Contacts of the helix formed by residues 8 - 34 (chain N) 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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7N VAL* 1.3 76.2 - - - +
9N THR* 1.3 67.6 + - - +
10N LYS* 3.9 25.2 - - + +
11N GLU* 3.1 43.7 + - - +
12N PHE* 3.2 10.0 + - - +
119N LEU* 3.8 8.1 - - - +
123N GLU* 3.6 13.9 - - - +
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Residues in contact with THR 9 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8N ASP* 1.3 74.6 - - - +
10N LYS* 1.3 63.1 + - - +
12N PHE* 3.4 3.7 + - + +
13N LEU* 3.1 32.3 + - + +
67N ILE* 3.8 15.5 - - + -
119N LEU* 4.1 9.0 + - - +
120N THR* 3.7 25.0 + - + +
123N GLU* 3.1 30.3 + - - +
125N ASP* 3.7 25.3 - - - +
128N THR* 4.2 8.7 - - + -
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Residues in contact with LYS 10 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8N ASP* 3.2 17.6 + - - +
9N THR* 1.3 79.4 - - - +
11N GLU* 1.3 61.9 + - - +
14N ASN* 3.1 24.4 + - - +
64N LEU* 3.6 18.1 - - + +
67N ILE* 3.8 31.0 - - + +
68N GLY 3.6 16.9 + - - -
69N GLY* 3.8 21.8 - - - -
70N SER 5.3 0.8 - - - +
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Residues in contact with GLU 11 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7N VAL* 3.0 37.3 - - + +
8N ASP* 3.1 28.0 + - - +
10N LYS* 1.3 73.4 - - - +
12N PHE* 1.3 69.1 + - - +
14N ASN* 3.2 7.4 + - - +
15N HIS* 2.9 22.6 + - - +
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Residues in contact with PHE 12 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7N VAL* 4.1 11.7 - - + +
8N ASP 3.2 9.0 + - - +
9N THR* 3.6 9.2 - - + +
11N GLU* 1.3 79.0 - - - +
13N LEU* 1.3 76.8 + - + +
15N HIS* 2.9 19.5 + - + +
16N GLN* 3.1 42.6 + - + +
112N GLU* 3.1 35.2 - - + -
113N TYR* 4.0 5.2 - - - -
115N GLN* 4.5 5.8 - - + -
116N GLY* 3.3 28.7 - - - -
119N LEU* 4.3 13.2 - - + -
120N THR* 5.8 2.0 - - + -
132N LEU* 3.9 21.5 - - + -
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Residues in contact with LEU 13 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9N THR* 3.1 13.3 + - + +
10N LYS 4.0 3.1 - - - +
12N PHE* 1.3 94.5 - - + +
14N ASN* 1.3 61.6 + - - +
16N GLN* 3.3 3.5 + - + +
17N VAL* 3.2 18.4 + - - +
60N VAL* 3.4 30.1 - - + +
63N ARG* 4.0 18.4 - - + -
64N LEU* 4.2 18.2 - - + +
67N ILE* 4.1 18.6 - - + -
128N THR* 3.5 38.4 - - + +
131N MET* 3.9 15.7 - - + -
132N LEU* 4.1 8.1 - - + -
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Residues in contact with ASN 14 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10N LYS 3.1 19.7 + - - +
11N GLU* 3.6 7.2 - - - +
12N PHE 3.1 0.2 - - - -
13N LEU* 1.3 76.7 - - - +
15N HIS* 1.3 59.2 + - - +
17N VAL* 3.3 5.9 + - - +
18N ALA 3.3 10.9 + - - -
64N LEU* 3.7 14.7 - - + +
70N SER 3.2 22.6 + - - +
71N PRO* 3.4 5.2 - - - +
72N PHE* 2.9 66.8 + - + +
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Residues in contact with HIS 15 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11N GLU 2.9 11.4 + - - +
12N PHE* 2.9 14.6 + + + +
14N ASN* 1.3 73.2 - - - +
16N GLN* 1.3 79.9 + - - +
18N ALA* 3.2 7.5 + - - +
