Contacts of the helix formed by residues 4 - 30 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 1.3 91.6 + - - +
6B ILE* 3.9 33.2 - - + +
7B GLU* 3.5 25.6 + - + +
8B VAL* 3.7 10.6 + - - +
63B ILE* 5.8 2.2 + - - +
113B ILE* 4.0 8.3 - - - +
117B SER* 4.6 7.3 + - - -
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Residues in contact with VAL 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLN* 1.3 88.8 + - - +
6B ILE* 1.3 67.2 + - - +
7B GLU 3.0 2.2 - - - -
8B VAL* 2.8 15.7 + - + +
9B LEU* 3.0 18.0 + - + +
63B ILE* 4.8 5.8 - - + -
110B GLY 5.4 0.7 - - - +
113B ILE* 3.4 27.8 - - + -
114B ALA* 4.2 9.6 - - + -
117B SER* 3.8 21.3 - - - +
119B ASP* 4.2 15.5 - - + +
122B THR* 3.8 31.0 - - + +
126B LEU* 6.1 0.2 - - + -
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Residues in contact with ILE 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLN* 4.1 27.6 - - + +
5B VAL* 1.3 79.6 - - - +
7B GLU* 1.3 60.1 + - - +
9B LEU* 3.7 8.9 - - - +
10B ASN* 2.8 55.0 + - - +
60B ILE* 4.3 11.7 - - + -
63B ILE* 4.0 21.5 - - + +
64B GLY 4.5 3.1 - - - +
65B GLY* 3.3 33.2 - - - +
66B LYS 4.4 3.6 - - - +
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Residues in contact with GLU 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLN* 3.5 21.7 + - + +
5B VAL 3.0 0.8 - - - -
6B ILE* 1.3 83.8 - - - +
8B VAL* 1.3 65.1 + - - +
10B ASN* 3.9 17.9 + - - +
11B LYS* 3.1 23.2 + - - +
77B ILE* 4.3 12.5 - - - +
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Residues in contact with VAL 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLN 3.8 7.2 - - - +
5B VAL* 2.8 7.5 + - + +
7B GLU* 1.3 76.1 - - + +
9B LEU* 1.3 67.8 + - + +
11B LYS* 3.1 9.7 + - - +
12B GLN* 3.0 24.9 + - + +
106B GLU 4.7 5.6 - - - +
107B LEU* 6.1 1.1 - - + -
110B GLY* 3.6 24.5 - - - -
113B ILE* 3.7 38.6 - - + -
126B LEU* 4.4 13.9 - - + -
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Residues in contact with LEU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 3.0 14.9 + - + +
6B ILE 3.7 4.7 - - - +
8B VAL* 1.3 79.9 - - + +
10B ASN* 1.3 55.9 - - - +
12B GLN* 2.9 10.2 + - + +
13B VAL* 2.8 30.1 + - - +
56B ILE* 3.4 17.2 - - + +
59B ARG* 3.9 16.2 - - + -
60B ILE* 3.1 37.5 - - + +
63B ILE* 4.1 12.3 - - + -
122B THR* 3.5 34.8 - - + -
125B LEU* 5.5 0.4 - - + -
126B LEU* 3.7 23.3 - - + -
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Residues in contact with ASN 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 2.8 47.8 + - - +
7B GLU* 4.0 19.2 + - - +
8B VAL 3.3 0.2 - - - -
9B LEU* 1.3 73.3 - - - +
11B LYS* 1.3 61.1 + - - +
13B VAL* 3.4 7.6 + - - +
14B ALA* 3.1 19.9 + - - +
60B ILE* 3.5 6.3 - - - +
66B LYS 3.5 12.1 + - - -
67B PRO* 3.2 6.6 - - - +
68B VAL* 2.7 53.1 + - + +
77B ILE* 3.7 4.6 - - + +
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Residues in contact with LYS 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLU 3.1 14.2 + - - +
8B VAL* 3.5 10.1 - - - +
