Contacts of the helix formed by residues 8 - 34 (chain V) 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 V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7V VAL* 1.3 79.6 - - - +
9V THR* 1.3 65.2 - - - +
10V LYS* 3.3 15.2 + - - +
11V GLU* 3.0 37.5 + - - +
12V PHE* 2.9 22.9 + - - +
119V LEU* 3.8 9.6 - - - +
123V GLU* 3.3 15.0 - - - +
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Residues in contact with THR 9 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8V ASP* 1.3 71.2 - - - +
10V LYS* 1.3 64.8 + - - +
12V PHE* 3.3 3.6 + - - +
13V LEU* 3.0 25.0 + - + +
67V ILE* 3.8 15.7 - - + -
119V LEU* 4.2 9.3 - - - +
120V THR* 3.6 23.7 + - - +
123V GLU* 2.8 40.5 + - - +
125V ASP* 3.6 23.8 - - - +
128V THR* 4.0 12.3 - - + -
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Residues in contact with LYS 10 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8V ASP* 3.3 13.4 + - - +
9V THR* 1.3 79.6 - - - +
11V GLU* 1.3 58.6 + - - +
13V LEU 3.6 0.2 + - - -
14V ASN* 3.1 25.8 + - - +
64V LEU* 3.4 32.9 - - + +
67V ILE* 3.2 34.1 + - + -
68V GLY* 3.7 20.0 + - - -
69V GLY* 4.5 4.9 - - - -
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Residues in contact with GLU 11 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7V VAL* 3.6 29.8 - - + +
8V ASP* 3.0 28.9 + - - +
10V LYS* 1.3 75.1 - - - +
12V PHE* 1.3 59.7 + - - +
14V ASN* 3.8 7.3 - - + +
15V HIS* 2.9 29.1 + - - +
72V PHE* 6.5 1.1 - - + -
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Residues in contact with PHE 12 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7V VAL* 5.0 8.2 - - + +
8V ASP 2.9 17.0 + - - +
9V THR* 3.6 4.7 - - + +
11V GLU* 1.3 73.8 - - - +
13V LEU* 1.3 72.7 + - + +
15V HIS* 3.0 10.9 + - + +
16V GLN* 2.8 63.4 + - + +
112V GLU* 3.2 32.1 - - + -
113V TYR* 4.0 6.1 - + - -
115V GLN* 4.7 2.7 - - + -
116V GLY* 3.4 27.6 - - - -
119V LEU* 3.9 15.0 - - + -
132V LEU* 3.8 22.0 - - + -
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Residues in contact with LEU 13 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9V THR* 3.0 19.3 + - + +
10V LYS 3.7 5.4 - - - +
12V PHE* 1.3 92.4 - - + +
14V ASN* 1.3 58.1 + - - +
16V GLN* 3.0 3.5 + - - +
17V VAL* 2.9 30.0 + - - +
60V VAL* 3.3 24.6 - - + +
63V ARG* 3.9 14.6 - - + -
64V LEU* 3.7 38.6 - - + +
67V ILE* 3.9 20.4 - - + -
128V THR* 3.7 24.2 - - + -
131V MET* 4.8 7.0 - - + -
132V LEU* 4.9 1.8 - - + -
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Residues in contact with ASN 14 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10V LYS 3.1 15.8 + - - +
11V GLU* 3.8 7.9 - - + +
13V LEU* 1.3 79.0 - - - +
15V HIS* 1.3 61.8 + - - +
17V VAL* 3.3 8.5 + - - +
18V ALA* 3.2 16.5 + - - +
64V LEU* 3.7 11.4 - - + +
70V SER 3.1 20.2 + - - -
71V PRO* 3.2 5.0 - - - +
72V PHE* 2.7 75.3 + - + +
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Residues in contact with HIS 15 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11V GLU 2.9 16.1 + - - +
12V PHE* 3.0 15.2 + + + +
14V ASN* 1.3 78.3 - - - +
16V GLN* 1.3 58.6 + - - +
18V ALA* 3.4 7.4 + - - +
