Contacts of the helix formed by residues 38 - 67 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36O GLY 2.9 2.6 + - - -
37O HIS* 1.3 86.1 + - - +
39O PHE* 1.3 63.1 + - - +
40O PHE 3.3 2.5 - - - -
41O THR* 4.2 12.6 - - - +
42O LEU* 3.2 40.4 + - + +
95O MET* 3.6 17.5 - - + +
149O PHE* 3.9 11.9 - - + -
38Q ASN* 4.6 8.1 - - - +
37Y HIS* 2.9 55.8 + - - +
38Y ASN* 4.9 3.2 - - - +
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Residues in contact with PHE 39 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31O HIS* 4.5 8.7 - + - -
34O MET* 3.4 37.4 - - + +
36O GLY 3.1 16.1 + - - +
37O HIS 3.4 2.6 - - - -
38O ASN* 1.3 77.8 - - - +
40O PHE* 1.3 76.1 + + - +
43O GLY* 3.1 27.6 + - - -
95O MET* 3.8 10.7 - - + +
144Q TRP* 3.9 25.1 - + - -
145Q MET* 3.5 52.0 - - + -
148Q ALA* 3.6 19.1 - - + +
149Q PHE* 4.2 12.1 - - + +
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Residues in contact with PHE 40 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37O HIS 5.0 1.3 + - - +
38O ASN 3.3 0.2 - - - -
39O PHE* 1.3 84.1 - + - +
41O THR* 1.3 66.1 + - - +
43O GLY* 3.3 9.2 + - - -
44O GLU* 3.3 19.9 + - - +
41Q THR* 4.0 16.2 - - - +
42Q LEU* 3.9 19.7 - - + -
45Q LYS* 3.4 40.2 - - + -
145Q MET* 4.0 31.9 - - + -
146Q PHE* 3.7 34.5 - + - -
149Q PHE* 3.9 29.2 - + + -
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Residues in contact with THR 41 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37O HIS 5.1 2.2 - - - +
38O ASN* 4.3 26.5 - - - +
39O PHE 3.6 0.2 - - - -
40O PHE* 1.3 79.4 - - + +
42O LEU* 1.3 67.4 + - + +
44O GLU* 3.6 13.9 - - - +
45O LYS* 3.5 22.4 + - - +
38Q ASN* 5.7 2.2 - - - +
41Q THR* 4.3 16.5 + - + +
37Y HIS 4.9 4.0 + - - +
38Y ASN* 6.0 0.2 - - - +
40Y PHE* 3.5 25.6 - - - +
41Y THR* 4.0 26.5 + - + -
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Residues in contact with LEU 42 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34O MET* 3.7 17.7 - - + -
38O ASN* 3.2 27.1 + - + +
41O THR* 1.3 83.0 - - + +
43O GLY* 1.3 60.5 + - - +
44O GLU 3.3 0.7 - - - -
45O LYS* 3.2 4.1 + - + +
46O MET* 2.9 36.1 + - + +
95O MET* 4.6 6.5 - - + -
99O MET* 3.5 34.5 - - + -
146O PHE* 4.0 18.4 - - + -
149O PHE* 3.7 33.4 - - + -
40Y PHE* 4.5 8.5 - - + -
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Residues in contact with GLY 43 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31O HIS* 3.1 38.2 + - - -
34O MET* 3.6 8.2 - - - -
39O PHE* 3.1 23.4 + - - -
40O PHE* 3.3 1.1 + - - -
42O LEU* 1.3 75.5 - - - +
44O GLU* 1.3 57.4 + - - +
46O MET* 3.4 1.4 + - - -
47O ASP* 3.2 19.0 + - - +
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Residues in contact with GLU 44 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40O PHE 3.3 14.2 + - - +
41O THR* 3.6 17.8 - - - +
43O GLY* 1.3 73.7 - - - +
45O LYS* 1.3 77.8 + - + +
46O MET 3.2 0.2 - - - -
47O ASP* 3.2 13.4 + - + +
48O ASP* 3.1 29.2 + - - +
44Y GLU* 4.2 15.1 - - - +
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Residues in contact with LYS 45 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41O THR 3.5 14.5 + - - +
42O LEU* 3.2 11.3 + - - +
44O GLU* 1.3 89.0 - - + +
46O MET* 1.3 67.2 + - + +
48O ASP* 3.4 19.4 + - + +
49O LEU* 3.0 33.6 + - + +
145O MET* 5.0 10.3 - - - +
