Contacts of the helix formed by residues 4 - 30 (chain A) in PDB entry 1JI5
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 4 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 1.3 90.9 + - - +
6A ILE* 3.2 36.0 - - + +
7A GLU* 3.5 23.6 + - + +
8A VAL* 3.7 10.6 + - - +
63A ILE* 5.8 2.2 + - - +
113A ILE* 4.1 9.4 - - - +
117A SER* 4.5 7.9 + - - -
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Residues in contact with VAL 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN* 1.3 85.2 + - - +
6A ILE* 1.3 61.4 + - - +
7A GLU 3.0 2.2 - - - -
8A VAL* 2.8 20.9 + - + +
9A LEU* 2.9 18.5 + - + +
63A ILE* 4.8 6.7 - - + -
110A GLY 5.4 0.2 - - - +
113A ILE* 3.4 28.7 - - + -
114A ALA* 4.2 10.3 - - + -
117A SER* 3.8 20.9 - - - -
119A ASP* 4.1 15.3 - - + +
122A THR* 3.7 30.7 - - + +
126A LEU* 6.1 0.2 - - + -
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Residues in contact with ILE 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN* 4.1 29.4 - - + +
5A VAL* 1.3 77.7 - - - +
7A GLU* 1.3 60.5 + - - +
9A LEU* 3.8 9.5 - - - +
10A ASN* 2.8 53.3 + - - +
60A ILE* 4.3 12.6 - - + -
63A ILE* 4.1 23.8 - - + +
64A GLY 4.6 2.9 - - - +
65A GLY* 3.5 30.1 - - - +
66A LYS 4.4 3.8 - - - +
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Residues in contact with GLU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN* 3.5 20.6 + - + +
5A VAL 3.0 0.8 - - - -
6A ILE* 1.3 86.4 - - - +
8A VAL* 1.3 65.5 + - + +
10A ASN* 3.4 16.4 + - - +
11A LYS* 3.1 23.4 + - - +
68A VAL* 5.6 2.1 - - - +
77A ILE* 4.4 12.3 - - - +
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Residues in contact with VAL 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN 3.8 7.4 - - - +
5A VAL* 2.8 7.7 + - + +
7A GLU* 1.3 77.1 - - + +
9A LEU* 1.3 66.3 - - + +
11A LYS* 3.1 8.7 + - - +
12A GLN* 3.1 25.0 + - + +
106A GLU 4.8 5.4 - - - +
107A LEU* 6.1 0.7 - - + -
110A GLY* 3.7 23.6 - - - +
113A ILE* 3.7 39.3 - - + -
126A LEU* 4.3 14.6 - - + -
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 2.9 17.6 + - + +
6A ILE 3.8 1.8 - - - +
8A VAL* 1.3 81.0 - - + +
10A ASN* 1.3 57.3 + - - +
12A GLN* 2.9 10.4 + - + +
13A VAL* 2.8 30.4 + - - +
56A ILE* 3.4 15.6 - - + +
59A ARG* 3.9 16.2 - - + -
60A ILE* 3.2 34.1 - - + -
63A ILE* 4.0 16.8 - - + -
122A THR* 3.5 35.7 - - + -
125A LEU* 5.6 0.7 - - + -
126A LEU* 3.8 22.9 - - + -
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Residues in contact with ASN 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 2.8 47.7 + - - +
7A GLU* 4.0 19.2 + - - +
8A VAL 3.3 0.2 - - - -
9A LEU* 1.3 72.9 - - - +
11A LYS* 1.3 61.4 + - - +
13A VAL* 3.5 7.4 - - - +
14A ALA* 3.1 17.7 + - - +
60A ILE* 3.5 6.4 - - - +
66A LYS 3.6 12.1 + - - -
67A PRO* 3.3 6.8 - - - +
68A VAL* 2.7 50.4 + - + +
77A ILE* 3.6 9.4 - - + +
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Residues in contact with LYS 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU 3.1 13.5 + - - +
8A VAL* 3.1 10.1 + - - +
