Contacts of the helix formed by residues 8 - 34 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 1.3 74.1 - - - +
9C THR* 1.3 65.6 + - - +
10C LYS* 3.1 16.6 + - - +
11C GLU* 3.0 32.9 + - - +
12C PHE* 3.1 15.6 + - - +
119C LEU* 3.6 10.4 - - - +
123C GLU* 3.3 17.9 - - - +
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Residues in contact with THR 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ASP* 1.3 74.8 - - - +
10C LYS* 1.3 64.6 + - - +
12C PHE* 3.2 5.4 + - + +
13C LEU* 3.0 30.7 + - + +
67C ILE* 4.0 9.6 - - + -
119C LEU* 3.8 7.4 - - - +
120C THR* 3.4 19.3 + - - +
123C GLU* 2.7 28.9 + - - +
125C ASP* 3.5 25.2 + - - +
128C THR* 3.9 21.1 - - + -
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Residues in contact with LYS 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ASP* 3.1 15.2 + - - +
9C THR* 1.3 80.5 - - - +
11C GLU* 1.3 64.5 + - + +
13C LEU 3.4 0.3 + - - -
14C ASN* 3.0 24.0 + - - +
64C LEU* 3.6 22.3 - - + +
67C ILE* 3.3 44.7 + - + -
68C GLY 4.0 6.8 + - - -
69C GLY* 4.0 16.6 - - - +
155H LEU* 5.9 1.4 - - - +
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Residues in contact with GLU 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 3.9 28.4 + - + +
8C ASP* 3.0 27.3 + - - +
10C LYS* 1.3 78.5 - - + +
12C PHE* 1.3 57.2 + - - +
14C ASN* 3.8 7.0 - - + +
15C HIS* 2.9 29.3 + - - +
72C PHE* 5.7 0.2 - - - -
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Residues in contact with PHE 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 5.0 9.5 - - + +
8C ASP 3.1 12.4 + - - +
9C THR* 3.2 10.1 + - + +
11C GLU* 1.3 78.0 - - - +
13C LEU* 1.3 73.6 + - + +
15C HIS* 3.1 9.1 + - + +
16C GLN* 3.0 54.6 + - + +
112C GLU* 3.1 29.8 - - + -
113C TYR* 3.9 10.1 - + - -
115C GLN* 4.6 2.7 - - + -
116C GLY* 3.5 29.2 - - - -
119C LEU* 4.0 14.4 - - + -
120C THR* 6.0 0.7 - - - -
132C LEU* 3.9 23.8 - - + -
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Residues in contact with LEU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C THR* 3.0 23.5 + - + +
10C LYS 3.8 3.6 - - - +
12C PHE* 1.3 84.9 - - + +
14C ASN* 1.3 56.9 + - - +
16C GLN* 3.0 4.7 + - + +
17C VAL* 2.9 24.2 + - - +
60C VAL* 3.3 34.5 - - + +
63C ARG* 4.3 12.3 - - + -
64C LEU* 4.4 14.4 - - + +
67C ILE* 4.2 14.6 - - + -
128C THR* 3.5 34.8 - - + -
131C MET* 3.8 16.4 - - + -
132C LEU* 4.0 14.4 - - + -
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Residues in contact with ASN 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LYS 3.0 16.9 + - - +
11C GLU* 3.8 7.6 - - - +
13C LEU* 1.3 74.3 - - - +
15C HIS* 1.3 64.0 + - - +
17C VAL* 3.2 13.8 + - - +
18C ALA 3.3 9.0 + - - -
64C LEU* 3.7 13.5 - - + +
70C SER 3.0 24.2 + - - +
71C PRO* 3.4 4.7 - - - +
72C PHE* 2.9 64.5 + - + +
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Residues in contact with HIS 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLU 2.9 19.6 + - - +
12C PHE* 3.4 9.4 - - + +
14C ASN* 1.3 75.4 - - - +
16C GLN* 1.3 63.5 + - - +
18C ALA* 3.4 5.7 + - - +
