Contacts of the helix formed by residues 8 - 34 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R THR* 1.3 64.8 + - - +
10R LYS* 3.5 21.5 + - - +
11R GLU* 3.4 39.5 + - + +
12R PHE* 3.2 17.0 + - - +
119R LEU* 3.7 31.9 - - - +
123R GLU* 3.5 15.4 + - - +
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Residues in contact with THR 9 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8R ASP* 1.3 73.5 - - - +
10R LYS* 1.3 64.2 + - - +
12R PHE* 3.3 5.2 + - + +
13R LEU* 3.0 24.0 + - + +
67R ILE* 3.8 21.8 - - + -
119R LEU* 4.2 9.1 - - - +
120R THR* 3.4 17.9 + - - +
123R GLU* 3.2 37.7 + - - +
125R ASP* 3.8 16.5 - - - +
128R THR* 4.0 20.2 - - + -
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Residues in contact with LYS 10 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8R ASP* 3.4 17.8 + - - +
9R THR* 1.3 76.9 - - - +
11R GLU* 1.3 62.3 + - - +
14R ASN* 3.0 27.3 + - - +
64R LEU* 3.4 27.7 - - + +
67R ILE* 4.2 25.1 + - + +
68R GLY* 4.3 14.5 + - - -
69R GLY* 3.9 20.2 - - - +
123R GLU* 6.1 0.2 - - - +
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Residues in contact with GLU 11 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8R ASP* 3.4 26.1 + - + +
9R THR 3.3 0.4 - - - -
10R LYS* 1.3 81.3 - - - +
12R PHE* 1.3 64.2 + - - +
14R ASN* 3.5 14.9 + - - +
15R HIS* 3.0 24.3 + - - +
72R PHE* 5.5 2.9 - - - -
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Residues in contact with PHE 12 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8R ASP 3.2 11.3 + - - +
9R THR* 3.3 8.3 + - + +
11R GLU* 1.3 78.3 - - - +
13R LEU* 1.3 70.1 + - + +
15R HIS* 3.2 9.5 + - + +
16R GLN* 3.1 56.9 + - + +
112R GLU* 3.2 29.4 - - + -
113R TYR* 3.9 10.3 - + - -
115R GLN* 5.2 2.9 - - + -
116R GLY* 3.5 22.2 - - - -
119R LEU* 3.9 14.6 - - + -
120R THR* 5.5 1.8 - - - -
128R THR* 5.8 0.2 - - + -
132R LEU* 3.5 34.5 - - + -
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Residues in contact with LEU 13 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R THR* 3.0 15.1 + - + +
10R LYS 3.8 4.3 - - - +
12R PHE* 1.3 88.8 - - + +
14R ASN* 1.3 58.1 + - - +
16R GLN* 3.2 4.4 + - + +
17R VAL* 2.8 25.0 + - - +
60R VAL* 3.3 35.6 - - + +
63R ARG* 4.2 7.6 - - + -
64R LEU* 4.0 24.5 - - + +
67R ILE* 3.9 28.5 - - + -
128R THR* 3.9 31.0 - - + -
131R MET* 4.2 10.5 - - + -
132R LEU* 4.4 5.6 - - + -
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Residues in contact with ASN 14 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10R LYS 3.0 17.7 + - - +
11R GLU* 3.8 15.4 + - - +
13R LEU* 1.3 75.1 - - - +
15R HIS* 1.3 65.4 + - - +
17R VAL* 3.1 6.9 + - - +
18R ALA 3.1 17.3 + - - -
64R LEU* 3.5 12.7 - - + +
70R SER 3.4 17.8 + - - -
71R PRO* 3.3 6.2 - - - +
72R PHE* 2.9 71.0 + - + +
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Residues in contact with HIS 15 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11R GLU 3.0 14.3 + - - +
12R PHE* 3.4 12.8 - - + +
14R ASN* 1.3 75.8 - - - +
16R GLN* 1.3 74.7 + - - +
18R ALA* 3.2 6.5 + - - +
19R ASN* 2.9 29.6 + - - +
72R PHE* 4.3 6.4 - - - -
81R ASN* 2.8 33.1 + - + -
