Contacts of the helix formed by residues 38 - 67 (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 ASN 38 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36N GLY 3.1 1.6 + - - -
37N HIS* 1.3 83.8 + - - +
39N PHE* 1.3 64.3 + - - +
40N PHE 3.3 2.7 - - - -
41N THR* 3.2 19.9 - - + +
42N LEU* 2.9 43.0 + - + +
95N MET* 3.7 11.4 - - + +
149N PHE* 4.0 4.6 - - - -
38R ASN* 4.8 8.9 - - - +
41R THR* 6.2 0.6 - - - +
37V HIS* 2.8 59.3 + - - +
38V ASN* 4.8 5.9 - - - +
41V THR* 5.8 1.2 - - - +
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Residues in contact with PHE 39 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31N HIS* 4.6 5.6 - + - -
32N TRP 5.5 0.4 - - - -
34N MET* 3.3 38.5 - - + +
36N GLY 3.0 17.2 + - - +
37N HIS 3.2 2.2 - - - -
38N ASN* 1.3 76.5 - - - +
40N PHE* 1.3 75.4 + + + +
43N GLY* 2.8 29.6 + - - -
95N MET* 3.7 10.2 - - + +
144R TRP* 3.8 31.9 - + - -
145R MET* 3.6 46.0 - - + -
148R ALA* 3.5 21.3 - - + +
149R PHE* 4.3 10.1 - - - +
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Residues in contact with PHE 40 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N HIS 4.8 1.1 + - - +
38N ASN 3.3 0.6 - - - -
39N PHE* 1.3 85.1 - + - +
41N THR* 1.3 63.0 + - - +
43N GLY* 3.1 11.0 + - - -
44N GLU* 3.1 27.3 + - - +
41R THR* 4.0 13.7 - - - +
42R LEU* 4.3 13.9 - - + -
44R GLU* 5.9 0.7 - - - +
45R LYS* 3.5 42.6 - - + -
145R MET* 3.9 36.8 - - + -
146R PHE* 3.6 39.3 - + - -
149R PHE* 3.9 32.3 - + + -
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Residues in contact with THR 41 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N HIS 5.2 0.2 - - - +
38N ASN* 3.2 42.2 - - + +
40N PHE* 1.3 78.7 - - - +
42N LEU* 1.3 64.1 + - + +
44N GLU* 3.8 9.3 + - - +
45N LYS* 3.4 23.7 + - - +
149N PHE* 5.4 0.9 - - + -
41R THR* 4.7 12.1 + - + -
37V HIS 5.2 1.8 - - - +
40V PHE* 3.8 17.7 - - + +
41V THR* 3.8 28.1 - - + +
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Residues in contact with LEU 42 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34N MET* 3.8 15.3 - - + -
38N ASN* 2.9 18.8 + - + +
41N THR* 1.3 81.7 - - + +
43N GLY* 1.3 60.0 + - - +
45N LYS* 3.7 5.7 - - + +
46N MET* 3.1 35.2 + - + +
95N MET* 3.5 28.0 - - + -
99N MET* 4.1 16.6 - - + -
146N PHE* 4.5 8.5 - - + -
149N PHE* 3.3 34.8 - - + -
40V PHE* 3.8 35.4 - - + -
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Residues in contact with GLY 43 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31N HIS* 3.1 38.8 + - - -
34N MET* 3.9 7.1 - - - -
39N PHE* 2.8 25.0 + - - -
40N PHE* 3.1 2.4 + - - -
42N LEU* 1.3 76.6 - - - +
44N GLU* 1.3 60.7 + - - +
47N ASP* 3.3 11.2 + - - +
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Residues in contact with GLU 44 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40N PHE* 3.1 26.8 + - - +
41N THR* 4.1 8.0 - - - +
43N GLY* 1.3 75.6 - - - +
45N LYS* 1.3 66.6 + - + +
47N ASP* 3.2 11.5 + - - +
48N ASP* 3.1 31.5 + - - +
44R GLU* 4.7 12.1 - - - +
45R LYS* 4.6 15.4 - - - -
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Residues in contact with LYS 45 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41N THR* 3.4 17.6 + - - +
42N LEU* 3.4 6.7 + - + +
43N GLY 3.4 0.2 - - - -
44N GLU* 1.3 81.3 - - + +
