Contacts of the helix formed by residues 8 - 34 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F VAL* 1.3 78.5 - - - +
9F THR* 1.3 65.1 + - - +
10F LYS* 3.7 13.7 + - - +
11F GLU* 3.3 34.4 + - - +
12F PHE* 3.0 23.2 + - - +
119F LEU* 3.6 7.3 - - - +
123F GLU* 3.8 19.1 - - - +
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Residues in contact with THR 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F ASP* 1.3 75.1 - - - +
10F LYS* 1.3 59.7 + - - +
12F PHE* 3.2 5.5 + - + +
13F LEU* 3.0 30.1 + - + +
67F ILE* 3.9 15.3 - - + -
119F LEU* 3.6 9.6 - - - +
120F THR* 3.6 23.2 + - - +
123F GLU* 2.9 31.2 + - - +
125F ASP* 3.7 26.1 + - - +
128F THR* 4.0 12.3 - - + -
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Residues in contact with LYS 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F ASP* 3.4 12.9 + - - +
9F THR* 1.3 76.3 - - - +
11F GLU* 1.3 64.1 + - + +
14F ASN* 3.1 22.3 + - - +
64F LEU* 3.4 20.3 - - + +
67F ILE* 3.7 40.8 - - + +
68F GLY 4.5 7.6 + - - -
69F GLY* 3.9 20.6 - - - +
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Residues in contact with GLU 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F VAL* 3.2 31.1 - - + +
8F ASP* 3.3 24.3 + - - +
10F LYS* 1.3 75.3 - - + +
12F PHE* 1.3 60.8 + - - +
14F ASN* 3.7 5.9 - - - +
15F HIS* 2.8 30.0 + - - +
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Residues in contact with PHE 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F VAL* 5.1 9.3 - - + +
8F ASP 3.0 18.4 + - - +
9F THR* 3.6 8.3 - - + +
11F GLU* 1.3 77.0 - - - +
13F LEU* 1.3 74.1 + - + +
15F HIS* 3.3 8.2 + + + +
16F GLN* 3.1 57.4 + - + +
112F GLU* 3.3 33.4 - - + -
113F TYR* 4.0 4.5 - - - -
115F GLN* 4.7 4.0 - - + -
116F GLY* 3.6 27.4 - - - -
119F LEU* 4.6 14.6 - - + -
120F THR* 5.8 1.3 - - - -
132F LEU* 3.9 22.9 - - + -
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Residues in contact with LEU 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F THR* 3.0 20.3 + - + +
10F LYS 3.9 4.0 - - - +
12F PHE* 1.3 87.3 - - + +
14F ASN* 1.3 62.1 + - - +
16F GLN* 3.1 3.3 + - + +
17F VAL* 2.8 26.1 + - - +
60F VAL* 3.3 34.3 - - + +
63F ARG* 4.2 13.0 - - + -
64F LEU* 4.1 16.2 - - + -
67F ILE* 3.9 23.8 - - + -
128F THR* 3.7 33.2 - - + -
131F MET* 4.3 9.2 - - + -
132F LEU* 4.3 7.6 - - + -
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Residues in contact with ASN 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F LYS 3.1 15.7 + - - +
11F GLU* 3.8 5.8 - - - +
13F LEU* 1.3 76.4 - - - +
15F HIS* 1.3 64.8 + - - +
17F VAL* 3.2 14.3 + - - +
18F ALA* 3.3 4.7 + - - +
64F LEU* 3.4 13.7 - - + +
70F SER 2.9 23.0 + - - +
71F PRO* 3.3 6.2 - - - +
72F PHE* 2.8 73.6 + - + +
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Residues in contact with HIS 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F GLU 2.8 19.7 + - - +
12F PHE* 3.5 10.9 - + + +
13F LEU 3.2 0.2 - - - -
14F ASN* 1.3 75.9 - - - +
16F GLN* 1.3 62.4 + - - +
18F ALA* 3.4 6.7 + - - +
19F ASN* 3.1 29.9 + - - -
72F PHE* 4.4 6.0 - - - -
81F ASN* 2.8 32.8 + - + -
