Contacts of the helix formed by residues 8 - 34 (chain S) in PDB entry 2BKC
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 8 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7S VAL* 1.3 76.8 - - - +
9S THR* 1.3 59.8 + - - +
10S LYS* 4.1 20.4 + - - +
11S GLU* 3.3 32.3 + - - +
12S PHE* 3.1 26.7 + - - +
119S LEU* 3.5 7.3 - - - +
123S GLU* 3.4 19.6 - - - +
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Residues in contact with THR 9 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8S ASP* 1.3 72.1 - - - +
10S LYS* 1.3 62.8 + - - +
12S PHE* 3.1 7.4 + - - +
13S LEU* 3.0 37.6 + - + +
67S ILE* 3.7 17.7 - - + -
119S LEU* 4.5 3.0 + - - +
120S THR* 3.6 23.7 + - - +
123S GLU* 2.9 33.2 + - - +
125S ASP* 3.4 25.2 + - - +
128S THR* 4.5 6.3 - - + -
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Residues in contact with LYS 10 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8S ASP* 4.1 17.8 + - - +
9S THR* 1.3 81.3 - - - +
11S GLU* 1.3 60.9 + - + +
14S ASN* 3.3 15.1 + - - +
64S LEU* 3.2 37.4 - - + +
67S ILE* 3.7 31.2 - - + -
68S GLY* 4.2 11.9 - - - +
69S GLY* 4.2 12.3 - - - -
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Residues in contact with GLU 11 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7S VAL* 3.7 28.9 - - + +
8S ASP* 3.3 20.2 + - - +
9S THR 3.2 0.8 - - - -
10S LYS* 1.3 78.9 - - + +
12S PHE* 1.3 61.7 + - - +
14S ASN* 3.8 4.9 - - + +
15S HIS* 2.9 30.1 + - - +
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Residues in contact with PHE 12 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7S VAL* 3.8 9.1 - - + +
8S ASP 3.1 18.7 + - - +
9S THR* 3.1 7.5 + - - +
11S GLU* 1.3 78.2 - - - +
13S LEU* 1.3 75.6 + - + +
15S HIS* 3.3 9.4 + - + +
16S GLN* 3.2 53.5 + - + +
112S GLU* 3.2 31.6 - - + -
113S TYR* 4.2 4.3 - + - -
115S GLN* 4.6 4.5 - - + -
116S GLY* 3.6 28.5 - - - -
119S LEU* 4.0 13.0 - - + -
120S THR* 5.7 2.2 - - - +
132S LEU* 3.9 21.8 - - + -
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Residues in contact with LEU 13 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9S THR* 3.0 20.8 + - + +
12S PHE* 1.3 92.6 - - + +
14S ASN* 1.3 63.8 + - - +
16S GLN* 2.9 5.4 + - + -
17S VAL* 2.9 19.0 + - - +
60S VAL* 3.2 32.4 - - + +
63S ARG* 4.6 2.5 - - + -
64S LEU* 4.0 22.4 - - + +
67S ILE* 3.8 25.4 - - + -
128S THR* 3.7 34.3 - - + +
131S MET* 4.2 14.6 - - + -
132S LEU* 4.3 7.2 - - + -
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Residues in contact with ASN 14 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10S LYS 3.3 15.9 + - - +
11S GLU* 3.8 6.3 - - + +
12S PHE 3.3 0.2 - - - -
13S LEU* 1.3 77.6 - - - +
15S HIS* 1.3 64.9 + - - +
17S VAL* 3.0 17.9 + - - +
18S ALA 3.1 9.5 + - - -
64S LEU* 3.2 13.2 - - - +
70S SER 3.1 21.4 + - - -
71S PRO* 3.2 8.5 - - - +
72S PHE* 2.9 64.7 + - + +
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Residues in contact with HIS 15 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7S VAL* 6.3 1.1 - - + -
11S GLU 2.9 18.8 + - - +
12S PHE* 3.5 9.4 - + + +
13S LEU 3.3 0.2 - - - -
14S ASN* 1.3 76.7 - - - +
16S GLN* 1.3 62.5 + - - +
18S ALA* 3.3 7.3 + - - +