19V ASN* 2.9 35.2 + - - +
72V PHE* 4.4 3.6 - - - -
81V ASN* 3.0 29.6 + - + -
83V SER* 3.2 39.9 + - - -
112V GLU* 3.8 10.2 + - - -
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Residues in contact with GLN 16 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12V PHE* 2.8 50.9 + - + +
13V LEU* 3.0 7.5 + - - +
15V HIS* 1.3 81.1 + - - +
17V VAL* 1.3 58.6 + - - +
19V ASN* 2.8 27.2 + - - +
20V LEU* 2.9 40.8 + - + +
60V VAL* 4.2 12.3 - - + -
109V LEU* 3.6 4.5 - - - +
112V GLU* 2.7 28.9 + - - +
113V TYR* 3.5 33.9 + - + +
132V LEU* 5.9 1.1 - - + -
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Residues in contact with VAL 17 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13V LEU 2.9 22.9 + - - +
14V ASN* 3.3 21.7 + - - +
16V GLN* 1.3 74.1 - - - +
18V ALA* 1.3 62.9 + - - +
20V LEU* 3.6 1.3 + - - +
21V ASN* 2.8 44.4 + - - +
57V MET* 4.3 17.0 - - - -
60V VAL* 4.1 13.6 - - + +
61V ALA* 4.4 17.3 - - + +
64V LEU* 4.8 2.2 - - + -
71V PRO* 4.6 4.3 - - + -
72V PHE* 3.9 21.8 - - + +
78V PHE* 4.1 3.6 - - + -
32Y TRP* 4.3 8.3 - - + -
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Residues in contact with ALA 18 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14V ASN 3.2 8.7 + - - +
15V HIS 3.5 9.9 - - - +
16V GLN 3.2 0.2 - - - -
17V VAL* 1.3 79.1 - - - +
19V ASN* 1.3 66.8 + - - +
20V LEU 3.4 0.2 + - - -
21V ASN* 3.4 2.9 + - - +
22V VAL* 3.4 23.9 + - - +
72V PHE* 4.3 4.9 - - + -
78V PHE* 3.9 37.5 - - - +
81V ASN* 4.2 11.2 - - + -
82V ALA* 3.9 15.0 - - + +
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Residues in contact with ASN 19 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15V HIS* 2.9 15.1 + - - +
16V GLN* 2.8 33.8 + - - +
18V ALA* 1.3 76.7 - - - +
20V LEU* 1.3 64.0 + - - +
22V VAL* 3.2 6.4 + - - +
23V PHE* 3.0 21.6 + - - +
82V ALA* 3.6 4.3 - - - +
83V SER* 3.1 32.6 + - - -
84V VAL* 3.3 20.2 + - + +
108V LEU* 4.4 0.4 - - - +
109V LEU* 3.8 15.4 - - + +
112V GLU* 2.8 23.4 + - - -
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Residues in contact with LEU 20 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16V GLN 2.9 26.6 + - - +
18V ALA 3.3 0.2 - - - -
19V ASN* 1.3 76.9 - - + +
21V ASN* 1.3 57.0 + - - +
23V PHE* 3.2 5.7 + - + +
24V THR* 2.8 33.2 + - - -
53V PHE* 4.1 24.0 - - + +
56V GLN* 4.2 8.5 - - + +
57V MET* 3.6 40.8 - - + +
60V VAL* 4.1 13.9 - - + -
109V LEU* 4.1 26.0 - - + -
113V TYR* 3.5 27.6 - - - +
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Residues in contact with ASN 21 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17V VAL* 2.8 25.8 + - - +
18V ALA 4.0 0.7 - - - +
19V ASN 3.2 0.6 - - - -
20V LEU* 1.3 78.3 - - - +
22V VAL* 1.3 61.1 + - - +
24V THR* 3.6 10.4 - - - +
25V VAL* 3.4 28.1 + - - +
57V MET* 3.3 38.1 - - - +
78V PHE* 3.5 48.8 - - + -
25Y VAL* 4.2 11.1 - - - +
28Y HIS* 5.3 1.7 - - - -
32Y TRP* 5.0 0.4 - - - -
50Y TYR* 5.6 0.9 + - - -
75Y LEU* 4.0 3.9 - - + +
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Residues in contact with VAL 22 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18V ALA 3.4 14.8 + - - +