83F SER* 3.0 38.4 + - - -
112F GLU* 3.1 20.9 + - - -
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Residues in contact with GLN 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F PHE* 3.1 50.6 + - + +
13F LEU* 3.1 8.3 + - + +
15F HIS* 1.3 81.7 + - - +
17F VAL* 1.3 65.0 + - - +
18F ALA 3.1 1.6 - - - -
19F ASN* 3.0 23.9 + - - +
20F LEU* 3.0 37.2 + - + +
60F VAL* 4.5 8.5 - - + -
109F LEU* 3.8 5.4 - - - +
112F GLU* 2.7 28.7 + - - +
113F TYR* 3.6 29.4 - - + +
132F LEU* 5.9 0.9 - - + -
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Residues in contact with VAL 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F LEU 2.8 19.6 + - - +
14F ASN* 3.2 19.5 + - - +
16F GLN* 1.3 76.7 - - - +
18F ALA* 1.3 60.5 + - - +
20F LEU* 4.9 0.2 - - - -
21F ASN* 2.7 38.3 + - - +
57F MET* 4.0 15.9 - - - +
60F VAL* 3.7 17.0 - - + +
61F ALA* 3.9 23.3 - - + +
64F LEU* 4.9 1.8 - - + -
71F PRO* 4.9 2.5 - - + -
72F PHE* 3.8 24.5 - - + +
78F PHE* 3.9 12.1 - - + -
32H TRP* 4.7 5.4 - - + -
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Residues in contact with ALA 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F ASN 3.3 8.4 + - - +
15F HIS 3.5 9.0 - - - +
16F GLN 3.1 0.6 - - - -
17F VAL* 1.3 76.4 - - - +
19F ASN* 1.3 66.6 + - - +
21F ASN* 3.2 6.1 + - - +
22F VAL* 3.1 22.7 + - - +
72F PHE* 4.3 3.1 - - + -
78F PHE* 3.6 41.7 - - + +
81F ASN* 4.1 17.0 - - + -
82F ALA* 4.1 7.0 - - - +
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Residues in contact with ASN 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F HIS* 3.1 16.4 + - - +
16F GLN* 3.0 30.4 + - - +
18F ALA* 1.3 80.1 - - - +
20F LEU* 1.3 55.4 + - - +
22F VAL* 3.1 4.0 + - - +
23F PHE* 2.8 27.8 + - - +
82F ALA* 3.3 6.8 - - - -
83F SER* 2.9 33.9 + - - -
84F VAL* 3.0 28.7 + - + +
108F LEU* 4.4 0.2 - - - +
109F LEU* 4.2 8.8 - - + +
112F GLU* 3.0 21.6 + - - -
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Residues in contact with LEU 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F GLN* 3.0 28.0 + - + +
19F ASN* 1.3 76.4 - - - +
21F ASN* 1.3 58.8 + - - +
23F PHE* 3.5 6.1 - - + +
24F THR* 2.8 33.8 + - - -
53F PHE* 3.9 42.0 - - + +
56F GLN* 4.2 4.0 - - - +
57F MET* 3.9 35.2 - - + +
60F VAL* 4.3 10.8 - - + -
109F LEU* 4.1 21.3 - - + -
113F TYR* 3.2 26.7 - - - +
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Residues in contact with ASN 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F VAL* 2.7 23.6 + - - +
18F ALA 3.2 6.5 + - - +
20F LEU* 1.3 77.9 - - - +
22F VAL* 1.3 59.4 + - - +
24F THR* 3.8 9.2 - - + +
25F VAL* 3.6 18.5 + - - +
57F MET* 3.3 41.3 - - - +
78F PHE* 3.3 46.1 - - + -
25H VAL* 4.1 10.7 - - - +
28H HIS* 5.7 0.2 - - - -
75H LEU* 3.7 12.5 - - + +
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Residues in contact with VAL 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F ALA 3.1 13.1 + - - +
19F ASN 3.1 8.5 + - - +
21F ASN* 1.3 75.5 - - - +
23F PHE* 1.3 62.6 + - - +
25F VAL* 3.7 2.6 + - - +
26F LYS* 3.3 19.8 + - - +
78F PHE* 4.4 5.4 - - + +
79F LEU* 5.0 5.4 - - + +