19S ASN* 3.0 34.1 + - - +
72S PHE* 4.4 7.5 - - - -
81S ASN* 3.1 26.8 + - + -
83S SER* 2.9 35.4 + - - -
112S GLU* 3.6 17.3 + - - -
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Residues in contact with GLN 16 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12S PHE* 3.2 46.5 + - + +
13S LEU* 2.9 10.1 + - + +
15S HIS* 1.3 85.5 + - - +
17S VAL* 1.3 65.4 + - - +
19S ASN* 3.1 21.7 + - - +
20S LEU* 2.9 40.2 + - + +
60S VAL* 4.4 9.4 - - + -
109S LEU* 3.8 5.7 - - - +
112S GLU* 2.9 28.0 + - - +
113S TYR* 3.7 25.7 + - + -
132S LEU* 5.8 0.7 - - + -
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Residues in contact with VAL 17 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32Q TRP* 4.3 11.9 - - + -
13S LEU 2.9 12.9 + - - +
14S ASN* 3.3 19.3 - - - +
16S GLN* 1.3 76.1 - - - +
18S ALA* 1.3 65.2 + - - +
20S LEU* 4.0 1.7 - - - +
21S ASN* 3.0 33.6 + - - +
57S MET* 4.6 9.2 - - - +
60S VAL* 3.5 25.1 - - + +
61S ALA* 4.2 18.6 - - + +
64S LEU* 4.8 3.1 - - + -
71S PRO* 4.8 1.1 - - + -
72S PHE* 3.8 24.5 - - + +
78S PHE* 3.8 12.3 - - + -
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Residues in contact with ALA 18 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14S ASN 3.1 6.8 + - - +
15S HIS 3.5 8.7 - - - +
17S VAL* 1.3 81.3 - - - +
19S ASN* 1.3 61.8 + - - +
21S ASN* 3.5 2.6 + - - +
22S VAL* 3.3 26.0 + - - +
72S PHE* 4.3 3.3 - - + -
78S PHE* 3.6 43.2 - - + +
81S ASN* 4.0 12.6 - - + -
82S ALA* 4.0 11.9 - - - +
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Residues in contact with ASN 19 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15S HIS* 3.0 16.3 + - - +
16S GLN* 3.1 23.0 + - - +
18S ALA* 1.3 76.9 - - - +
20S LEU* 1.3 57.4 + - + +
22S VAL* 3.1 4.0 + - - +
23S PHE* 2.9 30.1 + - - +
82S ALA* 3.4 7.2 - - - -
83S SER* 3.0 33.0 + - - -
84S VAL* 3.4 23.9 + - + +
108S LEU* 4.1 0.4 - - - +
109S LEU* 3.7 14.6 - - + +
112S GLU* 3.1 28.5 + - - -
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Residues in contact with LEU 20 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16S GLN* 2.9 38.1 + - + +
19S ASN* 1.3 73.9 - - - +
21S ASN* 1.3 57.0 + - - +
23S PHE* 3.7 6.0 - - + +
24S THR* 2.8 32.4 + - - -
53S PHE* 3.9 40.1 - - + +
56S GLN* 4.1 2.9 - - + +
57S MET* 3.8 32.8 - - + +
60S VAL* 4.5 9.6 - - + -
109S LEU* 4.3 20.0 - - + -
113S TYR* 3.3 27.4 - - + +
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Residues in contact with ASN 21 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Q VAL* 4.3 10.4 - - - +
28Q HIS* 5.6 0.3 - - - -
50Q TYR* 5.5 1.0 + - - -
75Q LEU* 4.0 3.8 - - + +
17S VAL* 3.0 27.0 + - - +
18S ALA 3.8 2.5 - - - +
20S LEU* 1.3 75.4 - - - +
22S VAL* 1.3 65.0 + - - +
24S THR* 3.6 11.5 - - - +
25S VAL* 3.4 28.3 + - + +
57S MET* 3.5 36.7 - - - +
78S PHE* 3.6 46.9 - - + -
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Residues in contact with VAL 22 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75Q LEU* 3.9 25.8 - - + -
18S ALA 3.3 14.8 - - - +
19S ASN 3.1 8.1 + - - +
21S ASN* 1.3 79.2 - - - +
23S PHE* 1.3 57.5 + - - +
25S VAL* 3.4 4.2 + - - +
26S LYS* 3.0 25.7 + - + +
