Contacts of the helix formed by residues 38 - 67 (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 ASN 38 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38N ASN* 4.8 5.3 - - - +
37R HIS* 3.0 55.6 + - - +
38R ASN* 4.5 7.1 - - - +
41R THR* 5.7 1.8 - - - +
36V GLY 2.9 2.0 + - - -
37V HIS* 1.3 80.2 + - - +
39V PHE* 1.3 56.5 + - - +
40V PHE 3.2 2.9 + - - -
41V THR* 3.3 13.2 + - - +
42V LEU* 2.9 49.8 + - + +
95V MET* 4.4 13.8 - - + +
149V PHE* 3.5 14.0 - - + -
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Residues in contact with PHE 39 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144N TRP* 4.1 24.7 - + - -
145N MET* 3.8 48.9 - - + -
148N ALA* 3.2 28.7 - - + +
149N PHE* 4.4 4.7 - - + -
31V HIS* 4.4 7.4 - + - -
32V TRP 5.5 0.2 - - - -
34V MET* 3.4 44.8 - - + +
35V ARG 4.8 0.4 - - - -
36V GLY 2.9 18.4 + - - +
37V HIS 3.3 2.4 + - - -
38V ASN* 1.3 76.4 - - - +
40V PHE* 1.3 75.6 + + - +
43V GLY* 3.0 26.3 + - - -
95V MET* 4.3 3.1 - - - +
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Residues in contact with PHE 40 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41N THR* 3.8 14.8 - - - +
42N LEU* 3.8 23.6 - - + -
45N LYS* 3.7 38.1 - - + -
145N MET* 4.0 35.2 - - + -
146N PHE* 3.5 40.6 - + - -
149N PHE* 3.9 24.5 - + + -
37V HIS 4.9 0.9 + - - +
38V ASN 3.3 0.6 - - - -
39V PHE* 1.3 85.5 - + - +
41V THR* 1.3 65.1 + - + +
43V GLY* 3.5 1.0 + - - -
44V GLU* 3.2 22.7 + - - +
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Residues in contact with THR 41 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38N ASN* 5.8 0.9 - - - +
41N THR* 3.8 25.1 - - + +
37R HIS 5.7 0.2 + - - -
40R PHE* 3.9 18.3 - - - +
41R THR* 3.7 29.3 - - + +
37V HIS 5.4 1.1 - - - +
38V ASN* 3.3 17.1 + - - +
40V PHE* 1.3 76.8 - - + +
42V LEU* 1.3 71.2 + - - +
44V GLU* 3.6 9.2 + - - +
45V LYS* 3.1 27.9 + - - +
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Residues in contact with LEU 42 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37R HIS 5.2 0.4 - - - +
40R PHE* 4.3 12.8 - - + -
34V MET* 3.8 19.1 - - + -
38V ASN* 2.9 34.5 + - + +
41V THR* 1.3 85.7 - - - +
43V GLY* 1.3 60.4 + - - +
45V LYS* 3.2 7.3 - - + +
46V MET* 2.9 32.4 + - + +
95V MET* 4.0 13.0 - - - -
99V MET* 3.4 34.3 - - + -
146V PHE* 4.1 14.8 - - + -
149V PHE* 3.7 22.7 - - + -
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Residues in contact with GLY 43 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31V HIS* 3.1 35.0 + - - -
34V MET* 3.6 13.1 - - - -
39V PHE* 3.0 23.5 + - - -
40V PHE 3.8 1.6 - - - -
41V THR 3.3 0.2 - - - -
42V LEU* 1.3 76.9 - - - +
44V GLU* 1.3 59.2 + - - +
46V MET* 3.2 1.4 + - - -
47V ASP* 3.1 10.6 + - - -
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Residues in contact with GLU 44 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40V PHE 3.2 16.0 + - - +
41V THR* 3.9 8.7 - - - +
42V LEU 3.3 0.2 - - - -
43V GLY* 1.3 72.1 - - - +
45V LYS* 1.3 73.7 + - + +
47V ASP* 3.2 14.6 + - - +
48V ASP* 3.1 49.1 + - - +
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Residues in contact with LYS 45 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R PHE* 3.6 43.6 - - + -
41V THR 3.1 17.2 + - - +
42V LEU* 3.2 17.0 - - + +
44V GLU* 1.3 83.6 - - + +