82F ALA* 3.8 17.9 - - + -
84F VAL* 3.7 32.9 - - + +
85F GLU 4.4 0.2 - - - +
86F GLU* 3.9 33.1 - - + +
75H LEU* 3.9 25.8 - - + -
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Residues in contact with PHE 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ASN 2.8 13.9 + - - +
20F LEU* 3.5 11.4 - - + +
22F VAL* 1.3 75.4 - - - +
24F THR* 1.3 59.3 + - - +
26F LYS* 3.0 13.9 + - + +
27F ILE* 2.9 44.6 + - + +
30F ILE* 5.9 0.2 - - + -
49F LEU* 4.7 1.3 - - + -
53F PHE* 3.5 48.9 - + + -
84F VAL* 4.4 5.8 - - + +
102F LEU* 3.6 31.2 - - + -
105F THR* 3.8 28.7 - - + -
106F LEU* 3.7 19.1 - - + -
109F LEU* 3.7 17.5 - - + -
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Residues in contact with THR 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F LEU 2.8 16.8 + - - +
21F ASN* 3.8 16.4 - - + +
23F PHE* 1.3 78.2 - - - +
25F VAL* 1.3 70.6 + - + +
27F ILE* 3.3 8.0 + - - +
28F HIS* 3.2 16.3 + - - +
50F TYR* 3.2 61.0 + - + +
53F PHE* 4.5 5.9 - - - +
54F GLY* 4.2 12.1 + - - -
57F MET* 5.9 4.3 - - + -
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Residues in contact with VAL 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F ASN 3.6 14.8 + - - +
22F VAL 4.2 1.8 - - - +
23F PHE 3.3 0.6 - - - -
24F THR* 1.3 83.2 - - + +
26F LYS* 1.3 58.3 + - - +
28F HIS* 3.2 13.5 + - + +
29F GLN* 2.9 25.8 + - - +
32F TRP* 6.0 0.4 - - + -
50F TYR* 6.0 0.7 - - + +
86F GLU* 4.9 1.1 - - - +
21H ASN* 4.0 10.1 - - - +
73H SER* 3.4 24.4 - - - +
74H THR* 3.8 7.6 - - - +
75H LEU* 3.8 16.8 - - + +
78H PHE* 3.5 36.6 - - + -
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Residues in contact with LYS 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F VAL 3.3 11.1 + - - +
23F PHE* 3.0 20.0 + - + +
25F VAL* 1.3 74.5 - - - +
27F ILE* 1.3 59.8 + - - +
29F GLN* 3.0 20.0 + - - +
30F ILE* 2.8 44.9 + - + +
84F VAL* 4.5 9.6 - - - -
85F GLU 2.9 30.5 + - - -
86F GLU* 4.1 12.3 - - + +
87F ALA 5.0 1.6 - - - +
101F ASP* 2.8 38.6 + - - +
102F LEU* 5.4 0.2 - - - -
105F THR* 3.7 22.2 - - - +
73H SER 5.1 1.1 - - - -
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Residues in contact with ILE 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F PHE* 2.9 59.7 + - + +
24F THR* 3.3 13.6 + - - +
26F LYS* 1.3 74.7 - - - +
28F HIS* 1.3 58.1 + - - +
30F ILE* 3.4 8.9 + - + +
31F HIS* 3.0 26.9 + - + +
46F MET* 3.2 42.0 - - + +
49F LEU* 4.0 30.7 - - + +
50F TYR* 3.9 13.7 - - + +
53F PHE* 4.4 2.5 - - + -
102F LEU* 4.6 4.9 - - + -
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Residues in contact with HIS 28 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F THR 3.2 7.5 + - - +
25F VAL* 3.4 13.9 - - + +
26F LYS 3.1 0.4 - - - -
27F ILE* 1.3 73.9 - - - +
29F GLN* 1.3 56.7 + - - +
31F HIS* 3.2 9.2 + + - +
32F TRP* 2.7 72.4 + + + -
47F ASP* 5.3 6.5 + - - -
50F TYR* 3.3 53.5 + + + +
21H ASN* 5.6 1.3 - - - -
57H MET* 3.7 23.4 - - + +
58H ASP* 3.3 30.4 + - - -
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Residues in contact with GLN 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F VAL 2.9 13.6 + - - +