46N MET* 1.3 61.0 + - + +
48N ASP* 3.4 20.9 + - - +
49N LEU* 3.0 29.4 + - - +
142N HIS* 4.6 9.3 - - - -
145N MET* 4.5 14.0 - - - +
146N PHE* 4.1 23.8 - - + -
40V PHE* 3.7 49.8 - - + -
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Residues in contact with MET 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27N ILE* 3.3 21.2 - - + +
30N ILE* 4.0 22.7 - - + -
31N HIS* 3.7 26.0 - - + +
34N MET* 3.8 16.8 - - + -
42N LEU* 3.1 23.8 + - + +
45N LYS* 1.3 77.1 - - + +
47N ASP* 1.3 59.7 + - - +
49N LEU* 4.4 7.0 - - + -
50N TYR* 2.8 30.9 + - - +
99N MET* 4.2 9.4 - - + -
102N LEU* 4.1 17.9 - - + -
146N PHE* 3.7 34.5 - - + -
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Residues in contact with ASP 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28N HIS* 5.7 4.7 - - - -
31N HIS* 3.1 22.7 + - - -
43N GLY 3.3 15.1 + - - +
44N GLU* 3.2 15.5 + - - +
46N MET* 1.3 76.7 - - - +
48N ASP* 1.3 66.3 + - - +
50N TYR* 3.4 7.6 + - - +
51N SER* 3.2 23.4 + - - -
58P ASP* 5.5 4.0 - - - +
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Residues in contact with ASP 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44N GLU* 3.1 17.4 + - - +
45N LYS* 3.6 28.4 - - - +
46N MET 3.3 0.2 - - - -
47N ASP* 1.3 78.1 - - - +
49N LEU* 1.3 60.6 + - + +
51N SER* 3.2 5.9 + - - -
52N GLU* 2.8 31.3 + - - +
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Residues in contact with LEU 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23N PHE* 4.4 5.2 - - + -
27N ILE* 4.1 19.3 - - + -
45N LYS* 3.0 18.4 + - - +
46N MET* 3.9 11.0 - - + +
48N ASP* 1.3 75.3 - - + +
50N TYR* 1.3 66.9 + - - +
52N GLU* 4.2 3.8 - - - +
53N PHE* 2.9 47.7 + - + +
102N LEU* 4.1 31.2 - - + -
106N LEU* 5.0 3.4 - - + -
142N HIS* 3.4 44.6 - - + +
146N PHE* 4.4 10.3 - - + -
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Residues in contact with TYR 50 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24N THR* 3.5 50.4 + - + +
27N ILE* 3.8 14.3 - - + +
28N HIS* 3.3 47.9 + + + +
46N MET 2.8 19.5 + - - +
47N ASP* 3.7 7.9 - - - +
48N ASP 3.1 0.2 - - - -
49N LEU* 1.3 78.3 - - - +
51N SER* 1.3 68.8 + - - +
53N PHE 4.0 0.2 - - - -
54N GLY* 3.1 21.9 + - - -
24P THR* 5.6 4.0 - - - +
50P TYR* 4.4 16.0 + + - -
54P GLY* 5.9 3.7 - - - -
57P MET* 4.7 7.1 - - - +
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Residues in contact with SER 51 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47N ASP 3.2 12.6 + - - -
48N ASP* 3.2 9.5 + - - -
50N TYR* 1.3 79.7 - - - +
52N GLU* 1.3 66.8 + - - +
54N GLY* 3.2 2.8 + - - -
55N GLU* 3.1 26.0 + - - +
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Residues in contact with GLU 52 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48N ASP 2.8 20.6 + - - +
49N LEU* 3.8 5.7 - - - +
51N SER* 1.3 74.3 - - - +
53N PHE* 1.3 71.8 + - + +
55N GLU* 3.3 19.4 + - - +
56N GLN* 3.1 35.1 + - + +
138N SER* 2.5 30.7 + - - -
142N HIS* 2.7 27.9 + - - -
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Residues in contact with PHE 53 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20N LEU* 4.2 14.5 - - + +
23N PHE* 3.6 33.4 - + + -
24N THR* 4.4 8.3 + - - +
27N ILE* 4.5 5.6 - - + -
49N LEU* 2.9 54.8 + - + +
50N TYR 4.5 0.9 - - - +
52N GLU* 1.3 89.5 - - + +