19C ASN* 3.0 35.2 + - - +
72C PHE* 4.3 6.0 - - - -
81C ASN* 2.9 32.4 + - + -
83C SER* 2.9 36.8 + - - -
112C GLU* 3.5 13.2 + - - -
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Residues in contact with GLN 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C PHE* 3.0 50.8 + - + +
13C LEU* 3.0 8.2 + - + +
15C HIS* 1.3 85.8 + - - +
17C VAL* 1.3 66.0 + - - +
19C ASN* 2.7 26.9 + - - +
20C LEU* 2.9 42.0 + - + +
60C VAL* 4.6 7.9 - - + -
109C LEU* 3.6 12.3 - - - +
112C GLU* 3.2 24.2 + - - +
113C TYR* 3.7 21.8 - - + +
132C LEU* 6.0 0.7 - - + -
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Residues in contact with VAL 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TRP* 4.2 12.8 - - + -
13C LEU 2.9 20.0 + - - +
14C ASN* 3.2 21.3 + - - +
16C GLN* 1.3 77.0 - - - +
18C ALA* 1.3 62.1 + - - +
20C LEU* 3.9 1.2 - - - +
21C ASN* 3.0 41.9 + - - +
57C MET* 4.5 8.7 - - + +
60C VAL* 3.6 17.4 - - + +
61C ALA* 4.3 17.7 - - + -
64C LEU* 4.7 1.8 - - + -
71C PRO* 4.5 5.6 - - + -
72C PHE* 3.9 12.3 - - + +
78C PHE* 3.9 14.8 - - + -
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Residues in contact with ALA 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ASN 3.3 8.6 + - - +
15C HIS 3.8 7.0 - - - +
16C GLN 3.2 0.4 - - - -
17C VAL* 1.3 77.8 - - - +
19C ASN* 1.3 66.4 + - - +
21C ASN* 3.4 3.3 + - - +
22C VAL* 3.2 25.3 + - - +
72C PHE* 4.3 3.6 - - + -
78C PHE* 3.5 44.4 - - + +
81C ASN* 4.3 10.3 - - + -
82C ALA* 3.9 11.9 - - - +
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Residues in contact with ASN 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C HIS* 3.0 16.3 + - - +
16C GLN* 2.7 33.0 + - - +
18C ALA* 1.3 74.9 - - - +
20C LEU* 1.3 58.4 + - - +
22C VAL* 3.1 7.8 + - - +
23C PHE* 2.9 27.2 + - - +
82C ALA* 3.5 5.5 - - - -
83C SER* 2.9 33.0 + - - -
84C VAL* 3.2 21.7 + - + +
108C LEU* 4.2 1.2 - - - +
109C LEU* 4.0 11.6 - - + +
112C GLU* 2.7 24.5 + - - -
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Residues in contact with LEU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLN* 2.9 30.0 + - + +
17C VAL 3.9 3.4 - - - +
19C ASN* 1.3 77.2 - - - +
21C ASN* 1.3 56.9 + - - +
23C PHE* 3.8 5.5 - - + +
24C THR* 3.0 33.4 + - - -
53C PHE* 3.9 39.1 - - + +
56C GLN* 4.3 2.9 - - + +
57C MET* 3.9 32.7 - - + +
60C VAL* 4.4 8.1 - - + -
109C LEU* 4.1 21.1 - - + -
113C TYR* 3.3 27.1 - - - +
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Residues in contact with ASN 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 4.0 12.3 - - - +
28A HIS* 5.4 1.4 - - - -
32A TRP* 4.8 0.6 - - - -
50A TYR* 5.6 0.5 + - - -
75A LEU* 3.9 3.9 - - + +
17C VAL* 3.0 28.7 + - - +
18C ALA 3.8 3.8 - - - +
19C ASN 3.3 0.4 - - - -
20C LEU* 1.3 78.1 - - - +
22C VAL* 1.3 58.6 + - - +
24C THR* 3.8 7.8 - - - +
25C VAL* 3.5 26.7 + - - +
57C MET* 3.3 37.2 - - - +
78C PHE* 3.4 48.1 - - + -
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Residues in contact with VAL 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.0 24.9 - - + -
18C ALA 3.2 14.8 + - - +