26F LYS* 3.4 25.4 + - - +
28F HIS* 1.3 77.4 - - - +
30F ILE* 1.3 66.5 + - - +
32F TRP* 4.5 3.1 - - - -
33F TYR* 3.1 33.6 + - + +
86F GLU* 6.3 0.4 - - - +
87F ALA 3.1 27.5 + - - +
89F TYR* 4.1 17.4 + - + -
93F LYS* 5.4 6.1 - - - +
98F LEU* 5.5 4.9 - - + +
101F ASP* 4.8 7.3 + - - -
73H SER* 2.9 44.9 + - - +
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Residues in contact with ILE 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F LYS* 2.8 41.6 + - + +
27F ILE* 3.7 7.6 - - + +
29F GLN* 1.3 77.9 - - - +
31F HIS* 1.3 61.6 + - - +
34F MET* 3.1 33.2 + - + +
46F MET* 3.9 7.0 - - - -
98F LEU* 3.9 36.5 - - + +
99F MET* 3.6 27.4 - - + -
101F ASP* 5.2 3.6 - - + +
102F LEU* 3.9 37.9 - - + +
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Residues in contact with HIS 31 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F ILE* 3.0 18.6 + - + +
28F HIS* 3.5 11.7 - + - +
30F ILE* 1.3 77.4 - - - +
32F TRP* 1.3 81.2 + + - +
33F TYR 3.6 0.2 + - - -
34F MET* 3.8 23.4 - - - +
39F PHE* 5.0 6.3 - - - -
43F GLY* 3.0 40.6 + - - -
46F MET* 3.5 13.7 - - + +
47F ASP* 3.7 25.3 + - - -
62H GLU* 4.1 16.0 + - - -
144J TRP* 5.1 11.3 - + - -
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Residues in contact with TRP 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F VAL* 6.0 0.4 - - + -
28F HIS* 2.7 64.6 + + + +
29F GLN 4.0 2.5 - - - +
31F HIS* 1.3 92.9 - + - +
33F TYR* 1.3 64.8 + - + +
34F MET 3.7 2.3 + - - +
39F PHE* 5.7 0.5 - - - -
17H VAL* 4.3 5.6 - - + -
21H ASN* 4.8 3.1 - - - -
57H MET* 3.8 23.3 - - + -
58H ASP* 4.9 7.0 + - - +
61H ALA* 3.5 23.4 - - + +
62H GLU* 4.9 9.4 + - + +
65H LEU* 3.8 40.3 - - + +
71H PRO* 3.8 27.6 - - + -
72H PHE 3.3 24.2 - - - -
73H SER* 4.0 18.8 - - - -
78H PHE* 4.9 3.4 - + - -
144J TRP* 4.7 6.7 + - - -
----------------------------------------------------------
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Residues in contact with TYR 33 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F GLN* 3.1 23.9 + - + +
30F ILE 4.0 0.4 - - - +
32F TRP* 1.3 79.9 - - + +
34F MET* 1.3 65.9 + - - +
35F ARG* 3.5 13.9 + - - +
89F TYR* 3.5 71.1 + + + +
93F LYS 5.5 0.5 - - - +
98F LEU* 4.5 5.9 - - + +
65H LEU* 5.1 2.9 - - + -
69H GLY 5.4 0.2 - - - -
70H SER* 3.0 25.3 + - - -
71H PRO* 2.6 55.0 + - + -
73H SER* 3.7 17.9 - - - -
----------------------------------------------------------
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Residues in contact with MET 34 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F ILE* 3.1 33.8 + - + +
31F HIS* 3.8 15.0 - - - +
32F TRP 3.4 3.3 - - - +
33F TYR* 1.3 77.9 - - - +
35F ARG* 1.3 67.7 + - - +
39F PHE* 3.5 36.6 - - + +
42F LEU* 3.8 22.4 - - + -
43F GLY* 3.5 29.4 - - - -
46F MET* 3.9 12.6 - - + -
95F MET* 3.8 23.1 - - + -
98F LEU* 4.0 10.8 - - + -
99F MET* 4.2 2.0 - - + -
144J TRP* 5.8 0.3 + - - -
148J ALA* 4.1 1.2 - - - +
----------------------------------------------------------
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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