146O PHE* 4.5 11.0 - - + -
40Y PHE* 3.5 51.5 - - + -
44Y GLU* 4.7 18.9 + - - -
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Residues in contact with MET 46 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27O ILE* 3.2 24.8 - - + +
30O ILE* 4.0 21.8 - - + -
31O HIS* 3.8 20.2 - - + -
34O MET* 3.7 18.4 - - + -
42O LEU* 2.9 23.5 + - + +
43O GLY 3.5 6.3 - - - +
44O GLU 3.2 0.2 - - - -
45O LYS* 1.3 80.3 - - + +
47O ASP* 1.3 60.5 + - - +
49O LEU* 4.0 12.1 - - + -
50O TYR* 3.0 30.7 + - - +
99O MET* 4.1 10.5 - - + -
102O LEU* 4.0 12.1 - - + -
146O PHE* 4.0 26.7 - - + -
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Residues in contact with ASP 47 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28O HIS* 5.8 3.5 - - - -
31O HIS* 3.3 29.5 + - - -
43O GLY 3.2 10.1 + - - +
44O GLU* 3.2 14.7 + - - +
46O MET* 1.3 76.3 - - - +
48O ASP* 1.3 64.5 + - - +
50O TYR* 3.3 7.3 + - - +
51O SER* 3.2 25.6 + - - -
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Residues in contact with ASP 48 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44O GLU* 3.1 18.9 + - - +
45O LYS* 3.7 27.3 + - + +
47O ASP* 1.3 75.3 - - - +
49O LEU* 1.3 64.6 + - + +
51O SER* 3.6 4.8 + - - -
52O GLU* 3.0 30.9 + - - +
142O HIS* 6.4 0.2 - - + -
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Residues in contact with LEU 49 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23O PHE* 4.8 2.7 - - + -
27O ILE* 3.9 14.8 - - + -
45O LYS* 3.0 19.8 + - + +
46O MET* 3.8 26.2 - - + +
48O ASP* 1.3 78.7 - - + +
50O TYR* 1.3 57.4 + - - +
52O GLU* 4.4 4.7 - - - -
53O PHE* 2.8 49.8 + - + +
102O LEU* 4.0 29.2 - - + -
106O LEU* 5.5 2.5 - - + -
142O HIS* 3.3 37.7 - - + +
146O PHE* 4.2 13.0 - - + -
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Residues in contact with TYR 50 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21M ASN* 5.6 1.0 + - - -
50M TYR* 4.7 13.1 + + - -
54M GLY* 5.9 2.6 - - - -
57M MET* 4.8 5.5 - - - +
58M ASP* 5.4 2.9 - - - -
24O THR* 3.5 51.1 + - + +
27O ILE* 4.0 13.5 - - + -
28O HIS* 3.2 49.4 + + + +
46O MET 3.0 18.5 + - - +
47O ASP* 3.5 7.4 - - - +
48O ASP 3.2 0.2 - - - -
49O LEU* 1.3 77.1 - - - +
51O SER* 1.3 70.0 + - - +
54O GLY* 3.0 22.5 + - - -
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Residues in contact with SER 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47O ASP 3.2 14.2 + - - -
48O ASP* 4.0 5.3 - - - -
50O TYR* 1.3 84.9 - - - +
52O GLU* 1.3 63.5 + - - +
54O GLY* 3.2 2.1 + - - -
55O GLU* 2.9 24.8 + - - +
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Residues in contact with GLU 52 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48O ASP 3.0 20.4 + - - +
49O LEU* 3.8 4.5 - - - +
51O SER* 1.3 78.3 - - - +
53O PHE* 1.3 67.8 + - + +
55O GLU* 3.4 5.4 + - + +
56O GLN* 3.0 32.9 + - + +
138O SER* 2.5 31.9 + - - -
142O HIS* 2.8 27.5 + - - -
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Residues in contact with PHE 53 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20O LEU* 4.2 16.2 - - + +
23O PHE* 3.7 36.8 - + + -
24O THR* 4.3 9.9 - - - +
27O ILE* 4.4 5.6 - - + -
49O LEU* 2.8 47.5 + - + +
50O TYR 4.5 0.9 - - - +
52O GLU* 1.3 92.6 - - + +
54O GLY* 1.3 57.0 + - - +
56O GLN* 3.5 37.6 + - - +
57O MET* 3.0 27.2 + - - +
