Contacts of the helix formed by residues 82 - 110 (chain W) in PDB entry 2JA7
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 ASP 82 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29W ASN* 5.2 1.3 - - - +
80W GLY 4.1 1.4 + - - -
81W TYR* 1.3 80.1 - - - +
83W PRO* 1.3 71.6 - - - +
84W LYS* 2.5 56.1 + - - +
85W ASP* 3.1 35.2 + - - +
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Residues in contact with PRO 83 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29W ASN* 3.8 16.2 - - - +
30W ALA* 5.1 1.1 - - - +
31W VAL* 3.5 30.3 - - + +
75W ILE* 3.9 35.2 - - + +
77W THR* 4.0 12.3 - - + +
81W TYR 3.4 6.2 - - - +
82W ASP* 1.3 87.1 - - - +
84W LYS* 1.3 67.0 + - - +
85W ASP 3.0 2.2 - - - -
86W ALA* 2.8 12.1 + - + +
87W LEU* 2.7 24.0 + - - +
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Residues in contact with LYS 84 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262O LEU* 4.4 15.6 - - + +
265O MET* 5.1 12.0 + - - +
266O ASP* 4.2 19.1 + - - -
21W ILE* 4.1 39.1 - - + +
31W VAL* 5.4 3.8 - - + -
33W ILE* 5.9 0.4 - - + -
82W ASP* 2.5 35.6 + - - +
83W PRO* 1.3 77.3 - - + +
85W ASP* 1.3 61.9 + - - +
87W LEU* 3.1 10.2 + - - +
88W LYS* 3.1 22.9 + - - +
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Residues in contact with ASP 85 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81W TYR* 4.0 11.0 - - + -
82W ASP* 3.1 27.5 + - - +
83W PRO 3.0 0.4 - - - -
84W LYS* 1.3 80.0 - - - +
86W ALA* 1.3 54.5 + - - +
88W LYS* 2.8 51.2 + - - +
89W ASN* 3.1 14.8 + - - +
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Residues in contact with ALA 86 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50W LEU* 4.5 5.7 - - + +
53W ASP* 4.1 7.2 - - - +
56W VAL* 4.1 20.0 - - + -
75W ILE* 5.0 0.7 - - + -
77W THR* 4.3 0.9 - - + -
81W TYR* 3.2 30.6 + - + +
82W ASP 3.4 2.2 + - - -
83W PRO* 2.8 21.0 + - + +
85W ASP* 1.3 75.0 - - - +
87W LEU* 1.3 65.2 + - - +
89W ASN* 3.5 3.5 + - - +
90W ALA* 3.0 27.4 + - - +
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Residues in contact with LEU 87 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258O ILE* 4.7 4.7 - - + -
262O LEU* 3.7 24.2 - - + -
19W LEU* 4.9 2.5 - - + -
21W ILE* 5.5 0.2 - - + -
33W ILE* 3.4 29.4 - - + -
35W PHE* 4.5 11.7 - - + -
46W ILE* 3.3 34.1 - - + -
50W LEU* 4.4 7.1 - - + +
73W LEU* 4.3 3.1 - - + -
75W ILE* 4.3 19.3 - - + +
83W PRO 2.7 14.4 + - - +
84W LYS* 3.3 11.9 - - - +
86W ALA* 1.3 74.2 - - - +
88W LYS* 1.3 69.3 + - - +
90W ALA* 3.5 3.6 + - + +
91W CYS* 2.8 27.6 + - - -
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Residues in contact with LYS 88 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259O LEU* 3.5 18.7 - - + +
262O LEU* 4.2 26.7 - - + +
263O THR* 5.3 8.2 + - - +
266O ASP* 4.2 18.4 + - - -
84W LYS 3.1 12.6 + - - +
85W ASP* 2.8 27.7 + - - +
87W LEU* 1.3 76.6 - - - +
89W ASN* 1.3 58.3 + - - +
91W CYS* 2.6 30.4 + - - +
92W ASN* 3.0 20.5 + - - +
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Residues in contact with ASN 89 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53W ASP* 4.5 6.0 + - - +