54N GLY* 1.3 62.7 + - - +
56N GLN* 3.6 34.6 - - - +
57N MET* 3.2 21.7 + - - +
106N LEU* 3.9 12.8 - - + -
109N LEU* 4.5 3.8 - - + -
139N ILE* 3.8 29.4 - - + -
142N HIS* 4.1 8.3 - + - -
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Residues in contact with GLY 54 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24N THR* 4.2 8.6 + - - -
50N TYR* 3.1 17.4 + - - -
51N SER* 3.2 3.3 + - - -
53N PHE* 1.3 78.4 - - - +
55N GLU* 1.3 55.6 + - - +
57N MET* 3.2 16.7 - - - +
58N ASP* 3.0 24.9 + - - +
28P HIS* 5.3 2.1 + - - -
50P TYR* 5.5 7.4 - - - -
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Residues in contact with GLU 55 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51N SER 3.1 13.1 + - - +
52N GLU* 3.7 21.2 - - - +
54N GLY* 1.3 72.4 - - - +
56N GLN* 1.3 63.6 + - - +
57N MET 3.1 1.6 - - - -
58N ASP* 3.3 8.0 + - - +
59N GLU* 3.0 39.5 + - + +
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Residues in contact with GLN 56 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20N LEU* 4.1 5.8 - - + +
52N GLU* 3.1 28.6 + - + +
53N PHE* 3.6 45.4 - - - +
54N GLY 3.4 0.2 - - - -
55N GLU* 1.3 75.0 - - - +
57N MET* 1.3 57.8 - - - +
59N GLU* 3.2 3.8 + - - +
60N VAL* 2.9 34.2 + - - +
113N TYR* 3.1 25.5 + - - -
135N PHE* 3.6 59.4 + - + +
138N SER* 4.7 0.8 + - - -
139N ILE* 4.2 1.4 - - - +
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Residues in contact with MET 57 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17N VAL* 4.2 8.2 - - - +
20N LEU* 3.5 32.1 - - + -
21N ASN* 3.0 46.4 - - - +
24N THR* 5.9 4.3 - - + -
53N PHE 3.2 13.1 + - - +
54N GLY* 3.2 17.3 - - - +
56N GLN* 1.3 82.4 - - - +
58N ASP* 1.3 60.2 + - - +
60N VAL* 3.8 3.8 + - - +
61N ALA* 3.2 19.1 + - - +
28P HIS* 3.6 31.2 - - + +
32P TRP* 3.9 15.9 - - + -
50P TYR* 4.6 7.6 - - - +
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Residues in contact with ASP 58 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54N GLY 3.0 14.9 + - - +
55N GLU* 3.8 8.5 - - - +
56N GLN 3.2 0.4 - - - -
57N MET* 1.3 77.2 - - - +
59N GLU* 1.3 63.5 + - - +
61N ALA* 3.4 4.4 + - - +
62N GLU* 2.7 58.5 + - - +
28P HIS* 4.8 13.9 - - + +
31P HIS* 4.5 6.5 + - - -
32P TRP* 3.5 22.3 + - - -
47P ASP* 5.4 3.0 - - - +
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Residues in contact with GLU 59 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55N GLU* 3.0 32.5 + - + +
56N GLN* 3.2 4.5 + - - +
58N ASP* 1.3 82.3 - - - +
60N VAL* 1.3 52.0 + - - +
62N GLU* 3.8 10.1 - - - +
63N ARG* 2.8 35.2 + - - +
131N MET* 3.9 11.3 - - - +
135N PHE* 3.4 29.4 - - + -
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Residues in contact with VAL 60 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13N LEU* 3.4 37.5 - - + +
16N GLN* 4.4 7.0 - - + -
17N VAL* 3.6 19.5 - - + +
20N LEU* 4.2 12.3 - - + -
56N GLN 2.9 18.9 + - - +
57N MET* 4.0 5.8 - - - +
58N ASP 3.3 0.2 - - - -
59N GLU* 1.3 73.7 - - - +
61N ALA* 1.3 59.9 + - - +
63N ARG* 3.4 2.0 + - - +
64N LEU* 2.9 28.4 + - - +
113N TYR* 5.0 1.1 - - + +
131N MET* 3.9 15.5 - - + -
132N LEU* 5.3 2.2 - - + -
135N PHE* 3.6 24.5 - - + -
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Residues in contact with ALA 61 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17N VAL* 4.1 15.7 - - + -