19V ASN 3.2 5.9 + - - +
21V ASN* 1.3 78.6 - - - +
23V PHE* 1.3 56.0 + - - +
25V VAL* 3.6 3.6 + - - +
26V LYS* 3.1 25.3 + - + +
78V PHE* 4.5 5.6 - - + +
79V LEU* 5.0 4.7 - - + +
82V ALA* 3.8 19.3 - - + -
84V VAL* 3.8 30.7 - - + +
85V GLU 4.7 0.2 - - - +
86V GLU* 3.9 33.9 - - + +
75Y LEU* 4.0 23.6 - - + -
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Residues in contact with PHE 23 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19V ASN 3.0 13.5 + - - +
20V LEU* 3.5 12.1 - - + +
22V VAL* 1.3 73.4 - - - +
24V THR* 1.3 60.7 + - - +
26V LYS* 3.3 14.0 + - + -
27V ILE* 2.9 38.8 + - + +
30V ILE* 6.1 0.7 - - + -
49V LEU* 4.7 2.9 - - + -
53V PHE* 3.8 40.4 - + + -
84V VAL* 4.5 5.6 - - + +
102V LEU* 3.6 33.0 - - + -
105V THR* 3.4 31.9 - - + -
106V LEU* 3.8 14.6 - - + -
109V LEU* 3.5 26.5 - - + -
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Residues in contact with THR 24 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20V LEU 2.8 15.8 + - - +
21V ASN* 3.6 17.0 - - - +
22V VAL 3.3 0.2 - - - -
23V PHE* 1.3 78.0 - - - +
25V VAL* 1.3 68.6 + - + +
27V ILE* 3.2 10.8 + - - +
28V HIS 3.2 16.3 + - - -
50V TYR* 3.2 44.5 + - + +
53V PHE* 4.2 7.1 + - - +
54V GLY* 4.0 22.7 + - - -
57V MET* 6.0 5.4 - - + +
50Y TYR* 5.7 3.8 - - - +
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Residues in contact with VAL 25 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21V ASN 3.4 17.4 + - - +
22V VAL 3.8 4.5 - - - +
24V THR* 1.3 80.7 - - + +
26V LYS* 1.3 59.6 + - - +
28V HIS* 3.4 13.3 + - + +
29V GLN* 3.0 24.1 + - - +
86V GLU* 4.9 1.6 - - - +
21Y ASN* 4.1 19.7 - - - +
73Y SER* 3.4 22.9 - - - +
74Y THR* 3.9 6.7 - - - -
75Y LEU* 3.7 16.4 - - + -
78Y PHE* 3.7 21.5 - - + -
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Residues in contact with LYS 26 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22V VAL* 3.1 15.6 + - + +
23V PHE* 3.4 18.6 - - + +
25V VAL* 1.3 75.6 - - - +
27V ILE* 1.3 59.7 + - - +
29V GLN* 3.1 22.0 + - - +
30V ILE* 2.9 39.3 + - + +
84V VAL* 4.3 8.1 - - - -
85V GLU 3.1 29.5 + - - -
86V GLU* 4.3 11.2 - - + +
87V ALA 5.2 1.4 - - - +
101V ASP* 2.4 38.5 + - - +
102V LEU 5.4 0.2 - - - +
105V THR* 3.5 25.4 - - - +
73Y SER 5.1 1.1 - - - -
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Residues in contact with ILE 27 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23V PHE* 2.9 50.0 + - + +
24V THR* 3.2 14.5 + - - +
26V LYS* 1.3 75.0 - - - +
28V HIS* 1.3 63.0 + - - +
30V ILE* 3.3 8.8 + - - +
31V HIS* 3.0 22.5 + - + +
46V MET* 3.3 45.6 - - + +
49V LEU* 4.0 17.9 - - + +
50V TYR* 3.9 27.6 - - + +
53V PHE* 4.5 5.4 - - + -
102V LEU* 5.2 2.0 - - + -
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Residues in contact with HIS 28 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24V THR 3.2 5.4 + - - +
25V VAL* 3.5 16.2 - - + +
26V LYS 3.3 0.2 - - - -
27V ILE* 1.3 79.7 - - - +
29V GLN* 1.3 61.6 + - - +
31V HIS* 3.4 7.1 + - - +
32V TRP* 3.0 58.7 + + + -
47V ASP* 6.1 0.4 - - - -
50V TYR* 3.1 54.4 + + + +
21Y ASN* 5.3 3.1 - - - -
54Y GLY 5.4 0.2 + - - -
57Y MET* 3.5 29.7 - - + +