10A ASN* 1.3 74.5 - - - +
12A GLN* 1.3 57.5 + - - +
14A ALA* 3.3 1.0 + - - +
15A ASP* 2.7 46.4 + - - +
77A ILE* 2.9 43.4 + - + +
78A SER 3.5 0.4 - - - -
79A SER* 3.0 36.7 - - - +
106A GLU* 2.9 43.1 - - - +
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Residues in contact with GLN 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 3.1 20.7 + - + +
9A LEU* 2.9 20.6 + - + +
11A LYS* 1.3 76.6 - - - +
13A VAL* 1.3 51.2 + - - +
15A ASP* 3.1 8.4 + - - +
16A TRP* 2.7 61.5 + - - -
56A ILE* 3.6 16.4 - - + -
103A MET* 2.9 38.4 + - - +
106A GLU* 5.3 5.9 + - - +
107A LEU* 3.8 24.0 - - + +
126A LEU* 5.4 2.9 - - + -
129A ILE* 3.8 9.5 - - - +
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Residues in contact with VAL 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU 2.8 20.7 + - - +
10A ASN* 3.5 17.7 - - - +
12A GLN* 1.3 76.7 - - - +
14A ALA* 1.3 56.3 + - - +
16A TRP* 3.7 4.3 - - - +
17A SER* 2.8 35.4 + - - +
53A ILE* 4.4 18.0 - - + +
56A ILE* 3.7 19.5 - - + -
57A ALA* 4.2 16.6 - - + +
60A ILE* 5.3 1.1 - - + -
67A PRO* 5.3 1.3 - - + -
68A VAL* 4.0 9.6 - - + +
74A TYR* 3.6 29.8 - - + +
28B TRP* 4.5 6.5 - - + -
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Residues in contact with ALA 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASN 3.1 11.1 + - - +
11A LYS 3.6 6.5 - - - +
13A VAL* 1.3 78.8 - - - +
15A ASP* 1.3 65.3 + - - +
17A SER* 3.1 3.8 + - - -
18A VAL* 3.0 26.3 + - - +
74A TYR* 3.4 44.3 - - + +
77A ILE* 3.9 10.8 - - + -
78A SER* 3.9 13.7 - - - +
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Residues in contact with ASP 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 2.7 46.6 + - - +
12A GLN* 3.6 12.9 + - - +
14A ALA* 1.3 73.3 - - - +
16A TRP* 1.3 59.2 + - - +
18A VAL* 2.9 5.9 + - - +
19A LEU* 2.8 31.7 + - - +
78A SER* 3.1 10.8 + - - -
79A SER* 3.1 29.8 + - - -
80A ILE* 3.7 16.7 - - + +
103A MET* 4.5 16.8 - - - +
106A GLU* 3.4 8.5 - - - +
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Residues in contact with TRP 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLN* 2.7 50.6 + - - +
13A VAL 3.8 1.3 - - - +
15A ASP* 1.3 72.8 - - - +
17A SER* 1.3 56.4 + - - +
19A LEU* 3.2 24.3 + - + +
20A PHE* 2.8 29.8 + - - +
23A LEU* 5.7 0.7 - - + -
45A LEU 5.5 0.4 - - - -
48A GLU* 6.2 0.4 - - + -
49A SER* 3.7 29.3 - - - +
52A HIS* 3.6 36.4 - + + +
53A ILE* 3.7 23.4 - - + +
56A ILE* 3.6 21.2 - - + +
100A TYR* 4.2 14.8 - + - -
103A MET* 3.3 24.3 - - + +
129A ILE* 3.6 13.1 - - + +
132A GLU* 4.7 0.4 - - - -
133A LEU* 3.6 24.9 - - + -
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Residues in contact with SER 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 2.8 25.1 + - - +
14A ALA 3.4 5.2 - - - -
16A TRP* 1.3 75.4 - - - +
18A VAL* 1.3 64.7 + - - +
20A PHE* 3.2 15.8 - - - +
21A THR* 3.4 10.4 + - - -
53A ILE* 3.7 7.9 - - - +
74A TYR* 3.5 32.1 + - - -
71B MET* 4.2 4.1 - - - +
2001B MPD 3.1 34.2 - - - +