19C ASN 3.1 7.2 + - - +
21C ASN* 1.3 75.3 - - - +
23C PHE* 1.3 58.4 + - - +
24C THR 3.2 0.6 + - - -
25C VAL* 3.4 3.8 + - - +
26C LYS* 3.0 26.2 + - + +
78C PHE 4.4 4.5 - - - +
79C LEU* 5.3 4.5 - - + -
82C ALA* 3.7 18.4 - - + -
84C VAL* 3.8 26.5 - - + +
85C GLU 4.6 0.4 - - - +
86C GLU* 3.8 38.3 - - + +
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Residues in contact with PHE 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ASN 2.9 15.4 + - - +
20C LEU* 3.4 8.7 + - + +
22C VAL* 1.3 75.8 - - - +
24C THR* 1.3 53.6 + - - +
26C LYS* 3.1 14.3 + - + +
27C ILE* 2.8 49.5 + - + +
30C ILE* 6.3 0.2 - - + -
49C LEU* 4.9 0.9 - - + -
53C PHE* 3.6 44.4 - + + -
84C VAL* 4.5 6.3 - - + +
102C LEU* 3.5 33.7 - - + -
105C THR* 3.4 32.3 - - + -
106C LEU* 3.6 23.6 - - + -
109C LEU* 3.8 12.8 - - + -
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Residues in contact with THR 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 5.8 2.7 - - - +
20C LEU 3.0 15.2 + - - +
21C ASN* 3.8 15.3 - - - +
23C PHE* 1.3 79.7 - - - +
25C VAL* 1.3 65.2 + - + +
27C ILE* 3.4 6.9 + - - -
28C HIS 3.2 13.3 + - - -
50C TYR* 3.2 50.3 + - + +
53C PHE* 4.0 8.3 - - - +
54C GLY* 3.9 24.3 + - - -
57C MET* 5.5 7.6 - - + +
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Residues in contact with VAL 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN* 4.1 11.4 - - + +
73A SER* 3.5 21.2 - - - +
74A THR* 3.8 9.0 - - - -
75A LEU* 3.8 17.0 - - + -
78A PHE* 3.8 31.0 - - + -
21C ASN 3.5 13.4 + - - +
22C VAL 3.4 8.2 + - - +
24C THR* 1.3 80.3 - - + +
26C LYS* 1.3 59.1 + - - +
28C HIS* 3.4 12.2 + - + +
29C GLN* 3.0 24.4 + - - +
32C TRP* 5.6 0.8 - - + -
50C TYR* 5.9 1.1 - - - +
86C GLU* 4.6 1.8 - - - +
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Residues in contact with LYS 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A SER 5.1 1.1 - - - -
22C VAL* 3.0 15.6 + - + +
23C PHE* 3.1 20.2 + - + +
25C VAL* 1.3 75.3 - - - +
27C ILE* 1.3 64.9 + - - +
29C GLN* 3.0 28.4 + - - +
30C ILE* 3.0 28.4 + - + +
84C VAL* 4.3 8.5 - - - -
85C GLU 2.7 31.6 + - - -
86C GLU* 3.9 12.2 - - + +
87C ALA 4.8 2.8 - - - +
101C ASP* 2.9 35.6 + - - +
102C LEU 5.2 0.2 - - - +
105C THR* 3.6 24.7 - - - +
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Residues in contact with ILE 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 2.8 58.2 + - + +
24C THR* 3.6 12.8 - - - +
25C VAL 3.4 0.2 - - - -
26C LYS* 1.3 71.1 - - - +
28C HIS* 1.3 64.2 + - - +
30C ILE* 3.3 10.2 + - + +
31C HIS* 3.0 22.5 + - + +
46C MET* 3.3 41.0 - - + +
49C LEU* 3.9 31.2 - - + +
50C TYR* 3.9 12.1 - - + +
53C PHE* 4.5 2.5 - - + -
102C LEU* 4.8 7.0 - - + -
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Residues in contact with HIS 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN* 5.4 1.1 - - - -
57A MET* 3.7 20.2 - - + +
58A ASP* 3.0 32.3 + - - -
24C THR 3.2 6.1 + - - +
25C VAL* 3.5 13.9 - - + +
27C ILE* 1.3 76.0 - - - +
29C GLN* 1.3 64.3 + - - +
31C HIS* 3.6 10.2 - + - +
32C TRP* 3.0 55.0 + + + -