81W TYR* 3.9 15.6 + - - -
85W ASP* 3.1 26.4 + - - +
86W ALA 3.9 2.5 - - - +
88W LYS* 1.3 77.9 - - - +
90W ALA* 1.3 57.3 + - - +
91W CYS 2.5 13.0 + - - -
92W ASN* 2.5 27.6 + - - +
93W SER* 2.7 14.8 + - - -
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Residues in contact with ALA 90 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46W ILE* 5.3 3.4 - - + +
49W GLU* 3.8 11.6 - - + +
50W LEU* 3.9 36.8 - - + +
53W ASP* 5.4 4.4 + - + +
86W ALA 3.0 16.6 + - - +
87W LEU* 3.6 5.2 - - + +
89W ASN* 1.3 78.8 - - - +
91W CYS* 1.3 57.4 + - - +
93W SER* 3.8 8.3 - - - -
94W ILE* 3.1 28.0 + - - +
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Residues in contact with CYS 91 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255O VAL* 3.6 28.0 - - + +
258O ILE* 4.2 13.7 - - - -
259O LEU* 3.4 20.4 - - + -
46W ILE* 4.3 11.2 - - - -
87W LEU* 2.8 41.7 - - - -
88W LYS 2.6 9.9 + - - +
89W ASN 2.5 4.2 + - - -
90W ALA* 1.3 70.6 - - - +
92W ASN* 1.3 67.1 + - - +
93W SER 3.1 1.3 - - - -
94W ILE* 2.7 16.3 + - - +
95W ILE* 2.9 12.0 + - - +
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Residues in contact with ASN 92 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259O LEU* 3.0 26.8 - - - +
88W LYS* 3.0 25.9 + - - +
89W ASN* 2.5 19.2 + - - +
91W CYS* 1.3 72.9 - - - +
93W SER* 1.3 64.9 + - - +
95W ILE* 2.8 14.3 + - - +
96W ASN* 2.7 37.7 + - - +
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Residues in contact with SER 93 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49W GLU* 3.0 24.3 + - - -
89W ASN* 2.7 18.6 + - - -
90W ALA* 3.8 6.5 - - - -
92W ASN* 1.3 72.7 - - - +
94W ILE* 1.3 63.3 + - - -
96W ASN* 3.3 10.3 + - - +
97W LYS* 2.9 43.2 + - - +
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Residues in contact with ILE 94 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29O MET* 4.1 6.9 - - + +
255O VAL* 3.7 31.9 - - + -
45W LEU* 3.4 51.6 - - + +
46W ILE* 4.0 9.4 - - + +
49W GLU* 3.3 18.8 - - + -
90W ALA 3.1 18.2 - - - +
91W CYS* 2.7 16.6 + - - +
93W SER* 1.3 73.4 - - - +
95W ILE* 1.3 62.5 + - - +
97W LYS* 3.4 7.7 + - - +
98W LEU* 3.1 30.4 + - + +
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Residues in contact with ILE 95 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252O GLN* 3.3 32.1 - - + +
255O VAL* 4.1 17.0 - - + +
256O ALA* 4.3 26.7 - - + -
259O LEU* 4.3 19.5 - - + -
91W CYS 2.9 14.3 + - - +
92W ASN* 2.8 16.4 + - - +
94W ILE* 1.3 70.5 - - - +
96W ASN* 1.3 57.0 + - - +
98W LEU* 2.6 16.6 + - - +
99W GLY* 2.6 33.6 + - - -
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Residues in contact with ASN 96 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92W ASN* 2.7 34.2 + - - +
93W SER* 3.5 9.1 - - - +
95W ILE* 1.3 78.8 - - - +
97W LYS* 1.3 62.7 + - + +
99W GLY* 3.2 3.1 + - - +
100W ALA* 3.1 21.3 + - - +
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Residues in contact with LYS 97 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5O GLY* 5.8 2.2 - - - -
6O PRO* 3.8 31.6 - - + +