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Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA 3.1 15.0 - - - +
15A ASP 2.9 5.8 + - - +
17A SER* 1.3 74.3 - - - +
19A LEU* 1.3 67.3 + - - +
21A THR* 3.0 5.4 + - - -
22A LYS* 2.8 20.9 + - + +
74A TYR* 4.8 5.6 - - + +
75A LEU* 4.9 7.2 - - + -
78A SER* 3.2 26.2 - - - +
80A ILE* 3.9 30.1 - - + +
82A GLU* 4.0 28.3 - - + +
71B MET* 4.2 17.9 - - - -
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Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASP 2.8 30.8 + - - +
16A TRP* 3.4 36.3 - - + +
18A VAL* 1.3 76.6 - - - +
20A PHE* 1.3 54.1 + - - +
22A LYS* 4.1 10.1 - - + -
23A LEU* 2.7 52.2 + - + +
49A SER* 4.6 0.2 - - - -
80A ILE* 4.0 25.4 - - + -
96A ILE* 5.2 6.1 - - + -
99A ASP* 4.1 28.3 - - + +
100A TYR* 4.6 12.6 - - + -
103A MET* 4.4 11.4 - - - -
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Residues in contact with PHE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP 2.8 12.4 + - - +
17A SER 3.2 12.6 - - - +
18A VAL 3.1 0.2 - - - -
19A LEU* 1.3 76.6 - - - +
21A THR* 1.3 59.3 + - - +
23A LEU* 3.5 2.6 + - - +
24A HIS* 2.7 60.3 + + - -
46A TYR* 3.6 13.4 - + - +
49A SER* 3.5 22.6 + - - +
50A ALA* 4.0 17.7 - - + -
53A ILE* 4.3 6.1 - - + -
20B PHE* 3.4 35.7 - + - -
50B ALA* 4.7 9.2 - - + -
53B ILE* 4.7 5.8 - - + -
2001B MPD 3.5 39.7 - - + -
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Residues in contact with THR 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER 3.4 4.5 + - - -
18A VAL 3.0 6.1 + - - -
20A PHE* 1.3 76.4 - - - +
22A LYS* 1.3 67.1 + - - +
24A HIS* 3.0 10.5 + - + +
25A ASN* 2.9 21.5 + - - +
82A GLU* 4.6 3.6 - - - +
69B ALA* 3.9 20.0 - - + +
70B THR* 4.1 6.5 - - - +
71B MET* 3.5 10.5 - - - +
74B TYR* 3.5 32.5 - - + +
2001B MPD 3.2 30.9 - - + +
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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
----------------------------------------------------------
18A VAL* 2.8 16.2 + - + +
19A LEU* 3.6 11.0 - - + +
21A THR* 1.3 77.6 - - - +
23A LEU* 1.3 57.7 + - + +
25A ASN* 3.3 9.4 - - + +
26A PHE* 3.1 63.2 + - + -
80A ILE* 4.1 10.4 - - + +
81A GLN* 4.0 10.7 - - - +
82A GLU* 3.8 46.0 + - + +
83A ALA 5.1 4.0 - - - +
84A ALA* 5.9 0.7 - - - -
87A GLU* 5.4 2.7 - - - -
95A ALA* 4.8 8.6 + - - +
96A ILE* 5.1 3.1 - - + -
99A ASP* 2.8 33.4 + - - +
69B ALA 5.3 2.0 - - - -
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP* 5.7 0.2 - - + -
19A LEU* 2.7 37.8 + - + +
20A PHE 3.8 0.2 - - - +
22A LYS* 1.3 70.7 - - - +
24A HIS* 1.3 57.4 + - - +
26A PHE* 3.5 3.0 + - - -
27A HIS* 2.8 31.7 + - - +
42A PHE* 3.7 24.4 - - + +
45A LEU* 3.5 29.2 - - + +
46A TYR* 3.4 44.0 - - + +
49A SER* 4.2 5.6 - - - -
96A ILE* 4.1 26.2 - - + -
100A TYR* 4.5 7.4 - - + +
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Residues in contact with HIS 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 2.7 60.6 + + - -
21A THR* 3.0 12.9 + - + +
23A LEU* 1.3 73.5 - - - +
25A ASN* 1.3 56.7 + - - +