82R ALA 4.1 0.2 - - - -
83R SER* 2.9 38.8 + - - -
112R GLU* 3.1 10.7 + - - -
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Residues in contact with GLN 16 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12R PHE* 3.1 44.8 + - + +
13R LEU* 3.6 8.3 - - + +
15R HIS* 1.3 85.9 + - - +
17R VAL* 1.3 67.7 + - - +
19R ASN* 2.7 24.8 + - - +
20R LEU* 2.9 41.2 + - + +
60R VAL* 4.4 8.3 - - + -
109R LEU* 3.6 14.0 - - - +
112R GLU* 3.0 24.4 + - - +
113R TYR* 3.6 22.1 - - + -
132R LEU* 5.9 1.1 - - + -
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Residues in contact with VAL 17 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R LEU 2.8 23.3 + - - +
14R ASN* 3.1 20.4 + - - +
16R GLN* 1.3 73.0 - - - +
18R ALA* 1.3 64.4 + - - +
20R LEU* 4.0 1.1 - - - +
21R ASN* 3.0 34.8 + - - +
57R MET* 4.6 8.5 - - - +
60R VAL* 3.7 17.5 - - + +
61R ALA* 3.9 21.3 - - + +
64R LEU* 4.8 3.8 - - + -
71R PRO* 4.8 1.1 - - + -
72R PHE* 3.7 23.3 - - + +
78R PHE* 4.0 11.0 - - + -
32T TRP* 4.5 11.7 - - + -
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Residues in contact with ALA 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R ASN 3.1 11.9 + - - +
15R HIS 3.6 7.0 - - - +
16R GLN 3.2 0.2 - - - -
17R VAL* 1.3 75.8 - - - +
19R ASN* 1.3 65.9 + - - +
21R ASN* 3.3 5.0 + - - +
22R VAL* 3.3 24.3 + - - +
72R PHE* 4.2 9.6 - - + -
78R PHE* 3.6 43.9 - - + +
81R ASN* 4.2 3.4 - - + -
82R ALA* 4.0 12.8 - - - +
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Residues in contact with ASN 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15R HIS* 2.9 14.6 + - - +
16R GLN* 2.7 34.3 + - - +
18R ALA* 1.3 75.8 - - - +
20R LEU* 1.3 58.0 + - - +
22R VAL* 3.1 5.0 + - - +
23R PHE* 3.0 28.7 + - - +
82R ALA* 3.5 4.3 - - - -
83R SER* 2.9 33.2 + - - -
84R VAL* 3.3 23.6 + - + +
108R LEU* 4.3 0.2 - - - +
109R LEU* 4.1 10.4 - - + +
112R GLU* 3.1 23.4 + - - -
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Residues in contact with LEU 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16R GLN* 2.9 31.3 + - + +
19R ASN* 1.3 74.5 - - + +
21R ASN* 1.3 62.3 + - - +
23R PHE* 3.9 5.1 - - + +
24R THR* 3.2 26.9 + - - -
53R PHE* 4.1 21.9 - - + +
56R GLN* 4.1 9.2 - - + +
57R MET* 3.5 46.2 - - + +
60R VAL* 4.0 15.5 - - + -
109R LEU* 4.3 20.0 - - + -
113R TYR* 3.6 26.7 - - - +
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Residues in contact with ASN 21 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R VAL* 3.0 22.4 + - - +
18R ALA 3.3 6.2 + - - +
19R ASN 3.3 0.6 - - - -
20R LEU* 1.3 81.4 - - - +
22R VAL* 1.3 58.6 + - - +
24R THR* 3.9 8.6 - - - +
25R VAL* 3.4 26.5 + - - +
57R MET* 3.2 40.5 - - - +
78R PHE* 3.1 49.0 - - + -
25T VAL* 4.0 12.1 - - - +
28T HIS* 5.5 0.9 - - - -
32T TRP* 5.0 0.2 - - - -
50T TYR* 5.6 0.5 + - - -
75T LEU* 3.8 4.1 - - + +
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Residues in contact with VAL 22 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18R ALA 3.3 13.2 + - - +
19R ASN 3.1 7.8 + - - +
21R ASN* 1.3 72.9 - - - +
23R PHE* 1.3 60.4 + - - +
24R THR 3.2 0.4 - - - -
