Contacts of the helix formed by residues 45 - 70 (chain B) in PDB entry 1JTY
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 THR 45 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 3.3 4.2 + - - -
44B LYS* 1.3 81.3 - - + +
46B LYS* 1.3 78.3 + - - +
47B GLU* 3.7 21.0 + - + +
48B ASN* 2.9 36.8 + - - +
49B LEU* 3.1 12.6 + - - +
106B TYR* 4.7 7.3 + - - -
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Residues in contact with LYS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 4.8 7.0 - - + -
20B TYR* 3.2 54.4 + - + +
21B ASN* 3.1 35.2 - - - +
23B THR 3.5 12.2 + - - -
24B THR* 5.0 7.6 + - - +
25B THR* 5.4 17.5 - - + +
45B THR* 1.3 80.0 + - - +
47B GLU* 1.3 64.5 + - - +
49B LEU* 3.3 11.2 + - + +
50B PHE* 2.9 23.6 + - - +
106B TYR* 4.3 14.3 - - + +
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Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 3.2 6.0 + - - +
45B THR* 3.1 16.7 + - + +
46B LYS* 1.3 78.1 - - - +
48B ASN* 1.3 55.6 + - - +
50B PHE* 3.1 2.3 + - - +
51B LEU* 2.5 39.5 + - + +
102B PHE* 3.8 12.8 - - + -
106B TYR* 2.8 61.2 - - + +
109B THR* 3.2 13.4 + - - -
111B SER* 3.2 32.4 + - - +
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Residues in contact with ASN 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B HIS 4.6 6.8 + - - +
43B PHE* 4.4 3.8 - - - -
44B LYS* 4.0 29.7 - - - +
45B THR* 2.9 32.9 + - - +
47B GLU* 1.3 72.9 - - - +
49B LEU* 1.3 67.8 + - - +
51B LEU* 4.0 5.6 - - - +
52B GLU* 2.7 29.2 + - + +
114B GLU* 5.3 6.5 + - - +
115B LYS* 5.0 17.0 - - - +
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Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 4.7 6.5 - - + -
8B LEU* 4.1 11.4 - - + -
11B ALA* 3.7 14.6 - - + -
15B PHE* 4.5 9.2 - - + -
28B ILE* 3.3 33.2 - - + -
39B LEU* 6.5 0.2 - - + -
43B PHE* 3.7 45.3 - - + +
45B THR 3.1 7.8 + - - +
46B LYS* 3.6 12.3 - - + +
48B ASN* 1.3 78.0 - - - +
50B PHE* 1.3 58.5 + - - +
52B GLU* 3.3 5.0 - - - +
53B ILE* 2.8 48.0 + - + +
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Residues in contact with PHE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.2 44.9 - + + -
20B TYR* 3.4 16.2 - + + -
46B LYS 2.9 13.9 + - - +
47B GLU 3.3 6.1 - - - +
49B LEU* 1.3 73.5 - - - +
51B LEU* 1.3 55.3 + - - +
52B GLU 2.6 15.4 + - - -
53B ILE* 2.9 15.1 + - + +
54B LEU* 2.9 47.8 + - + +
95B LEU* 5.4 3.6 - - + -
98B ALA* 3.8 27.1 - - + -
99B ILE* 3.8 10.5 - - + -
102B PHE* 3.1 49.6 - + + -
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLU 2.5 21.4 + - - +
48B ASN* 4.0 4.7 - - - +
50B PHE* 1.3 74.1 - - - +
52B GLU* 1.3 58.8 + - - +
54B LEU* 3.5 16.4 - - + +
55B ASN 3.6 0.2 + - - -
102B PHE* 3.5 31.9 - - + -
111B SER* 4.5 5.2 - - - +
114B GLU* 4.9 2.9 - - - +
115B LYS* 3.9 15.9 - - + -
116B MET* 3.5 54.7 - - + +
118B LYS* 3.6 18.1 + - - +
119B LEU* 3.8 16.8 - - + -
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Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 4.2 12.9 - - + +
42B HIS 6.1 0.7 - - - +
43B PHE* 5.1 8.7 - - + -
48B ASN 2.7 22.9 + - - +
49B LEU* 3.3 7.0 - - - +
50B PHE 2.6 4.6 + - - -
51B LEU* 1.3 67.7 - - - +
53B ILE* 1.3 66.4 + - - +
54B LEU 3.0 2.4 + - - -
55B ASN* 3.3 7.7 + - - +
56B ILE* 3.1 50.5 + - + +
115B LYS* 2.7 39.2 + - - +
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Residues in contact with ILE 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 4.0 23.1 - - + +
