 1.3 69.0 + - + +
65a GLN* 2.9 23.7 + - - +
66a TYR* 3.0 39.3 + - + -
117a VAL* 5.3 1.1 - - + +
120a ALA* 4.0 16.6 - - + +
121a VAL* 4.8 6.5 - - + +
124a ILE* 3.6 32.1 - - + -
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Residues in contact with LEU 63 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59a VAL* 2.9 35.2 + - + +
60a SER* 3.1 7.6 + - - +
62a VAL* 1.3 78.8 - - + +
64a THR* 1.3 61.3 + - - +
66a TYR* 3.2 2.9 + - - +
67a GLY 3.0 4.7 + - - -
68a ILE* 2.9 42.4 + - + +
73a ARG* 3.5 48.0 - - + +
76a TYR* 3.6 34.5 - - + -
77a GLN* 4.0 10.3 - - + +
117a VAL* 4.1 10.8 - - + -
121a VAL* 5.1 0.9 - - + -
----------------------------------------------------------
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Residues in contact with THR 64 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60a SER 3.0 6.1 + - - -
61a ALA* 3.6 9.8 - - - -
62a VAL 3.2 0.2 - - - -
63a LEU* 1.3 77.4 - - - +
65a GLN* 1.3 61.8 + - + +
67a GLY 3.1 9.5 + - - -
73a ARG* 3.0 21.9 + - - +
90c ILE* 2.6 33.9 + - + +
91c GLY 3.8 7.2 - - - +
92c SER 3.3 27.8 - - - +
93c GLY* 4.6 1.3 - - - -
94c PRO* 3.3 4.8 - - + +
95c ALA* 3.3 19.4 + - + +
----------------------------------------------------------
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Residues in contact with GLN 65 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926 SER* 5.8 5.3 - - - -
1266 THR* 3.9 22.7 + - - +
1276 GLY 5.8 0.7 - - - -
1286 SER* 4.9 4.8 + - - -
1346 SER* 3.7 29.9 + - - +
61a ALA* 3.1 18.4 + - - +
62a VAL* 2.9 16.7 + - - +
64a THR* 1.3 77.5 - - + +
66a TYR* 1.3 66.6 + - + +
94c PRO* 3.4 24.0 - - + +
----------------------------------------------------------
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Residues in contact with TYR 66 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62a VAL* 3.0 36.9 + - + +
63a LEU* 3.2 6.7 + - - +
65a GLN* 1.3 84.1 - - + +
67a GLY* 1.3 62.9 + - - +
68a ILE* 3.2 21.7 + - + +
116a GLN* 2.9 43.6 + - - -
117a VAL* 4.1 16.2 - - + -
120a ALA* 3.5 27.6 - - + +
94c PRO* 4.6 0.7 - - - -
----------------------------------------------------------
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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