27A HIS* 3.0 8.7 + - - +
28A TRP* 2.7 78.6 + + + -
46A TYR* 3.4 40.3 + + - -
50B ALA* 5.1 6.3 + - - +
53B ILE* 4.2 12.7 - - + +
54B ASP* 4.5 6.8 - - + +
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Residues in contact with ASN 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR 2.9 9.7 + - - +
22A LYS* 3.3 13.2 - - + +
24A HIS* 1.3 76.1 - - - +
26A PHE* 1.3 68.4 + - + +
28A TRP* 3.0 6.4 + - - -
29A TYR* 2.7 48.6 + - - +
83A ALA 4.7 11.1 + - - -
84A ALA 4.8 4.5 - - - +
85A TYR* 3.7 25.0 - - - +
92A MET* 4.5 1.7 - - - +
69B ALA* 2.8 45.3 + - + +
70B THR* 5.0 0.2 - - - +
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Residues in contact with PHE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 3.1 40.6 + - + +
23A LEU* 3.8 4.5 - - - +
25A ASN* 1.3 86.9 - - - +
27A HIS* 1.3 63.0 + - - +
30A VAL* 3.1 30.0 + - - +
42A PHE* 3.4 23.6 - + + -
83A ALA 4.7 1.6 - - - -
87A GLU* 3.3 27.4 - - - -
92A MET* 3.3 55.9 - - + -
95A ALA* 3.8 11.0 - - + -
96A ILE* 3.4 26.9 - - + -
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Residues in contact with HIS 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU 2.8 16.9 + - - +
24A HIS* 3.1 13.9 - - - +
26A PHE* 1.3 79.7 - - - +
28A TRP* 1.3 73.1 + + - +
30A VAL* 3.7 6.1 - - - +
35A PHE* 5.0 0.5 - - - -
39A HIS* 2.7 74.1 + + - -
42A PHE* 3.7 11.4 - - + -
43A GLU* 3.7 25.0 + - + +
46A TYR* 3.7 17.3 + + + -
54B ASP* 3.3 14.4 - - - -
58B GLU* 3.2 3.4 + - - -
151B FE 2.1 31.4 - - - -
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Residues in contact with TRP 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A HIS* 2.7 55.6 + + + +
25A ASN* 3.6 7.2 - - - +
27A HIS* 1.3 88.0 - + - +
29A TYR* 1.3 62.6 + - + +
30A VAL* 3.5 3.5 + - - +
31A LYS* 5.0 2.6 + - - -
35A PHE* 5.3 0.7 - - - -
13B VAL* 4.4 2.9 - - + -
53B ILE* 3.4 28.9 - - + -
54B ASP* 2.6 22.4 + - - -
57B ALA* 3.2 31.9 - - + +
58B GLU* 3.9 16.1 - - + +
61B LEU* 3.3 34.7 - - + +
67B PRO* 4.2 16.8 - - + -
68B VAL 3.8 9.6 - - - -
69B ALA* 4.1 10.3 - - + -
74B TYR* 3.7 21.3 - - - -
138C TRP* 4.4 7.8 + - - -
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Residues in contact with TYR 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASN* 2.7 44.8 + - - +
28A TRP* 1.3 74.8 - - + +
30A VAL* 1.3 67.2 + - - +
31A LYS* 3.3 28.5 + - - +
85A TYR* 3.7 35.2 - + - +
87A GLU 5.1 3.3 - - - +
92A MET* 3.9 16.2 - - + +
61B LEU* 4.8 5.2 - - + -
66B LYS* 2.9 33.8 - - + +
67B PRO* 2.6 56.6 + - + -
69B ALA* 4.3 2.7 - - + -
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE 3.1 20.8 + - - +
27A HIS 3.7 12.1 - - - +
28A TRP 4.4 1.7 - - - +
29A TYR* 1.3 78.1 - - - +
31A LYS* 1.3 73.6 + - - +
35A PHE* 3.4 35.8 - - + +
38A LEU* 4.0 22.0 - - + -
39A HIS* 4.0 16.8 - - - +
42A PHE* 4.1 6.7 - - + -
89A ALA* 4.0 24.2 - - + -
92A MET* 3.9 12.7 - - - +
142C ALA* 4.2 1.9 - - - +
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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