19N ASN* 2.9 35.4 + - - +
72N PHE* 4.4 6.7 - - - -
81N ASN* 3.0 31.6 + - + -
82N ALA 4.3 0.2 - - - -
83N SER* 3.0 34.3 + - - -
112N GLU* 3.3 13.4 + - - -
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Residues in contact with GLN 16 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N PHE* 3.1 39.6 + - + +
13N LEU* 3.6 8.7 - - + +
15N HIS* 1.3 92.6 + - - +
17N VAL* 1.3 57.4 + - - +
19N ASN* 2.9 18.5 + - - +
20N LEU* 2.7 50.8 + - + +
60N VAL* 4.4 7.9 - - + -
109N LEU* 3.5 10.2 - - - +
112N GLU* 2.9 23.1 + - - +
113N TYR* 3.4 32.2 - - + +
132N LEU* 5.7 1.6 - - + -
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Residues in contact with VAL 17 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13N LEU 3.2 10.5 + - - +
14N ASN* 3.3 20.3 + - - +
16N GLN* 1.3 73.0 - - - +
18N ALA* 1.3 63.1 + - - +
20N LEU* 4.1 0.7 - - - +
21N ASN* 2.8 45.3 + - - +
57N MET* 4.4 13.5 - - - +
60N VAL* 3.6 23.7 - - + +
61N ALA* 4.1 20.0 - - + +
64N LEU* 4.9 1.1 - - + -
71N PRO* 4.6 4.5 - - + -
72N PHE* 3.9 13.2 - - + +
78N PHE* 3.8 15.9 - - + -
32P TRP* 4.5 7.2 - - + -
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Residues in contact with ALA 18 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N ASN 3.3 6.5 + - - +
15N HIS 3.2 9.1 + - - +
16N GLN 3.1 0.6 - - - -
17N VAL* 1.3 80.7 - - - +
19N ASN* 1.3 62.7 + - - +
21N ASN* 3.3 4.7 + - - +
22N VAL* 3.1 24.4 + - - +
72N PHE* 4.3 2.4 - - + -
78N PHE* 3.6 42.1 - - + +
81N ASN* 4.0 18.2 - - + -
82N ALA* 4.0 6.5 - - - +
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Residues in contact with ASN 19 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15N HIS* 2.9 18.3 + - - +
16N GLN* 2.9 24.9 + - - +
18N ALA* 1.3 75.5 - - - +
20N LEU* 1.3 58.2 + - - +
22N VAL* 3.1 4.5 + - - +
23N PHE* 2.8 31.0 + - - +
82N ALA* 3.3 8.9 - - - +
83N SER* 3.0 33.0 + - - -
84N VAL* 3.8 21.0 - - + +
108N LEU* 4.4 0.2 - - - +
109N LEU* 3.9 10.8 - - + +
112N GLU* 2.8 30.1 + - - -
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Residues in contact with LEU 20 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16N GLN* 2.7 32.6 + - + +
19N ASN* 1.3 73.4 - - + +
21N ASN* 1.3 58.0 + - - +
23N PHE* 3.4 5.8 + - + +
24N THR* 2.9 32.3 + - - -
53N PHE* 4.2 19.9 - - + +
56N GLN* 4.1 10.8 - - - +
57N MET* 3.5 40.2 - - + +
60N VAL* 4.2 13.7 - - + -
109N LEU* 3.9 28.0 - - + -
113N TYR* 3.4 28.3 - - - +
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Residues in contact with ASN 21 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17N VAL* 2.8 29.5 + - - +
18N ALA 3.7 2.0 - - - +
19N ASN 3.2 0.2 - - - -
20N LEU* 1.3 78.5 - - - +
22N VAL* 1.3 58.3 + - - +
24N THR* 3.7 11.1 - - - +
25N VAL* 3.6 23.9 + - - +
57N MET* 3.0 43.4 - - - +
78N PHE* 3.3 48.2 - - + -
25P VAL* 4.1 10.9 - - - +
28P HIS* 5.2 0.3 - - - -
32P TRP* 4.7 0.8 - - - -
75P LEU* 3.8 4.7 - - - +
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Residues in contact with VAL 22 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18N ALA 3.1 14.3 + - - +
19N ASN 3.1 6.1 + - - +
21N ASN* 1.3 72.8 - - - +
23N PHE* 1.3 66.9 + - - +