47C ASP* 5.6 5.2 - - - -
50C TYR* 2.9 59.3 + + + +
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Residues in contact with GLN 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A SER* 3.0 46.3 + - - +
74A THR* 4.1 1.0 - - - +
25C VAL 3.0 13.2 + - - +
26C LYS* 3.0 26.9 + - - +
28C HIS* 1.3 75.7 - - - +
30C ILE* 1.3 69.7 + - + +
32C TRP* 4.5 1.1 - - - -
33C TYR* 3.1 35.9 + - + +
86C GLU* 5.9 0.3 - - - +
87C ALA 2.9 27.2 + - - +
89C TYR* 4.0 18.0 + - + +
98C LEU* 5.2 6.4 - - + +
101C ASP* 4.8 8.3 + - - -
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Residues in contact with ILE 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LYS* 3.0 31.1 + - + +
27C ILE* 3.7 10.5 - - + +
29C GLN* 1.3 80.6 - - - +
31C HIS* 1.3 63.2 + - - +
34C MET* 3.0 35.6 + - + +
46C MET* 3.7 14.8 - - + -
98C LEU* 3.5 48.8 - - + +
99C MET* 3.4 26.2 - - + -
101C ASP* 5.0 2.7 - - + +
102C LEU* 4.0 24.2 - - + +
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Residues in contact with HIS 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLU* 4.3 15.6 + - - -
27C ILE 3.0 18.1 + - - +
28C HIS* 3.6 14.4 - + - +
30C ILE* 1.3 76.2 - - - +
32C TRP* 1.3 79.0 + + + +
34C MET* 3.9 21.0 + - - +
39C PHE* 4.4 11.7 - + - -
43C GLY* 3.1 39.4 + - - -
46C MET* 3.7 14.6 - - + +
47C ASP* 3.3 25.7 + - - -
144E TRP* 5.0 10.5 - + - -
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Residues in contact with TRP 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 4.4 5.6 - - + -
21A ASN* 4.8 2.5 - - - -
57A MET* 3.7 30.3 - - + -
58A ASP* 4.0 10.7 + - - +
61A ALA* 3.5 25.8 - - + +
62A GLU* 4.9 10.3 + - + +
65A LEU* 3.6 42.4 - - + +
71A PRO* 3.9 25.1 - - + -
72A PHE 3.6 21.3 - - - -
73A SER* 4.3 14.6 - - - -
78A PHE* 5.1 3.6 - + - -
25C VAL* 5.6 0.7 - - + -
28C HIS* 3.0 54.0 + + + +
29C GLN 4.0 2.5 - - - +
31C HIS* 1.3 94.4 - + - +
33C TYR* 1.3 62.5 + - + +
34C MET 4.7 2.3 - - - +
39C PHE* 5.6 0.3 - - - -
144E TRP* 4.6 7.9 + + - -
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Residues in contact with TYR 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 5.1 3.8 - - + -
70A SER* 3.1 34.4 + - - -
71A PRO* 2.5 43.6 + - + -
73A SER* 3.7 13.5 - - - -
29C GLN* 3.1 29.6 + - + +
30C ILE 3.9 0.7 - - - +
32C TRP* 1.3 79.5 - - + +
34C MET* 1.3 68.0 + - - +
35C ARG* 3.5 11.9 + - - +
89C TYR* 3.2 76.6 + + + +
93C LYS 5.6 0.7 - - - +
98C LEU* 4.6 5.0 - - + +
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Residues in contact with MET 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ILE* 3.0 33.0 + - + +
31C HIS* 4.1 11.0 - - - +
32C TRP 3.6 2.5 - - - +
33C TYR* 1.3 79.4 - - - +
35C ARG* 1.3 67.5 + - - +
39C PHE* 3.4 51.8 - - + +
42C LEU* 3.6 29.8 - - + -
43C GLY* 3.7 15.0 - - - -
46C MET* 4.2 6.5 - - + -
95C MET* 3.6 24.5 - - + -
98C LEU* 4.0 13.2 - - + -
99C MET* 4.7 0.4 - - + -
144E TRP* 5.8 0.3 + - - -
148E ALA* 4.0 2.3 - - - +
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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