11B ALA* 3.4 32.8 - - + -
12B LYS* 3.8 29.8 - - + +
15B PHE* 3.7 19.3 - - + -
49B LEU* 2.8 30.0 + - + +
50B PHE* 2.9 6.6 + - + +
52B GLU* 1.3 72.2 - - - +
54B LEU* 1.3 67.0 + - + +
56B ILE* 3.3 13.4 + - + +
57B GLU* 3.0 31.0 + - + +
95B LEU* 5.4 5.6 - - + -
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 2.9 55.0 + - + +
51B LEU* 3.5 28.7 - - + +
52B GLU 3.0 0.2 - - - -
53B ILE* 1.3 81.1 - - + +
55B ASN* 1.3 66.3 + - - +
57B GLU* 2.9 5.3 + - - +
58B GLU* 2.9 20.6 + - - +
92B TYR* 4.0 6.7 - - + -
95B LEU* 4.1 14.8 - - + -
99B ILE* 3.6 25.8 - - + -
116B MET* 4.1 12.1 - - + -
119B LEU* 3.4 22.9 - - + -
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Residues in contact with ASN 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU 3.6 0.4 + - - +
52B GLU* 3.3 8.8 + - - +
54B LEU* 1.3 78.5 - - - +
56B ILE* 1.3 70.6 + - - +
58B GLU* 3.0 1.9 + - - +
59B SER* 2.8 29.4 + - - -
115B LYS* 5.1 3.7 - - - +
118B LYS* 2.8 49.5 - - - +
119B LEU* 3.5 15.0 - - - +
122B LYS* 2.8 32.0 + - - +
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Residues in contact with ILE 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 4.0 30.3 - - + -
52B GLU* 3.1 35.3 + - - +
53B ILE* 3.4 18.6 - - + +
55B ASN* 1.3 84.7 - - - +
57B GLU* 1.3 65.2 + - + +
59B SER* 2.9 23.2 + - - -
60B LYS* 3.2 21.4 + - + +
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS* 2.6 40.5 + - + +
16B ILE* 6.0 1.1 - - - +
53B ILE* 3.4 21.9 - - + +
54B LEU* 2.9 11.8 + - - +
56B ILE* 1.3 77.1 - - + +
58B GLU* 1.3 66.5 + - - +
59B SER 2.9 2.7 + - - -
60B LYS* 3.0 25.9 + - - +
61B TRP* 3.1 12.5 + - - +
90B GLU 4.4 0.9 - - - +
91B TYR* 3.4 28.4 - - - +
92B TYR* 3.9 21.8 + - + +
95B LEU* 4.9 10.8 - - + -
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU 2.9 5.8 + - - +
55B ASN 3.4 8.1 - - - +
57B GLU* 1.3 75.4 - - - +
59B SER* 1.3 56.2 + - - +
61B TRP* 3.2 13.2 + - + +
62B GLN* 2.9 39.3 + - - +
82B TYR* 5.2 1.0 + - - -
92B TYR* 3.4 44.0 - - + -
119B LEU* 3.6 20.9 - - + -
122B LYS* 3.0 26.5 - - + +
123B TYR* 3.4 26.4 + - - +
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Residues in contact with SER 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASN* 2.8 17.6 + - - -
56B ILE* 2.9 12.8 + - - -
58B GLU* 1.3 77.2 - - - +
60B LYS* 1.3 58.4 + - - +
61B TRP 2.9 1.6 - - - -
62B GLN* 3.7 6.0 - - - +
63B GLU* 2.8 31.4 + - - +
122B LYS* 2.9 24.2 + - - -
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Residues in contact with LYS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS* 6.1 0.4 - - - +
56B ILE* 3.4 25.6 - - + +
57B GLU* 3.6 25.1 - - - +
59B SER* 1.3 75.4 - - - +
61B TRP* 1.3 56.9 + - - +
63B GLU* 3.7 7.5 + - - +
64B GLN* 3.0 26.5 + - - +
91B TYR* 3.3 37.2 + - + -
199B SO4 2.7 33.0 + - - -
1000B SO4 4.7 6.4 + - - -
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Residues in contact with TRP 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLU 3.1 10.5 + - - +
58B GLU* 3.2 31.4 + - + +
60B LYS* 1.3 73.7 - - - +
62B GLN* 1.3 66.9 + - - +
63B GLU 3.0 1.1 - - - -
64B GLN* 2.9 12.3 + - + -
65B TRP* 2.7 43.9 + + + -
82B TYR* 3.0 53.5 + + - -
85B LEU* 3.8 25.4 - - + -
86B SER* 3.9 17.7 - - - -
89B THR* 3.1 40.6 - - + -
91B TYR* 3.7 19.7 - - + +
92B TYR* 4.6 2.7 - + + -
93B TYR* 3.9 20.3 - + - -