58Y ASP* 3.9 25.8 + - - -
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Residues in contact with GLN 29 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25V VAL 3.0 13.5 + - - +
26V LYS* 3.3 26.1 - - - +
28V HIS* 1.3 77.1 - - - +
30V ILE* 1.3 68.7 + - - +
32V TRP* 3.4 0.8 + - - -
33V TYR* 3.2 34.6 + - + +
87V ALA 3.1 26.1 + - - +
89V TYR* 4.0 16.8 + - + -
93V LYS* 5.7 3.0 - - - +
98V LEU* 5.3 6.0 - - + +
101V ASP* 5.0 5.5 + - - -
73Y SER* 3.1 44.7 + - - +
74Y THR* 3.8 3.8 - - - +
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Residues in contact with ILE 30 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23V PHE* 6.1 0.7 - - + -
26V LYS* 2.9 36.9 + - + +
27V ILE* 3.3 7.2 + - + +
29V GLN* 1.3 79.3 - - + +
31V HIS* 1.3 56.9 + - - +
33V TYR 4.0 0.2 - - - -
34V MET* 3.1 42.0 + - + +
46V MET* 3.8 8.3 - - - -
98V LEU* 3.7 46.3 - - + +
99V MET* 3.5 27.8 - - + -
101V ASP* 5.0 3.1 - - - +
102V LEU* 4.2 25.6 - - + +
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Residues in contact with HIS 31 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144N TRP* 4.9 9.2 - + - -
27V ILE 3.0 16.5 + - - +
28V HIS* 3.9 9.6 - - - +
30V ILE* 1.3 78.2 - - - +
32V TRP* 1.3 79.8 + + - +
34V MET* 3.4 22.9 - - - +
39V PHE* 4.4 9.5 - + - -
43V GLY* 3.1 31.8 + - - -
46V MET* 3.7 13.6 - - + +
47V ASP* 3.0 32.6 + - - -
58Y ASP* 5.3 2.8 + - - -
62Y GLU* 4.0 17.6 + - - -
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Residues in contact with TRP 32 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144N TRP* 4.2 9.7 + + - -
25V VAL* 6.2 0.2 - - + -
28V HIS* 3.0 56.7 + + + +
29V GLN 4.1 2.0 - - - +
31V HIS* 1.3 93.3 - + - +
33V TYR* 1.3 63.2 + - + +
34V MET 3.9 2.6 + - - +
39V PHE* 5.5 0.5 - - - -
17Y VAL* 4.5 5.8 - - + -
21Y ASN* 4.9 2.0 - - - -
57Y MET* 3.7 27.1 - - - -
58Y ASP* 3.8 18.3 + - - -
61Y ALA* 3.4 25.9 - - + +
62Y GLU* 4.8 7.8 - - + +
65Y LEU* 3.8 42.7 - - + +
71Y PRO* 3.9 24.2 - - + -
72Y PHE 3.6 19.7 - - - -
73Y SER* 4.2 15.0 - - - -
78Y PHE* 5.0 3.6 - + - -
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Residues in contact with TYR 33 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29V GLN* 3.2 22.9 + - + +
30V ILE 4.0 0.7 - - - +
32V TRP* 1.3 80.3 - - + +
34V MET* 1.3 67.0 + - - +
35V ARG* 3.6 11.8 + - - +
89V TYR* 3.3 73.9 + + + +
93V LYS 5.5 1.2 - - - +
98V LEU* 4.5 6.8 - - + +
65Y LEU* 4.9 5.6 - - + -
70Y SER* 3.1 21.6 - - - -
71Y PRO* 2.7 51.8 + - + -
73Y SER* 3.5 22.2 - - - -
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Residues in contact with MET 34 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148N ALA* 4.0 2.1 - - - +
30V ILE* 3.1 40.9 + - + +
31V HIS* 3.4 15.0 - - - +
32V TRP 3.6 2.1 - - - +
33V TYR* 1.3 79.4 - - - +
35V ARG* 1.3 65.8 + - - +
39V PHE* 3.4 43.9 - - + +
42V LEU* 3.8 22.9 - - + -
43V GLY* 3.6 25.4 - - - -
46V MET* 3.8 14.8 - - + -
95V MET* 3.5 17.9 - - + -
98V LEU* 3.7 13.7 - - + +
99V MET* 4.3 2.0 - - + -
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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