46V MET* 1.3 66.7 + - + +
48V ASP* 3.5 20.9 + - - +
49V LEU* 3.1 26.4 + - + +
142V HIS* 4.9 7.3 + - - -
145V MET* 3.9 17.6 - - - +
146V PHE* 4.0 20.6 - - + -
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Residues in contact with MET 46 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27V ILE* 3.3 21.8 - - + +
30V ILE* 3.8 22.0 - - + -
31V HIS* 3.7 20.4 - - + -
34V MET* 3.8 18.2 - - + -
42V LEU* 2.9 21.0 + - + +
43V GLY 3.2 6.7 + - - +
45V LYS* 1.3 77.4 - - + +
47V ASP* 1.3 61.1 + - - +
49V LEU* 4.1 6.1 - - + -
50V TYR* 2.9 31.4 + - - +
99V MET* 4.0 6.7 - - + -
102V LEU* 3.5 33.0 - - + -
146V PHE* 3.7 23.1 - - + -
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Residues in contact with ASP 47 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28V HIS* 6.1 0.7 - - - -
31V HIS* 3.0 30.0 + - - -
43V GLY 3.1 10.8 + - - +
44V GLU* 3.4 14.9 - - - +
46V MET* 1.3 75.8 - - - +
48V ASP* 1.3 62.5 - - - +
50V TYR* 3.6 6.5 + - - +
51V SER* 3.2 26.0 + - - -
58Y ASP* 5.7 1.6 - - - +
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Residues in contact with ASP 48 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44V GLU* 3.1 33.0 + - - +
45V LYS* 3.7 24.3 - - - +
46V MET 3.3 0.2 - - - -
47V ASP* 1.3 75.0 - - - +
49V LEU* 1.3 64.4 + - + +
51V SER* 3.5 6.8 + - - -
52V GLU* 3.0 28.8 + - - +
142V HIS* 6.6 0.2 - - + -
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Residues in contact with LEU 49 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23V PHE* 4.7 1.1 - - + -
27V ILE* 4.0 13.7 - - + -
45V LYS* 3.1 18.1 + - - +
46V MET* 3.3 15.5 + - + +
48V ASP* 1.3 78.6 - - + +
50V TYR* 1.3 67.9 + - - +
52V GLU* 3.2 2.8 + - - +
53V PHE* 3.0 47.9 + - + +
102V LEU* 3.7 41.3 - - + -
106V LEU* 5.1 2.9 - - + -
142V HIS* 3.6 38.8 - - + +
146V PHE* 4.2 11.7 - - + -
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Residues in contact with TYR 50 (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 53.4 + - + +
25V VAL* 6.0 0.2 - - - +
27V ILE* 3.9 14.2 - - + +
28V HIS* 3.1 47.3 + + + +
46V MET 2.9 18.2 + - - +
47V ASP* 3.6 7.0 - - - +
49V LEU* 1.3 77.3 - - - +
51V SER* 1.3 65.8 + - - +
53V PHE 4.0 0.2 - - - -
54V GLY* 3.0 23.5 + - - -
21Y ASN* 5.5 0.9 + - - -
24Y THR* 5.8 2.8 - - - +
50Y TYR* 4.7 12.4 + + - -
54Y GLY* 6.0 2.9 - - - -
57Y MET* 4.5 6.4 - - - +
58Y ASP* 5.7 1.1 - - - -
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Residues in contact with SER 51 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47V ASP 3.2 14.1 + - - -
48V ASP* 3.8 8.9 - - - -
50V TYR* 1.3 82.9 - - - +
52V GLU* 1.3 64.4 + - - +
54V GLY* 3.4 1.6 + - - -
55V GLU* 3.1 31.0 + - - +
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Residues in contact with GLU 52 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48V ASP 3.0 17.0 + - - +
49V LEU* 3.2 5.6 + - - +
51V SER* 1.3 77.5 - - - +
53V PHE* 1.3 69.7 + - + +
55V GLU* 3.3 10.0 + - + +
56V GLN* 3.0 34.3 + - + +
138V SER* 2.6 32.5 + - - -
142V HIS* 2.8 27.7 + - - -
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Residues in contact with PHE 53 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20V LEU* 4.1 15.0 - - + +
23V PHE* 3.8 35.4 - + + -
24V THR* 4.2 8.2 + - - +
27V ILE* 4.5 7.9 - - + -
49V LEU* 3.0 49.1 + - + +