78S PHE 4.6 3.4 - - - +
79S LEU* 4.6 5.4 - - + -
82S ALA* 3.8 17.3 - - + -
84S VAL* 4.0 26.9 - - + +
86S GLU* 3.9 36.0 - - + +
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Residues in contact with PHE 23 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19S ASN 2.9 16.5 + - - +
20S LEU* 3.7 8.7 - - + +
22S VAL* 1.3 76.5 - - - +
24S THR* 1.3 58.7 + - - +
26S LYS* 3.2 11.9 + - + +
27S ILE* 3.0 39.3 + - + +
49S LEU* 4.4 2.5 - - + -
53S PHE* 3.9 30.5 - + + -
84S VAL* 4.5 8.2 - - + +
102S LEU* 3.4 30.3 - - + -
105S THR* 3.9 20.4 - - + -
106S LEU* 3.4 29.4 - - + -
109S LEU* 3.4 31.6 - - + -
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Residues in contact with THR 24 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Q TYR* 5.7 4.0 - - - +
20S LEU 2.8 16.4 + - - +
21S ASN* 3.6 19.7 - - - +
22S VAL 3.3 0.2 - - - -
23S PHE* 1.3 76.3 - - - +
25S VAL* 1.3 72.0 + - + +
27S ILE* 3.3 17.5 + - - +
28S HIS* 3.3 8.8 + - - +
50S TYR* 3.4 51.9 + - + +
53S PHE* 4.3 4.9 + - - +
54S GLY* 4.0 15.9 + - - -
57S MET* 6.0 2.3 - - + +
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Residues in contact with VAL 25 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Q ASN* 4.1 11.4 - - + +
73Q SER* 3.6 22.8 - - - +
74Q THR* 3.9 7.4 - - - -
75Q LEU* 3.6 17.7 - - + -
78Q PHE* 3.7 30.7 - - + -
21S ASN* 3.4 14.0 + - + +
22S VAL 3.7 7.4 - - - +
23S PHE 3.3 0.2 - - - -
24S THR* 1.3 84.4 - - + +
26S LYS* 1.3 57.8 + - - +
28S HIS* 3.4 13.0 - - + +
29S GLN* 3.0 23.6 + - - +
32S TRP* 6.1 0.4 - - + -
86S GLU* 5.0 0.9 - - - +
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Residues in contact with LYS 26 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73Q SER 5.0 1.8 - - - -
22S VAL* 3.0 14.6 + - + +
23S PHE* 3.5 24.9 - - + +
24S THR 3.2 0.2 - - - -
25S VAL* 1.3 76.3 - - - +
27S ILE* 1.3 64.7 + - - +
29S GLN* 3.2 20.0 + - - +
30S ILE* 3.1 32.2 + - + +
84S VAL* 4.5 7.4 - - + -
85S GLU 3.1 28.7 + - - -
86S GLU* 4.5 11.7 - - + +
87S ALA 5.3 1.6 - - - +
101S ASP* 2.2 45.7 + - - +
102S LEU* 5.6 0.2 - - - -
105S THR* 3.9 20.0 - - + +
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Residues in contact with ILE 27 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23S PHE* 3.0 53.6 + - + +
24S THR* 3.3 11.2 + - - +
26S LYS* 1.3 72.5 - - - +
28S HIS* 1.3 63.3 + - - +
30S ILE* 3.1 10.4 + - - +
31S HIS* 2.9 27.5 + - + +
46S MET* 3.2 41.2 - - + +
49S LEU* 3.9 30.1 - - + +
50S TYR* 3.9 13.5 - - + +
53S PHE* 4.6 2.9 - - + -
102S LEU* 4.3 9.9 - - + -
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Residues in contact with HIS 28 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Q ASN* 5.5 2.2 - - - -
57Q MET* 3.5 29.1 - - + +
58Q ASP* 3.3 34.1 + - - -
24S THR 3.3 3.8 + - - +
25S VAL* 3.4 15.0 - - + +
27S ILE* 1.3 79.5 - - - +
29S GLN* 1.3 65.1 + - - +
31S HIS* 3.2 9.6 + + - +
32S TRP* 2.8 56.0 + + + -
47S ASP* 5.7 4.5 - - - -
50S TYR* 3.2 48.7 - + + +
----------------------------------------------------------
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Residues in contact with GLN 29 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73Q SER* 3.0 46.9 + - - +