57N MET 3.2 17.5 + - - +
58N ASP 3.8 3.6 - - - +
59N GLU 3.4 0.2 - - - -
60N VAL* 1.3 79.9 - - - +
62N GLU* 1.3 56.3 + - - +
64N LEU* 3.6 5.0 + - - +
65N LEU* 3.1 33.5 + - - +
71N PRO* 4.1 5.8 - - + +
32P TRP* 3.6 41.1 - - + +
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Residues in contact with GLU 62 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58N ASP* 2.7 47.3 + - - +
59N GLU* 3.8 9.8 - - - +
61N ALA* 1.3 75.3 - - - +
63N ARG* 1.3 64.9 + - - +
65N LEU* 3.4 10.4 + - + +
66N ALA* 3.0 24.9 + - - +
31P HIS* 4.3 11.4 + - - -
32P TRP* 5.2 2.9 - - + +
47P ASP* 5.6 1.0 - - - +
141S LYS* 4.2 18.8 - - + +
144S TRP* 3.7 35.1 - - + -
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Residues in contact with ARG 63 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13N LEU* 4.0 9.2 - - + -
59N GLU 2.8 22.9 + - - +
60N VAL 3.4 3.8 + - - +
62N GLU* 1.3 73.6 - - - +
64N LEU* 1.3 59.9 + - - +
66N ALA* 3.3 17.0 + - - +
67N ILE* 3.3 32.0 + - - +
125N ASP* 2.9 27.7 + - - -
127N VAL* 3.2 33.7 - - + +
128N THR* 2.9 22.7 + - + +
131N MET* 3.7 24.7 - - + -
136S LYS* 4.3 4.0 - - - +
137S ALA 5.2 1.0 + - - -
140S ASP* 3.1 38.8 + - - +
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Residues in contact with LEU 64 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10N LYS* 3.6 35.9 - - + +
13N LEU* 4.2 12.2 - - + +
14N ASN* 3.7 41.5 - - + +
17N VAL* 4.9 2.2 - - + -
60N VAL 2.9 17.2 + - - +
61N ALA* 3.6 5.6 - - - +
63N ARG* 1.3 73.5 - - - +
65N LEU* 1.3 57.5 + - - +
66N ALA 3.4 0.3 + - - -
67N ILE* 3.4 11.7 + - + +
69N GLY* 2.7 52.2 + - - -
70N SER 4.2 1.8 - - - +
71N PRO* 3.8 22.4 - - + -
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Residues in contact with LEU 65 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61N ALA 3.1 29.0 + - - +
62N GLU* 3.6 7.6 - - - +
64N LEU* 1.3 76.7 - - - +
66N ALA* 1.3 59.1 + - - +
68N GLY* 3.1 16.3 + - - -
69N GLY 3.8 10.4 - - - +
71N PRO* 3.7 24.4 - - + +
32P TRP* 3.6 46.0 - - + +
33P TYR* 5.2 5.4 - - + -
144S TRP* 3.7 37.7 - - + +
154S PRO* 3.3 16.7 - - - +
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Residues in contact with ALA 66 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62N GLU 3.0 18.1 + - - +
63N ARG* 3.6 23.5 + - - +
64N LEU 3.2 0.4 - - - -
65N LEU* 1.3 76.5 - - - +
67N ILE* 1.3 59.4 + - - +
68N GLY 3.3 1.7 + - - -
140S ASP* 4.2 20.6 - - - +
141S LYS* 4.7 4.7 - - - +
144S TRP* 4.1 23.6 - - + -
154S PRO* 4.2 11.7 - - - +
155S LEU* 4.8 3.6 - - - +
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Residues in contact with ILE 67 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9N THR* 3.8 30.1 - - + -
10N LYS* 3.8 30.5 - - + +
13N LEU* 4.1 16.4 - - + -
63N ARG* 3.3 39.4 + - - +
64N LEU* 3.5 15.5 - - + +
65N LEU 3.3 0.2 - - - -
66N ALA* 1.3 78.3 - - - +
68N GLY* 1.3 57.8 + - - +
69N GLY 3.6 0.2 + - - -
125N ASP* 4.1 7.9 - - - +
128N THR* 4.6 0.2 - - - +
155S LEU* 3.7 20.4 - - + +
----------------------------------------------------------
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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).
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