106O LEU* 4.0 19.1 - - + -
109O LEU* 4.4 4.7 - - + -
138O SER* 5.0 0.4 - - - -
139O ILE* 4.0 18.6 - - + -
142O HIS* 4.4 11.7 - + - -
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Residues in contact with GLY 54 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M HIS* 5.6 0.5 + - - -
50M TYR* 5.9 3.4 - - - -
24O THR* 4.1 7.8 + - - -
50O TYR* 3.0 17.7 + - - -
51O SER* 3.2 3.8 + - - -
53O PHE* 1.3 75.6 - - - +
55O GLU* 1.3 58.0 + - - +
57O MET* 3.3 14.1 + - - +
58O ASP* 3.0 27.0 + - - +
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Residues in contact with GLU 55 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51O SER 2.9 16.3 + - - +
52O GLU* 4.0 4.9 - - - +
54O GLY* 1.3 73.2 - - - +
56O GLN* 1.3 68.4 + - - +
58O ASP* 3.3 11.1 + - - +
59O GLU* 2.9 47.9 + - + +
135O PHE* 6.5 0.2 - - + -
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Residues in contact with GLN 56 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20O LEU* 4.2 5.6 - - + +
52O GLU* 3.0 28.4 + - + +
53O PHE* 3.6 45.2 - - - +
54O GLY 3.4 0.2 - - - -
55O GLU* 1.3 75.2 - - - +
57O MET* 1.3 58.0 + - - +
59O GLU* 3.2 2.4 + - - +
60O VAL* 2.9 33.9 + - - +
113O TYR* 3.1 27.9 + - - -
135O PHE* 3.5 59.5 + - + +
138O SER* 4.6 2.0 - - - -
139O ILE* 4.5 0.8 - - - +
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Residues in contact with MET 57 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M HIS* 3.6 32.1 - - + +
32M TRP* 3.7 21.3 - - + -
50M TYR* 4.7 6.5 - - - +
17O VAL* 4.2 9.4 - - - +
20O LEU* 3.6 31.2 - - + +
21O ASN* 3.5 40.4 - - - +
24O THR* 6.3 2.5 - - + -
53O PHE 3.0 16.7 + - - +
54O GLY* 3.6 12.1 - - - +
55O GLU 3.1 0.2 - - - -
56O GLN* 1.3 77.6 - - - +
58O ASP* 1.3 60.3 + - - +
60O VAL* 3.2 4.5 + - - +
61O ALA* 2.9 25.1 + - - +
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Residues in contact with ASP 58 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M HIS* 4.3 16.1 - - - +
31M HIS* 4.6 7.1 + - - -
32M TRP* 3.2 28.8 + - - -
47M ASP* 5.5 2.6 - - - +
54O GLY 3.0 16.8 + - - +
55O GLU* 3.3 13.6 + - - +
57O MET* 1.3 81.5 - - - +
59O GLU* 1.3 58.6 + - - +
61O ALA* 3.4 2.5 + - - +
62O GLU* 2.8 57.2 + - - +
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Residues in contact with GLU 59 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55O GLU* 2.9 45.6 + - + +
56O GLN 3.5 8.1 - - - +
58O ASP* 1.3 74.8 - - - +
60O VAL* 1.3 58.7 + - - +
62O GLU* 3.8 5.0 - - - +
63O ARG* 2.9 31.4 + - - +
131O MET* 3.8 8.6 - - + +
135O PHE* 3.7 22.7 - - + -
141T LYS* 3.4 26.4 + - - +
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Residues in contact with VAL 60 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13O LEU* 3.2 42.0 - - + +
16O GLN* 4.3 5.8 - - + -
17O VAL* 3.6 15.0 - - + +
20O LEU* 3.8 17.9 - - + -
56O GLN 2.9 19.5 + - - +
57O MET* 3.4 9.2 - - - +
59O GLU* 1.3 73.9 - - - +
61O ALA* 1.3 64.5 + - - +
63O ARG* 3.4 2.9 + - - +
64O LEU* 3.0 20.6 + - - +
113O TYR* 4.7 2.7 - - - +
131O MET* 4.4 12.1 - - + -
132O LEU* 5.5 2.7 - - + -
135O PHE* 3.9 18.6 - - + -
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Residues in contact with ALA 61 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32M TRP* 3.4 46.9 - - + -
17O VAL* 4.0 16.6 - - + -