10B ASN* 1.3 74.9 - - - +
12B GLN* 1.3 55.7 + - - +
14B ALA* 3.3 0.9 + - - +
15B ASP* 2.8 46.5 + - - +
77B ILE* 2.9 43.0 + - + +
78B SER 3.5 0.2 - - - -
79B SER* 3.0 35.8 - - - +
106B GLU* 2.8 43.7 - - - +
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Residues in contact with GLN 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 3.0 20.9 + - + +
9B LEU* 2.9 20.8 + - + +
11B LYS* 1.3 77.5 - - - +
13B VAL* 1.3 51.0 + - - +
15B ASP* 3.2 8.0 + - - +
16B TRP* 2.7 64.2 + - - -
56B ILE* 3.6 20.0 - - + +
103B MET* 2.9 37.6 + - - +
106B GLU* 5.3 7.1 + - - +
107B LEU* 3.9 18.0 - - + +
126B LEU* 5.4 3.1 - - + -
129B ILE* 3.9 9.4 - - - +
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Residues in contact with VAL 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TRP* 4.4 6.3 - - + -
9B LEU 2.8 19.7 + - - +
10B ASN* 3.5 18.2 - - - +
12B GLN* 1.3 76.6 - - - +
14B ALA* 1.3 57.7 + - - +
16B TRP* 3.7 5.8 - - - +
17B SER* 2.8 35.9 + - - +
53B ILE* 4.4 17.1 - - + +
56B ILE* 3.7 18.6 - - + -
57B ALA* 4.2 16.6 - - + +
60B ILE* 5.3 1.3 - - + -
67B PRO* 5.3 1.6 - - + -
68B VAL* 4.0 9.6 - - + +
74B TYR* 3.6 29.6 - - + +
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Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASN 3.1 11.7 + - - +
11B LYS 3.6 7.0 - - - +
12B GLN 3.3 0.2 - - - -
13B VAL* 1.3 79.9 - - - +
15B ASP* 1.3 63.6 + - - +
17B SER* 3.1 3.3 + - - -
18B VAL* 3.0 26.3 + - - +
74B TYR* 3.5 43.5 - - + +
77B ILE* 3.9 17.5 - - + -
78B SER* 3.9 5.8 - - - +
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Residues in contact with ASP 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LYS* 2.8 45.0 + - - +
12B GLN* 3.6 13.5 + - - +
14B ALA* 1.3 73.3 - - - +
16B TRP* 1.3 58.1 + - - +
18B VAL* 3.0 6.4 + - - +
19B LEU* 2.9 32.1 + - - +
78B SER* 3.1 10.6 + - - -
79B SER* 3.0 31.8 + - - -
80B ILE* 3.7 16.0 - - + +
103B MET* 4.5 17.0 - - - +
106B GLU* 3.5 7.8 - - - +
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Residues in contact with TRP 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLN* 2.7 49.6 + - - +
13B VAL 3.8 1.1 - - - +
15B ASP* 1.3 74.3 - - - +
17B SER* 1.3 57.0 + - - +
19B LEU* 3.2 22.4 + - + +
20B PHE* 2.8 29.6 + - - +
23B LEU* 5.7 0.7 - - + -
45B LEU 5.5 0.9 - - - -
48B GLU* 6.2 0.4 - - + -
49B SER* 3.7 29.7 - - - +
52B HIS* 3.6 30.2 - + + +
53B ILE* 3.6 22.1 - - + +
56B ILE* 3.5 22.2 - - + +
100B TYR* 4.3 14.4 - + - -
103B MET* 3.3 25.0 - - + +
129B ILE* 3.6 19.4 - - + +
132B GLU* 4.6 0.4 - - - -
133B LEU* 3.6 25.6 - - + -
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Residues in contact with SER 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A MET* 4.4 1.8 - - - -
13B VAL* 2.8 26.0 + - - +
14B ALA 3.4 4.9 - - - -
16B TRP* 1.3 75.6 - - - +
18B VAL* 1.3 63.3 + - - +
20B PHE* 3.2 8.0 - - - +
53B ILE* 3.7 20.9 - - - +
74B TYR* 3.5 41.5 + - - -
2001B MPD 2.5 34.3 + - - +