74Q THR* 3.7 1.9 - - - +
25S VAL 3.0 12.5 + - - +
26S LYS* 3.3 26.1 + - - +
27S ILE 3.2 0.2 - - - -
28S HIS* 1.3 74.9 - - - +
30S ILE* 1.3 68.7 + - - +
32S TRP* 4.5 1.0 - - - -
33S TYR* 3.1 39.6 + - + +
86S GLU* 5.9 0.3 - - - +
87S ALA 2.9 27.2 + - - +
89S TYR* 3.9 19.3 + - + +
93S LYS* 6.3 0.4 - - - +
98S LEU* 5.6 5.2 - - + +
101S ASP* 5.2 2.6 + - - -
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Residues in contact with ILE 30 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26S LYS* 3.1 23.2 + - + +
27S ILE* 3.1 7.8 + - - +
29S GLN* 1.3 81.7 - - + +
31S HIS* 1.3 61.1 + - - +
33S TYR 4.0 0.2 - - - -
34S MET* 3.1 36.9 + - + +
46S MET* 3.8 7.2 - - - -
98S LEU* 3.9 41.0 - - + +
99S MET* 3.4 25.8 - - + -
101S ASP* 5.1 3.8 - - + +
102S LEU* 3.8 37.7 - - + +
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Residues in contact with HIS 31 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58Q ASP* 5.1 3.1 - - - -
62Q GLU* 4.1 17.0 + - - -
27S ILE* 2.9 15.1 + - + +
28S HIS* 3.5 15.9 - + - +
30S ILE* 1.3 73.8 - - - +
32S TRP* 1.3 85.7 + + - +
34S MET* 3.3 26.4 - - - +
39S PHE* 4.6 10.0 - + - -
43S GLY* 3.1 43.7 + - - -
46S MET* 3.8 11.4 - - + +
47S ASP* 3.4 23.3 + - - -
144U TRP* 4.9 10.3 - + - -
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Residues in contact with TRP 32 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Q VAL* 4.4 5.2 - - + -
21Q ASN* 5.1 2.5 - - - -
57Q MET* 3.6 28.9 - - + -
58Q ASP* 3.5 18.5 + - - -
61Q ALA* 3.6 25.7 - - + +
62Q GLU* 4.8 7.0 - - + +
65Q LEU* 3.7 41.3 - - + +
71Q PRO* 4.1 19.1 - - + -
72Q PHE 3.4 25.6 - - - -
73Q SER* 4.2 15.9 - - - -
78Q PHE* 5.0 3.4 - + - -
25S VAL* 5.5 0.9 - - + -
28S HIS* 2.8 57.2 + + + +
29S GLN 4.0 1.8 - - - +
31S HIS* 1.3 91.3 - + - +
33S TYR* 1.3 65.0 + + + +
34S MET 3.8 2.4 + - - +
39S PHE* 5.4 0.2 - - - -
144U TRP* 4.2 11.6 + - - -
----------------------------------------------------------
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Residues in contact with TYR 33 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65Q LEU* 5.2 4.0 - - + -
70Q SER* 3.1 35.6 - - - -
71Q PRO* 2.4 45.5 + - + -
73Q SER* 3.7 17.4 + - - -
29S GLN* 3.1 29.6 + - + +
30S ILE* 4.0 1.6 - - - +
32S TRP* 1.3 82.0 - - + +
34S MET* 1.3 61.1 + - - +
35S ARG* 3.8 11.7 + - - +
89S TYR* 3.4 72.6 + + + +
93S LYS 5.2 1.2 - - - +
98S LEU* 4.3 5.0 - - + +
----------------------------------------------------------
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Residues in contact with MET 34 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30S ILE* 3.1 47.4 + - + +
31S HIS* 3.3 15.3 - - - +
32S TRP 3.5 2.5 - - - +
33S TYR* 1.3 79.3 - - - +
35S ARG* 1.3 66.1 + - - +
39S PHE* 3.4 35.7 - - + +
42S LEU* 4.0 9.9 - - + +
43S GLY* 3.6 26.7 - - - -
46S MET* 3.5 21.1 - - + -
95S MET* 3.5 25.8 - - + -
98S LEU* 3.8 14.6 - - + -
99S MET* 4.6 0.7 - - + -
144U TRP* 5.5 0.3 + - - -
148U ALA* 3.9 2.4 - - - +
----------------------------------------------------------
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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