57O MET 2.9 13.3 + - - +
58O ASP 4.0 2.0 - - - +
60O VAL* 1.3 75.5 - - - +
62O GLU* 1.3 57.0 + - - +
64O LEU* 3.2 7.0 + - - +
65O LEU* 3.1 32.8 + - - +
71O PRO* 4.4 5.4 - - + +
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Residues in contact with GLU 62 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M HIS* 4.3 12.3 + - - -
32M TRP* 4.8 6.1 - - + +
58O ASP* 2.8 46.3 + - - +
59O GLU* 3.9 3.0 - - - +
61O ALA* 1.3 76.6 - - - +
63O ARG* 1.3 60.4 + - - +
65O LEU* 3.5 8.4 + - - +
66O ALA* 3.0 26.9 + - - +
141T LYS* 2.6 46.3 + - - +
144T TRP* 3.6 35.7 - - + -
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Residues in contact with ARG 63 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13O LEU* 4.5 3.8 - - + -
59O GLU 2.9 19.0 + - - +
60O VAL 3.8 3.4 - - - +
62O GLU* 1.3 77.2 - - - +
64O LEU* 1.3 63.0 + - - +
66O ALA* 3.4 8.2 + - - +
67O ILE* 3.3 38.1 + - - +
125O ASP* 2.8 31.5 + - - -
127O VAL* 3.4 30.6 - - + +
128O THR* 3.0 21.8 + - - +
131O MET* 3.7 27.6 - - + -
136T LYS* 3.9 6.3 - - - +
137T ALA* 5.0 1.8 + - - +
140T ASP* 2.7 41.2 + - - +
141T LYS* 4.9 6.2 - - - +
----------------------------------------------------------
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Residues in contact with LEU 64 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10O LYS* 3.5 41.3 - - + +
13O LEU* 4.3 12.5 - - + +
14O ASN* 3.5 39.7 - - + +
17O VAL* 4.9 2.2 - - + -
60O VAL 3.0 14.4 + - - +
61O ALA* 3.2 9.8 + - - +
63O ARG* 1.3 76.2 - - - +
65O LEU* 1.3 59.9 + - - +
67O ILE* 3.1 18.7 - - + +
69O GLY* 3.1 27.9 + - - -
70O SER 3.8 9.0 - - - +
71O PRO* 3.5 24.7 - - + -
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Residues in contact with LEU 65 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32M TRP* 4.0 32.5 - - + +
33M TYR* 5.0 6.1 - - + -
61O ALA 3.1 27.3 + - - +
62O GLU* 3.7 8.5 - - - +
63O ARG 3.3 0.2 - - - -
64O LEU* 1.3 75.1 - - - +
66O ALA* 1.3 59.0 + - - +
68O GLY* 2.9 19.1 + - - -
69O GLY 3.3 21.0 - - - +
70O SER* 4.8 0.2 - - - -
71O PRO* 3.5 27.4 - - + -
144T TRP* 4.0 34.3 - - + +
154T PRO* 3.2 18.1 - - + +
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Residues in contact with ALA 66 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62O GLU 3.0 15.7 + - - +
63O ARG* 3.6 17.3 - - - +
65O LEU* 1.3 79.5 - - - +
67O ILE* 1.3 58.0 + - - +
68O GLY 3.3 2.3 + - - -
140T ASP* 4.0 37.7 - - + +
141T LYS* 4.5 4.9 - - - +
143T ILE* 6.0 0.7 - - - +
144T TRP* 4.0 15.0 - - + +
154T PRO* 3.9 11.8 - - - +
155T LEU* 4.6 8.1 - - - +
----------------------------------------------------------
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Residues in contact with ILE 67 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9O THR* 4.1 25.8 - - + -
10O LYS* 2.8 51.5 + - + +
13O LEU* 4.3 11.4 - - + -
63O ARG* 3.3 41.3 + - - +
64O LEU* 3.1 15.5 - - + +
66O ALA* 1.3 75.5 - - - +
68O GLY* 1.3 56.2 + - - +
125O ASP* 4.2 6.7 - - - +
128O THR* 5.1 0.2 - - - +
140T ASP* 6.2 0.4 - - - -
155T LEU* 4.0 15.6 - - + +
----------------------------------------------------------
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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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