25R VAL* 3.4 3.3 + - - +
26R LYS* 3.0 26.2 + - - +
78R PHE 4.7 3.6 - - - +
79R LEU* 5.1 7.0 - - + -
82R ALA* 3.9 19.1 - - + -
84R VAL* 3.9 27.4 - - + +
85R GLU 4.5 0.4 - - - +
86R GLU* 3.8 34.2 - - + +
75T LEU* 3.8 25.1 - - + -
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Residues in contact with PHE 23 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19R ASN 3.0 16.2 + - - +
20R LEU* 3.9 8.5 - - + +
22R VAL* 1.3 77.1 - - - +
24R THR* 1.3 56.8 + - - +
26R LYS* 3.2 14.2 + - + +
27R ILE* 2.9 41.0 + - + +
49R LEU* 4.8 0.7 - - + -
53R PHE* 3.6 48.0 - + + -
84R VAL* 4.4 5.1 - - + +
102R LEU* 3.9 31.2 - - + -
105R THR* 3.6 31.0 - - + -
106R LEU* 3.9 12.3 - - + -
109R LEU* 3.4 21.5 - - + -
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Residues in contact with THR 24 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20R LEU 3.2 17.4 + - - +
21R ASN* 3.9 13.9 - - - +
22R VAL 3.2 0.2 - - - -
23R PHE* 1.3 74.8 - - - +
25R VAL* 1.3 70.6 + - + +
27R ILE* 3.2 9.0 + - - +
28R HIS* 3.2 16.3 + - - +
50R TYR* 3.4 44.1 + - + +
53R PHE* 4.2 6.1 - - - +
54R GLY* 3.9 24.2 + - - -
57R MET* 5.9 4.8 - - + +
50T TYR* 5.7 4.5 - - - +
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Residues in contact with VAL 25 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21R ASN 3.4 14.3 + - - +
22R VAL 3.4 3.0 + - - +
23R PHE 3.4 0.2 - - - -
24R THR* 1.3 84.1 - - + +
26R LYS* 1.3 56.2 + - - +
28R HIS* 3.3 10.8 + - + +
29R GLN* 3.0 24.4 + - - +
32R TRP* 6.3 0.4 - - + -
50R TYR* 5.3 0.7 - - + +
86R GLU* 4.6 1.6 - - - +
21T ASN* 4.2 11.0 - - - +
73T SER* 3.4 23.4 - - - +
74T THR* 3.9 6.7 - - - -
75T LEU* 3.6 22.9 - - + -
78T PHE* 3.6 32.1 - - + -
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Residues in contact with LYS 26 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22R VAL* 3.0 14.9 + - + +
23R PHE* 3.2 18.4 + - + +
25R VAL* 1.3 73.8 - - - +
27R ILE* 1.3 67.3 + - - +
29R GLN* 3.1 23.5 + - - +
30R ILE* 3.0 34.5 + - + +
84R VAL* 4.4 7.4 - - - -
85R GLU 3.1 29.1 + - - -
86R GLU* 4.3 11.3 - - + +
87R ALA 5.0 2.2 - - - +
101R ASP* 2.6 38.2 + - - +
102R LEU* 5.5 0.4 - - - -
105R THR* 3.6 24.2 - - - +
73T SER 5.2 1.6 - - - -
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Residues in contact with ILE 27 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23R PHE* 2.9 50.6 + - + +
24R THR* 3.2 13.9 + - - +
26R LYS* 1.3 75.7 - - - +
28R HIS* 1.3 64.8 + - - +
30R ILE* 3.2 9.9 + - + +
31R HIS* 3.2 19.8 + - + +
46R MET* 3.2 41.3 - - + +
49R LEU* 3.9 36.6 - - + +
50R TYR* 3.8 16.8 - - + +
53R PHE* 4.5 3.8 - - + -
102R LEU* 5.5 2.9 - - + -
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Residues in contact with HIS 28 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24R THR 3.2 6.7 + - - +
25R VAL* 3.6 13.0 - - + +
26R LYS 3.2 0.4 - - - -
27R ILE* 1.3 75.7 - - - +
29R GLN* 1.3 66.3 + - - +
31R HIS* 3.3 9.4 + + - +
32R TRP* 2.9 55.3 + + + -
47R ASP* 5.4 6.3 - - - -
50R TYR* 3.2 55.8 + + + +
21T ASN* 5.6 0.7 - - - -
57T MET* 3.5 30.9 - - + +
58T ASP* 3.7 27.1 + - - -