50V TYR 4.6 0.4 - - - +
52V GLU* 1.3 87.1 - - + +
54V GLY* 1.3 63.8 + - - +
56V GLN* 3.6 37.9 - - - +
57V MET* 3.1 22.9 + - - +
106V LEU* 3.8 22.2 - - + -
109V LEU* 4.7 3.4 - - + -
139V ILE* 3.9 19.3 - - + -
142V HIS* 4.4 8.5 - + - -
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Residues in contact with GLY 54 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24V THR* 4.0 8.2 + - - -
50V TYR* 3.0 20.3 + - - -
51V SER 3.8 1.8 - - - -
53V PHE* 1.3 78.3 - - - +
55V GLU* 1.3 54.7 + - - +
57V MET* 3.3 11.6 - - - +
58V ASP* 3.1 33.4 + - - +
50Y TYR* 6.2 1.3 - - - -
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Residues in contact with GLU 55 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51V SER* 3.1 21.4 + - - +
52V GLU* 3.3 10.3 + - - +
54V GLY* 1.3 71.9 - - - +
56V GLN* 1.3 65.7 + - - +
57V MET 3.2 1.6 - - - -
58V ASP* 3.5 7.6 - - - +
59V GLU* 3.0 40.6 + - - +
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Residues in contact with GLN 56 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20V LEU* 4.2 7.8 - - + +
52V GLU* 3.0 30.8 + - + +
53V PHE* 3.6 40.0 - - + +
55V GLU* 1.3 73.5 - - - +
57V MET* 1.3 58.9 + - - +
59V GLU* 3.1 3.3 + - - +
60V VAL* 2.8 34.3 + - - +
113V TYR* 3.0 30.8 + - - -
135V PHE* 3.6 58.9 + - + +
138V SER* 5.0 2.0 - - - -
139V ILE* 4.0 2.4 - - - +
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Residues in contact with MET 57 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17V VAL* 4.2 10.1 - - + +
20V LEU* 3.6 28.0 - - + -
21V ASN* 3.3 40.2 - - - +
24V THR* 6.0 5.4 - - + +
53V PHE 3.1 11.7 + - - +
54V GLY* 3.3 13.0 - - - +
55V GLU 3.2 0.2 - - - -
56V GLN* 1.3 77.6 - - - +
58V ASP* 1.3 67.9 + - - +
60V VAL* 2.8 14.6 + - - +
61V ALA* 2.8 13.7 + - - +
28Y HIS* 3.4 31.9 - - + +
32Y TRP* 3.8 21.5 - - - -
50Y TYR* 4.7 6.5 - - + +
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Residues in contact with ASP 58 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54V GLY 3.1 13.3 + - - +
55V GLU* 3.5 11.9 - - - +
57V MET* 1.3 78.8 - - - +
59V GLU* 1.3 56.6 + - + +
61V ALA* 3.2 7.2 + - - +
62V GLU* 2.8 53.9 + - - +
28Y HIS* 3.3 33.0 + - - -
31Y HIS* 6.0 1.7 + - - -
32Y TRP* 5.0 7.4 + - - +
47Y ASP* 5.4 3.8 - - - +
50Y TYR* 5.5 1.0 - - - -
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Residues in contact with GLU 59 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55V GLU* 3.0 34.2 + - + +
56V GLN 3.1 3.3 + - - +
58V ASP* 1.3 79.8 - - + +
60V VAL* 1.3 60.8 + - - +
62V GLU* 4.1 10.1 - - - +
63V ARG* 3.0 29.8 + - - +
131V MET* 3.7 10.3 - - - +
135V PHE* 3.4 28.6 - - + -
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Residues in contact with VAL 60 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13V LEU* 3.3 42.6 - - + +
16V GLN* 4.2 12.3 - - + -
17V VAL* 4.1 8.1 - - + +
20V LEU* 4.1 12.1 - - + -
56V GLN 2.8 19.7 + - - +
57V MET* 3.4 9.0 - - - +
59V GLU* 1.3 76.9 - - - +
61V ALA* 1.3 58.3 + - - +
63V ARG* 3.3 2.6 + - - +
64V LEU* 2.9 27.7 + - - +
113V TYR* 4.9 1.6 - - - +
131V MET* 4.1 11.9 - - + -
132V LEU* 5.2 3.4 - - + -
135V PHE* 3.7 23.8 - - + -
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Residues in contact with ALA 61 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17V VAL* 4.4 12.7 - - + +