25O VAL* 6.4 1.3 - - - -
26O ASP* 4.8 7.0 - - - +
29O MET* 4.6 18.4 - - - -
49W GLU* 3.0 30.5 - - + +
52W ASN* 5.4 1.0 - - - +
93W SER* 2.9 35.0 + - - +
94W ILE* 3.7 5.8 - - - +
96W ASN* 1.3 75.0 - - + +
98W LEU* 1.3 59.7 + - - +
100W ALA* 3.1 9.3 + - - +
101W LEU* 2.9 25.9 + - - +
----------------------------------------------------------
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Residues in contact with LEU 98 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29O MET* 3.1 30.5 - - + -
33O LEU* 5.6 4.0 - - + -
248O ILE* 3.4 29.3 - - + +
251O LEU* 4.2 19.5 - - + -
252O GLN* 3.8 37.7 - - + +
94W ILE* 3.1 31.6 + - + +
95W ILE* 2.6 13.1 + - - +
97W LYS* 1.3 68.6 - - - +
99W GLY* 1.3 55.7 + - - +
101W LEU* 2.9 11.8 + - + +
102W LYS* 2.6 36.6 + - - +
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Residues in contact with GLY 99 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252O GLN* 3.2 16.5 - - - +
95W ILE* 2.6 15.8 + - - -
96W ASN* 3.2 6.0 + - - -
98W LEU* 1.3 73.2 - - - +
100W ALA* 1.3 60.9 + - - +
102W LYS* 3.8 8.0 + - - +
103W THR* 3.5 21.0 + - - -
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Residues in contact with ALA 100 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4O GLU* 3.6 38.1 - - + +
5O GLY 4.4 13.0 - - - +
96W ASN 3.1 10.1 + - - +
97W LYS* 3.1 12.2 + - - +
98W LEU 3.0 0.2 - - - -
99W GLY* 1.3 75.0 - - - +
101W LEU* 1.3 55.6 + - - +
103W THR* 3.0 5.9 + - - -
104W ASN* 2.7 38.9 + - - +
----------------------------------------------------------
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Residues in contact with LEU 101 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6O PRO* 4.1 34.7 + - + +
7O GLN 6.1 0.2 - - - -
8O VAL* 4.6 8.7 - - + +
22O LEU* 4.2 34.1 - - + -
25O VAL* 4.6 2.7 - - + -
29O MET* 5.1 6.5 - - + -
33O LEU* 4.9 7.0 - - + -
244O VAL* 6.0 0.7 - - + -
248O ILE* 3.3 34.5 - - + -
97W LYS 2.9 12.1 + - - +
98W LEU* 3.4 18.6 - - + +
100W ALA* 1.3 77.2 - - - +
102W LYS* 1.3 63.9 + - - +
104W ASN* 4.5 2.0 - - - +
105W PHE* 2.9 35.6 + - + +
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Residues in contact with LYS 102 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245O VAL* 3.8 20.8 - - + +
248O ILE* 4.0 18.1 - - + +
249O ASP* 3.6 35.1 + - - +
252O GLN* 3.9 20.1 + - - +
98W LEU 2.6 20.0 + - - +
99W GLY* 3.9 8.5 - - - +
100W ALA 3.2 0.2 - - - -
101W LEU* 1.3 75.1 - - - +
103W THR* 1.3 66.2 - - - +
105W PHE* 3.7 2.3 - - - +
106W GLU* 3.2 38.7 + - - +
----------------------------------------------------------
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Residues in contact with THR 103 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2O SER* 5.3 4.7 - - - +
4O GLU* 5.1 5.6 - - - +
99W GLY 3.5 11.7 + - - -
100W ALA* 3.0 9.6 + - - -
102W LYS* 1.3 76.9 - - - +
104W ASN* 1.3 61.1 + - - +
105W PHE 2.6 16.3 + - - -
106W GLU* 2.8 23.9 + - - +
107W THR* 2.9 22.7 + - - +
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Residues in contact with ASN 104 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2O SER* 3.5 31.0 + - - +