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A MET* 4.2 16.6 - - - -
14B ALA 3.0 15.0 + - - +
15B ASP 3.0 6.2 + - - +
17B SER* 1.3 74.3 - - - +
19B LEU* 1.3 66.4 + - - +
21B THR* 3.0 5.2 + - - -
22B LYS* 2.8 22.9 + - + +
74B TYR* 4.7 5.6 - - + +
75B LEU* 5.0 6.1 - - + -
78B SER* 3.2 27.4 - - - +
80B ILE* 3.9 27.6 - - + +
82B GLU* 4.0 31.4 - - + +
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASP 2.9 29.7 + - - +
16B TRP* 3.4 35.2 - - + +
18B VAL* 1.3 77.1 - - - +
20B PHE* 1.3 54.9 + - - +
22B LYS* 3.1 9.0 + - + -
23B LEU* 2.7 52.9 + - + +
49B SER* 4.6 0.2 - - - -
80B ILE* 3.9 33.4 - - + -
96B ILE* 5.2 5.6 - - + -
99B ASP* 4.1 20.6 - - + +
100B TYR* 4.7 12.8 - - + -
103B MET* 4.4 11.4 - - - -
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Residues in contact with PHE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 3.4 33.4 - + - -
50A ALA* 4.7 8.5 - - + -
53A ILE* 4.7 2.2 - - + -
16B TRP 2.8 12.7 + - - +
17B SER 3.2 11.0 - - - +
19B LEU* 1.3 76.6 - - - +
21B THR* 1.3 56.1 + - - +
23B LEU* 3.5 2.4 + - - +
24B HIS* 2.7 62.3 + + - -
46B TYR* 3.7 13.4 - + - +
49B SER* 3.5 22.6 + - - +
50B ALA* 4.0 17.9 - - + -
53B ILE* 4.2 6.5 - - + -
2001B MPD 3.2 54.3 - - + +
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Residues in contact with THR 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ALA* 3.9 19.5 - - - +
70A THR* 4.1 6.1 - - - +
71A MET* 3.4 13.6 - - - +
74A TYR* 3.5 28.7 - - + +
17B SER 3.4 1.1 + - - -
18B VAL 3.0 5.9 + - - -
20B PHE* 1.3 75.7 - - - +
22B LYS* 1.3 67.2 + - - +
24B HIS* 3.0 9.7 + - + +
25B ASN* 2.9 21.7 + - - +
82B GLU* 4.6 3.4 - - - +
2001B MPD 2.2 52.1 + - + +
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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
----------------------------------------------------------
69A ALA 5.3 1.6 - - - -
18B VAL* 2.8 18.7 + - + +
19B LEU* 3.6 10.1 - - + +
21B THR* 1.3 77.0 - - - +
23B LEU* 1.3 56.8 + - + +
25B ASN* 3.3 9.1 - - - +
26B PHE* 3.1 58.4 + - + -
80B ILE* 4.2 10.2 - - + +
81B GLN* 2.6 35.1 + - - +
82B GLU* 4.4 2.2 + - + -
83B ALA* 3.9 25.8 - - + +
87B GLU* 5.7 0.4 - - - -
95B ALA* 4.8 8.9 + - - +
96B ILE* 5.1 2.5 - - + -
99B ASP* 2.9 33.1 + - - +
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TRP* 5.7 0.4 - - + -
19B LEU* 2.7 39.0 + - + +
22B LYS* 1.3 71.4 - - - +
24B HIS* 1.3 61.0 + - - +
26B PHE* 3.6 2.6 + - + +
27B HIS* 2.8 27.4 + - - +
42B PHE* 3.7 23.3 - - + +
45B LEU* 3.6 28.7 - - + +
46B TYR* 3.5 44.8 - - + +
49B SER* 4.2 6.5 - - - -
96B ILE* 4.1 26.7 - - + -
100B TYR* 4.5 7.6 - - + +
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Residues in contact with HIS 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ALA* 5.1 5.5 + - - +
53A ILE* 4.2 12.7 - - + +
54A ASP* 4.4 7.2 - - + +
20B PHE* 2.7 61.7 + + - -
21B THR* 3.0 12.7 + - + +
23B LEU* 1.3 74.5 - - - +
25B ASN* 1.3 55.0 + - - +
27B HIS* 3.0 9.0 + - - +
28B TRP* 2.6 79.2 + + + -
46B TYR* 3.5 39.1 + + - -