24N THR 3.1 2.0 + - - -
25N VAL* 3.3 4.0 + - - +
26N LYS* 3.0 21.1 + - - +
78N PHE 4.5 5.8 - - - +
79N LEU* 5.0 6.5 - - + -
82N ALA* 3.6 22.4 - - + -
84N VAL* 3.7 28.3 - - + +
85N GLU 4.3 3.8 - - - +
86N GLU* 3.9 29.3 - - + +
75P LEU* 4.0 19.5 - - + +
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Residues in contact with PHE 23 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19N ASN 2.8 16.9 + - - +
20N LEU* 3.6 8.1 - - + +
22N VAL* 1.3 76.9 - - - +
24N THR* 1.3 57.0 + - - +
26N LYS* 3.3 11.4 + - + +
27N ILE* 3.0 40.1 + - + +
49N LEU* 4.4 2.5 - - + -
53N PHE* 3.6 37.5 - + + -
84N VAL* 4.4 5.4 - - + +
102N LEU* 3.5 27.6 - - + -
105N THR* 3.4 31.2 - - + -
106N LEU* 3.4 29.4 - - + -
109N LEU* 3.7 18.2 - - + -
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Residues in contact with THR 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20N LEU 2.9 17.4 + - - +
21N ASN* 3.7 18.2 - - - +
22N VAL 3.1 0.2 - - - -
23N PHE* 1.3 74.9 - - - +
25N VAL* 1.3 73.4 + - + +
27N ILE* 3.3 14.6 + - - +
28N HIS* 3.4 8.5 + - - +
50N TYR* 3.5 44.2 + - + +
53N PHE* 4.4 6.6 + - - +
54N GLY* 4.2 22.1 + - - -
57N MET* 5.9 3.8 - - + -
50P TYR* 5.7 3.6 - - - +
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Residues in contact with VAL 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21N ASN 3.6 7.6 + - - +
22N VAL 3.3 3.6 + - - +
24N THR* 1.3 83.6 - - + +
26N LYS* 1.3 55.8 + - - +
28N HIS* 3.3 12.2 + - + +
29N GLN* 3.0 25.3 + - - +
32N TRP* 6.1 0.7 - - + -
86N GLU* 4.7 1.3 - - - +
21P ASN* 4.2 10.1 - - - +
73P SER* 3.5 22.9 - - - +
74P THR* 4.1 1.8 - - - -
75P LEU* 3.6 31.0 - - + -
78P PHE* 3.5 32.8 - - + -
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Residues in contact with LYS 26 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22N VAL* 3.0 13.0 + - + +
23N PHE* 3.5 18.2 - - + +
24N THR 3.2 0.2 - - - -
25N VAL* 1.3 75.0 - - - +
27N ILE* 1.3 58.3 + - - +
29N GLN* 3.2 22.0 + - - +
30N ILE* 2.9 43.0 + - + +
84N VAL* 4.1 11.0 - - - -
85N GLU 2.6 31.9 + - - -
86N GLU* 3.9 12.7 - - + +
87N ALA 5.0 1.4 - - - +
101N ASP* 3.0 37.4 + - - +
102N LEU 5.2 0.4 - - - +
105N THR* 3.5 23.6 - - - +
73P SER 5.1 1.8 - - - -
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Residues in contact with ILE 27 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23N PHE* 3.0 54.3 + - + +
24N THR* 3.6 13.5 - - - +
25N VAL 3.3 0.4 - - - -
26N LYS* 1.3 75.8 - - - +
28N HIS* 1.3 63.8 + - - +
30N ILE* 3.3 10.5 + - - +
31N HIS* 3.1 21.9 + - + +
46N MET* 3.3 40.7 - - + +
49N LEU* 4.0 32.3 - - + +
50N TYR* 3.8 14.1 - - + +
53N PHE* 4.5 3.4 - - + -
102N LEU* 4.7 4.5 - - + -
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Residues in contact with HIS 28 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24N THR 3.4 2.8 + - - +
25N VAL* 3.3 15.0 + - + +
26N LYS 3.2 0.2 - - - -
27N ILE* 1.3 77.2 - - - +
29N GLN* 1.3 59.6 + - - +
31N HIS* 3.2 9.3 + + - +
32N TRP* 2.8 65.2 + + + -
47N ASP* 5.7 4.5 - - - -
50N TYR* 3.3 53.6 + + + +
21P ASN* 5.3 1.6 - - - -
54P GLY 5.4 1.4 + - - -
57P MET* 3.7 28.4 - - + +
58P ASP* 4.3 20.4 + - + +