57V MET 2.8 9.6 + - - +
58V ASP 3.6 5.4 - - - +
60V VAL* 1.3 77.3 - - - +
62V GLU* 1.3 57.0 + - - +
64V LEU* 3.3 5.7 + - - +
65V LEU* 2.9 32.7 + - - +
71V PRO* 4.4 11.1 - - + +
32Y TRP* 3.5 45.8 - - + +
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Residues in contact with GLU 62 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141O LYS* 4.0 23.8 - - + +
144O TRP* 3.9 33.1 - - + -
145O MET* 5.9 0.7 - - - +
58V ASP* 2.8 40.0 + - - +
59V GLU* 4.1 8.5 - - - +
61V ALA* 1.3 72.6 - - - +
63V ARG* 1.3 58.3 + - - +
65V LEU* 3.2 12.3 + - + +
66V ALA* 2.9 27.8 + - - +
31Y HIS* 4.8 11.4 + - + -
32Y TRP* 5.1 8.3 + - + +
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Residues in contact with ARG 63 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136O LYS* 4.1 5.3 - - - +
137O ALA 5.0 0.8 + - - -
140O ASP* 2.8 43.0 + - - +
13V LEU* 3.9 9.2 - - + -
59V GLU 3.0 19.5 + - - +
60V VAL 3.8 3.1 - - - +
61V ALA 3.3 0.2 - - - -
62V GLU* 1.3 75.4 - - - +
64V LEU* 1.3 63.8 + - - +
66V ALA* 3.1 10.3 + - - +
67V ILE* 3.1 45.8 + - + +
125V ASP* 3.0 24.9 + - - -
127V VAL* 3.4 29.2 - - - +
128V THR* 2.9 24.2 + - - +
131V MET* 4.0 20.2 - - + -
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Residues in contact with LEU 64 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10V LYS* 3.4 45.5 - - + +
13V LEU* 3.7 14.0 - - + +
14V ASN* 3.7 43.7 - - + +
17V VAL* 4.8 2.2 - - + -
60V VAL 2.9 17.1 + - - +
61V ALA* 3.6 5.6 - - - +
63V ARG* 1.3 74.0 - - - +
65V LEU* 1.3 62.4 + - - +
67V ILE* 3.5 8.9 + - + +
69V GLY* 2.8 38.8 + - - -
70V SER 4.0 2.7 - - - +
71V PRO* 3.8 19.5 - - + -
----------------------------------------------------------
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Residues in contact with LEU 65 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144O TRP* 3.7 38.6 - - + +
154O PRO* 3.4 16.5 - - - +
61V ALA 2.9 19.1 + - - +
62V GLU* 3.4 10.5 - - - +
64V LEU* 1.3 76.2 - - - +
66V ALA* 1.3 61.3 + - - +
68V GLY* 3.2 12.3 + - - -
69V GLY 3.7 11.2 + - - +
70V SER* 4.8 0.4 - - - -
71V PRO* 3.4 27.8 - - + -
32Y TRP* 3.5 50.9 - - + +
33Y TYR* 5.0 6.1 - - + -
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Residues in contact with ALA 66 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140O ASP* 3.9 27.5 - - - +
141O LYS* 4.6 5.2 - - + -
144O TRP* 4.0 14.6 - - + -
154O PRO* 4.0 12.3 - - - +
155O LEU* 4.5 7.4 - - - +
62V GLU 2.9 16.4 + - - +
63V ARG* 3.1 24.3 + - - +
65V LEU* 1.3 77.9 - - - +
67V ILE* 1.3 60.2 + - - +
68V GLY 3.4 1.5 + - - -
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Residues in contact with ILE 67 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140O ASP* 6.1 0.2 - - - -
155O LEU* 3.9 18.7 - - + +
9V THR* 3.8 29.2 - - + -
10V LYS* 3.2 37.4 + - + -
13V LEU* 3.9 19.5 - - + -
63V ARG* 3.1 44.5 + - - +
64V LEU* 3.7 9.4 - - + +
65V LEU 3.3 0.2 - - - -
66V ALA* 1.3 78.2 - - - +
68V GLY* 1.3 54.5 + - - +
125V ASP* 4.0 7.9 - - - +
128V THR* 4.6 1.1 - - - +
----------------------------------------------------------
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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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