2001B MPD 5.4 1.3 - - + -
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Residues in contact with ASN 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ALA* 2.9 45.5 + - + +
21B THR 2.9 9.9 + - - +
22B LYS* 3.3 13.2 - - - +
24B HIS* 1.3 75.9 - - - +
26B PHE* 1.3 64.1 + - + +
28B TRP* 3.0 5.9 + - - -
29B TYR* 2.7 49.4 + - - +
83B ALA* 4.0 17.2 - - + +
84B ALA 5.2 0.3 - - - +
85B TYR* 3.5 23.4 - - - -
87B GLU* 4.8 4.2 - - - +
92B MET* 4.4 1.9 - - - +
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Residues in contact with PHE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LYS* 3.1 35.7 + - + +
23B LEU* 3.9 4.3 - - - +
25B ASN* 1.3 81.2 - - - +
27B HIS* 1.3 65.6 + - - +
30B VAL* 3.1 30.3 + - - +
42B PHE* 3.5 24.9 - + + -
83B ALA* 3.7 24.9 - - + -
87B GLU* 4.2 14.6 - - - -
92B MET* 3.3 49.4 - - + -
95B ALA* 3.8 11.0 - - + -
96B ILE* 3.4 35.0 - - + -
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Residues in contact with HIS 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ASP* 3.3 14.6 - - - -
152A FE 1.9 32.9 - - - -
23B LEU 2.8 16.9 + - - +
24B HIS* 3.0 13.4 + - - +
26B PHE* 1.3 77.9 - - - +
28B TRP* 1.3 72.5 + + - +
30B VAL* 3.8 6.2 - - - +
35B PHE* 5.0 0.7 - - - -
39B HIS* 2.7 76.4 + + - -
42B PHE* 3.8 11.9 - - + -
43B GLU* 3.6 23.8 + - + +
46B TYR* 3.6 17.7 + + + -
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Residues in contact with TRP 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 4.5 2.7 - - + -
53A ILE* 3.5 27.4 - - + -
54A ASP* 2.7 21.4 + - - -
57A ALA* 3.3 31.1 - - + +
58A GLU* 4.0 16.3 - - + +
61A LEU* 3.4 35.0 - - + +
67A PRO* 4.2 16.2 - - + -
68A VAL 3.9 9.9 - - - -
69A ALA* 4.1 15.0 - - + -
74A TYR* 3.8 20.9 - - - -
21B THR* 5.5 0.4 - - + -
24B HIS* 2.6 54.9 + + + +
25B ASN* 3.6 2.5 - - - +
27B HIS* 1.3 89.3 - + - +
29B TYR* 1.3 63.1 + + + +
30B VAL 3.6 3.4 + - - +
31B LYS* 5.0 3.8 + - - -
35B PHE* 5.3 3.5 - - - -
39B HIS* 5.2 0.7 - - - -
2001B MPD 6.3 0.2 - - + -
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Residues in contact with TYR 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 4.8 5.2 - - + -
66A LYS* 3.0 32.7 + - + +
67A PRO* 2.6 56.8 + - + -
69A ALA* 4.3 2.5 - - + -
25B ASN* 2.7 44.4 + - - +
28B TRP* 1.3 75.0 - - + +
30B VAL* 1.3 65.8 + - - +
31B LYS* 3.4 28.2 + - - +
85B TYR* 3.7 28.3 - + - -
86B GLY* 6.1 5.2 - - - +
87B GLU 5.4 2.3 - - - +
92B MET* 3.9 17.2 - - + +
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Residues in contact with VAL 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE 3.1 21.7 + - - +
27B HIS 3.8 11.4 - - - +
28B TRP 3.6 2.0 - - - +
29B TYR* 1.3 77.2 - - - +
31B LYS* 1.3 74.5 + - - +
35B PHE* 3.4 35.6 - - + +
38B LEU* 3.9 22.0 - - + -
39B HIS* 4.0 17.3 - - - +
42B PHE* 4.1 8.1 - - + -
89B ALA* 4.0 23.8 - - + -
92B MET* 3.8 12.0 - - - +
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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