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Residues in contact with GLN 29 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25N VAL 3.0 11.4 + - - +
26N LYS* 3.2 28.6 + - - +
28N HIS* 1.3 76.3 - - - +
30N ILE* 1.3 65.5 + - + +
32N TRP* 3.3 4.1 + - - -
33N TYR* 3.1 34.6 + - + +
86N GLU* 6.1 1.2 - - - +
87N ALA 3.0 27.8 + - - +
89N TYR* 3.8 17.4 + - + -
93N LYS* 4.6 11.7 - - - +
98N LEU* 5.2 6.7 - - + +
101N ASP* 4.7 7.7 + - - -
73P SER* 2.9 46.7 + - - +
74P THR* 5.3 0.2 - - - -
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Residues in contact with ILE 30 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26N LYS* 2.9 30.6 + - + +
27N ILE* 3.6 11.9 - - - +
28N HIS 3.2 0.2 - - - -
29N GLN* 1.3 77.5 - - + +
31N HIS* 1.3 58.8 + - - +
33N TYR 3.9 0.2 - - - -
34N MET* 3.0 44.5 + - + +
46N MET* 4.0 6.5 - - - -
98N LEU* 3.9 36.8 - - + +
99N MET* 3.5 27.1 - - + -
101N ASP* 5.5 2.5 - - - +
102N LEU* 3.7 41.7 - - + +
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Residues in contact with HIS 31 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27N ILE* 3.1 16.8 + - + +
28N HIS* 3.5 11.4 - + - +
30N ILE* 1.3 75.4 - - - +
32N TRP* 1.3 82.6 + + - +
34N MET* 3.2 27.5 - - - +
39N PHE* 4.6 9.3 - + - -
43N GLY* 3.1 37.9 + - - -
46N MET* 3.7 14.2 - - + +
47N ASP* 3.1 25.0 + - - -
58P ASP* 4.8 4.1 + - - -
62P GLU* 4.0 16.5 + - - -
144R TRP* 4.9 10.5 - + - -
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Residues in contact with TRP 32 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25N VAL* 6.1 0.4 - - + -
28N HIS* 2.8 54.4 + + + +
29N GLN 3.9 2.2 - - - +
31N HIS* 1.3 91.5 - + - +
33N TYR* 1.3 68.4 + - + +
34N MET 3.9 2.1 + - - +
39N PHE* 5.5 0.2 - - - -
17P VAL* 4.3 7.0 - - + -
21P ASN* 4.9 2.5 - - - -
57P MET* 3.7 29.4 - - + -
58P ASP* 3.3 21.3 + - - -
61P ALA* 3.4 25.3 - - + +
62P GLU* 4.9 4.5 - - + +
65P LEU* 3.7 42.7 - - + +
71P PRO* 3.9 18.4 - - + -
72P PHE 3.4 23.6 - - - -
73P SER* 4.1 15.0 - - - -
78P PHE* 4.9 3.4 - + - -
144R TRP* 4.3 9.3 + + - -
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Residues in contact with TYR 33 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N GLN* 3.1 27.5 + - + +
30N ILE 3.9 0.7 - - - +
32N TRP* 1.3 84.4 - - + +
34N MET* 1.3 65.4 + - - +
35N ARG* 3.5 13.2 + - - +
89N TYR* 3.2 71.0 + + + +
93N LYS 5.5 0.9 - - - +
98N LEU* 4.4 3.9 - - + +
65P LEU* 5.2 4.7 - - + -
70P SER* 3.3 32.1 + - - -
71P PRO* 2.6 42.9 + - + -
73P SER* 3.7 17.0 + - - -
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Residues in contact with MET 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30N ILE* 3.0 39.3 + - + +
31N HIS* 3.2 20.0 - - - +
32N TRP 3.5 1.4 - - - +
33N TYR* 1.3 79.4 - - - +
35N ARG* 1.3 62.6 - - - +
39N PHE* 3.3 44.8 - - + +
42N LEU* 3.7 28.7 - - + +
43N GLY* 3.9 9.0 - - - -
46N MET* 3.8 9.6 - - + -
95N MET* 3.4 31.2 - - - -
98N LEU* 3.9 10.5 - - + -
99N MET* 4.4 1.3 - - + -
144R TRP* 5.8 0.2 + - - -
148R ALA* 4.0 1.7 - - - +
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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