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Residues in contact with GLN 29 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25R VAL 3.0 13.8 + - - +
26R LYS* 3.2 28.9 - - - +
28R HIS* 1.3 75.3 - - - +
30R ILE* 1.3 61.5 + - + +
32R TRP* 4.5 2.1 - - - -
33R TYR* 3.0 46.6 + - + +
87R ALA 3.0 27.7 + - - +
88R PRO* 4.1 0.3 - - - +
89R TYR* 3.8 21.9 + - + +
93R LYS* 5.6 4.9 - - - +
98R LEU* 5.8 4.5 - - + +
101R ASP* 5.2 3.2 + - - -
73T SER* 2.7 44.6 + - - +
74T THR* 4.2 0.6 - - - +
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Residues in contact with ILE 30 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23R PHE* 6.4 0.4 - - + -
26R LYS* 3.0 27.7 + - + +
27R ILE* 3.6 9.6 - - + +
28R HIS 3.2 0.2 - - - -
29R GLN* 1.3 83.8 - - + +
31R HIS* 1.3 56.0 + - - +
34R MET* 3.0 51.2 + - + +
46R MET* 3.8 11.7 - - - -
98R LEU* 3.7 46.4 - - + +
99R MET* 3.7 15.3 - - + -
101R ASP* 5.5 2.9 - - + +
102R LEU* 4.2 24.7 - - + +
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Residues in contact with HIS 31 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27R ILE* 3.2 13.6 + - + +
28R HIS* 3.8 11.5 + + - +
30R ILE* 1.3 77.7 - - - +
32R TRP* 1.3 80.7 + + - +
34R MET* 3.3 25.8 - - - +
39R PHE* 4.3 10.4 - + - -
43R GLY* 3.2 29.5 + - - -
46R MET* 3.9 12.2 - - + +
47R ASP* 3.1 32.6 + - - -
58T ASP* 5.6 2.9 + - - -
62T GLU* 4.4 13.3 + - - -
144V TRP* 4.6 14.5 - + - -
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Residues in contact with TRP 32 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25R VAL* 5.8 0.4 - - + -
28R HIS* 2.9 55.9 + + + +
29R GLN 3.8 2.9 - - - +
31R HIS* 1.3 92.8 - + - +
33R TYR* 1.3 67.3 + - + +
34R MET 4.8 1.0 - - - +
17T VAL* 4.4 4.0 - - + -
21T ASN* 5.0 2.2 - - - -
57T MET* 3.7 24.5 - - + -
58T ASP* 3.8 16.9 + - - -
61T ALA* 3.5 24.0 - - + +
62T GLU* 4.8 8.7 + - + +
65T LEU* 3.6 42.5 - - + +
71T PRO* 3.7 20.0 - - + -
72T PHE 3.4 23.6 - - - -
73T SER* 4.2 14.8 - - - -
78T PHE* 5.0 2.9 - + - -
144V TRP* 4.3 9.8 + - - -
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Residues in contact with TYR 33 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29R GLN* 3.0 30.1 + - + +
30R ILE* 4.6 1.3 - - - +
32R TRP* 1.3 84.9 - - + +
34R MET* 1.3 67.3 + - - +
35R ARG* 3.6 11.4 + - - +
89R TYR* 3.4 71.6 + + + +
93R LYS 5.8 0.2 - - - +
98R LEU* 4.6 3.9 - - + +
65T LEU* 4.9 4.0 - - + -
69T GLY 5.4 0.2 - - - -
70T SER* 3.0 20.6 - - - -
71T PRO* 2.6 55.9 + - + -
73T SER* 3.9 16.2 - - - -
----------------------------------------------------------
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Residues in contact with MET 34 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30R ILE* 3.0 41.1 + - + +
31R HIS* 3.3 17.0 - - - +
32R TRP 3.6 1.4 - - - +
33R TYR* 1.3 79.5 - - - +
35R ARG* 1.3 65.2 - - - +
39R PHE* 3.4 33.4 - - + +
42R LEU* 3.6 14.6 - - + -
43R GLY* 3.6 30.3 - - - -
46R MET* 4.2 7.4 - - + -
95R MET* 3.5 33.2 - - + -
98R LEU* 3.8 10.5 - - + +
99R MET* 4.3 2.5 - - + -
144V TRP* 5.6 0.5 + - - -
148V ALA* 4.1 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