3O GLU 4.5 1.0 - - - -
4O GLU* 3.9 22.0 - - - +
5O GLY 3.7 10.7 + - - -
6O PRO 3.9 10.2 + - - +
7O GLN* 3.6 36.2 - - + +
8O VAL* 3.9 11.7 + - + +
100W ALA 2.7 20.3 + - - +
101W LEU* 4.2 2.2 - - - +
103W THR* 1.3 75.9 - - - +
105W PHE* 1.3 58.6 + - - +
107W THR* 3.9 9.5 - - - -
108W GLU* 4.0 16.1 + - - +
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Residues in contact with PHE 105 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8O VAL* 3.9 28.3 - - + -
10O ILE* 4.2 6.2 - - + +
18O VAL* 3.8 21.5 - - + -
20O PHE* 4.0 22.4 - + - -
22O LEU* 6.3 0.4 - - + -
241O ASP* 4.2 20.2 - - - -
244O VAL* 3.9 28.3 - - + -
245O VAL* 4.3 14.8 - - + -
248O ILE* 4.5 6.7 - - + -
101W LEU* 2.9 22.8 + - + +
102W LYS 3.7 3.4 - - - +
103W THR 2.6 5.3 + - - -
104W ASN* 1.3 74.4 - - - +
106W GLU* 1.3 66.0 + - + +
107W THR 3.1 1.6 - - - -
108W GLU* 3.0 8.1 + - - +
109W TRP* 2.9 40.0 + + + +
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Residues in contact with GLU 106 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242O GLN* 5.1 1.9 - - - +
245O VAL* 3.8 30.9 - - + +
102W LYS* 3.2 29.8 + - - +
103W THR* 2.8 12.1 + - - +
105W PHE* 1.3 84.0 - - + +
107W THR* 1.3 60.8 + - - +
109W TRP* 3.4 10.9 - - + +
110W ASN* 2.9 39.6 + - - +
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Residues in contact with THR 107 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2O SER 3.3 28.0 + - - +
103W THR* 2.9 24.8 + - - +
104W ASN 4.1 7.9 - - - -
106W GLU* 1.3 79.1 - - - +
108W GLU* 1.3 68.2 + - + +
110W ASN* 3.6 14.5 + - - +
111W LEU* 4.0 13.6 - - + +
----------------------------------------------------------
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Residues in contact with GLU 108 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8O VAL 3.7 26.4 - - - +
9O LYS* 4.0 6.6 - - - +
10O ILE* 3.1 40.3 + - + +
104W ASN 4.0 10.3 - - - +
105W PHE* 3.0 8.1 + - - +
107W THR* 1.3 85.2 - - + +
109W TRP* 1.3 63.7 + - - +
111W LEU* 3.6 22.1 + - - +
112W GLN* 4.2 8.3 + - - -
----------------------------------------------------------
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Residues in contact with TRP 109 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10O ILE* 3.2 19.3 - - + +
13O ALA* 3.9 21.3 - - + -
14O SER 3.6 24.2 - - - -
18O VAL* 3.6 35.0 - - + -
240O VAL* 5.0 1.8 - - + -
241O ASP* 3.6 39.8 + - + +
105W PHE* 2.9 23.5 + + + +
106W GLU* 3.1 16.1 + - + +
108W GLU* 1.3 76.0 - - - +
110W ASN* 1.3 62.7 + - - +
111W LEU* 2.3 22.8 + - - -
112W GLN* 4.2 11.1 - - + +
----------------------------------------------------------
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Residues in contact with ASN 110 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106W GLU* 2.9 26.9 + - - +
107W THR* 4.0 9.7 + - - +
108W GLU 3.5 1.4 - - - -
109W TRP* 1.3 82.2 - - - +
111W LEU* 1.3 77.5 + - + +
----------------------------------------------------------
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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