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Residues in contact with GLN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU* 2.9 35.3 + - - +
59B SER* 3.8 7.2 - - - +
61B TRP* 1.3 81.6 + - - +
63B GLU* 1.3 60.4 + - - +
65B TRP* 3.5 9.0 - - - +
66B LYS* 3.2 58.4 + - + +
82B TYR* 5.0 1.2 + - - -
122B LYS* 3.3 29.8 - - + +
125B ASP* 4.3 6.8 + - - +
126B ALA* 3.4 29.4 - - - +
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Residues in contact with GLU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B SER 2.8 18.4 + - - +
60B LYS* 3.7 8.0 - - - +
62B GLN* 1.3 76.0 - - - +
64B GLN* 1.3 65.6 + - - +
66B LYS* 3.1 9.4 + - + +
67B LYS* 3.1 40.5 + - + +
1000B SO4 5.1 2.2 - - - +
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Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LYS 3.0 15.7 + - - +
61B TRP* 2.9 10.5 + - + +
63B GLU* 1.3 75.8 - - - +
65B TRP* 1.3 66.9 + - - +
67B LYS* 3.1 12.2 + - - +
68B GLU* 2.9 52.0 - - + +
85B LEU* 4.3 7.6 - - - +
88B THR* 5.3 0.3 + - - -
89B THR* 3.0 36.0 + - + +
90B GLU* 3.8 6.7 + - - -
91B TYR* 3.4 9.9 - - - -
1000B SO4 2.9 35.6 + - - +
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Residues in contact with TRP 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B TRP* 2.7 39.6 + + + +
62B GLN* 3.5 17.3 - - - +
64B GLN* 1.3 75.1 - - - +
66B LYS* 1.3 88.5 + - + +
68B GLU* 3.2 5.3 + - + -
69B GLN* 2.9 69.1 + - + +
78B LYS* 3.6 32.1 - - + -
81B LEU* 4.0 11.9 - - + -
82B TYR* 3.6 38.8 - + + -
85B LEU* 4.9 5.4 - - + -
126B ALA* 3.8 15.0 + - + +
130B ILE* 4.4 13.1 - - + +
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Residues in contact with LYS 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLN* 3.2 40.7 + - + +
63B GLU* 3.1 10.9 + - + +
64B GLN 3.1 0.6 - - - -
65B TRP* 1.3 91.4 - - + +
67B LYS* 1.3 55.9 + - + +
68B GLU 2.5 18.3 + - - -
69B GLN* 3.0 35.8 + - - +
70B ILE* 3.6 10.5 - - - +
125B ASP* 4.6 6.7 + - - -
126B ALA* 4.5 7.1 - - - +
129B VAL* 5.1 6.5 - - - +
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Residues in contact with LYS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLU* 3.1 31.4 + - + +
64B GLN* 3.1 6.2 + - - +
66B LYS* 1.3 77.1 - - + +
68B GLU* 1.3 66.6 + - + +
70B ILE* 5.1 6.9 - - - +
71B LYS* 4.9 5.9 + - - -
1000B SO4 3.2 34.0 + - - -
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Residues in contact with GLU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLN* 2.9 44.7 - - + +
65B TRP* 3.8 8.3 - - + +
66B LYS 2.5 14.6 + - - -
67B LYS* 1.3 81.8 - - + +
69B GLN* 1.3 53.5 + - - +
70B ILE* 2.7 17.4 + - - +
71B LYS* 3.1 27.7 + - - +
81B LEU* 4.1 5.9 - - - +
85B LEU* 3.3 35.9 - - + +
1000B SO4 5.4 2.9 + - - -
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Residues in contact with GLN 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B TRP* 2.9 51.2 + - + +
66B LYS* 3.0 58.5 + - - +
68B GLU* 1.3 74.6 - - - +
70B ILE* 1.3 59.6 + - + +
71B LYS 3.0 0.2 - - - -
72B ALA* 2.8 38.0 + - - +
78B LYS* 3.6 26.3 + - + -
81B LEU* 4.0 4.0 - - - -
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Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LYS 3.6 18.6 - - - +
67B LYS* 5.1 4.5 - - - +
68B GLU* 2.7 6.4 + - - +
69B GLN* 1.3 83.8 - - + +
71B LYS* 1.3 71.3 + - + +
72B ALA 3.1 8.3 + - - +
73B LYS* 3.9 6.6 + - - -
78B LYS* 5.7 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