Contacts of the helix formed by residues 38 - 67 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLY 3.2 1.2 - - - -
37B HIS* 1.3 84.8 + - - +
39B PHE* 1.3 62.4 + - - +
40B PHE 3.2 3.0 + - - -
41B THR* 3.4 17.4 + - + +
42B LEU* 3.0 42.0 + - + +
95B MET* 4.0 11.6 - - + +
149B PHE* 3.6 12.4 - - + -
38F ASN* 5.1 4.8 - - - +
37J HIS* 2.7 54.1 + - - +
38J ASN* 4.8 6.3 - - - +
41J THR* 5.8 1.0 - - - +
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Residues in contact with PHE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B HIS* 4.5 5.8 - - - -
32B TRP 5.4 0.2 - - - -
34B MET* 3.2 45.8 - - + +
35B ARG 4.7 0.2 - - - -
36B GLY 3.1 18.4 + - - +
37B HIS 3.3 1.8 - - - +
38B ASN* 1.3 76.0 - - - +
40B PHE* 1.3 78.9 + + + +
43B GLY* 3.0 28.9 + - - -
95B MET* 3.9 10.0 - - + +
144F TRP* 4.0 30.3 - + - -
145F MET* 3.8 40.6 - - + -
148F ALA* 3.8 13.5 - - + -
149F PHE* 4.2 11.0 - - + -
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Residues in contact with PHE 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B HIS 4.7 1.2 + - - -
38B ASN 3.2 1.2 - - - -
39B PHE* 1.3 86.9 - + - +
41B THR* 1.3 64.0 + - - +
44B GLU* 2.7 42.1 + - - +
41F THR* 3.8 13.7 - - + +
42F LEU* 3.8 25.8 - - + -
45F LYS* 3.7 35.2 - - + -
145F MET* 3.9 37.2 - - + -
146F PHE* 3.5 41.5 - + - -
149F PHE* 4.0 19.3 - + + -
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Residues in contact with THR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ASN* 3.4 22.0 + - + +
40B PHE* 1.3 77.8 - - - +
42B LEU* 1.3 61.4 + - - +
44B GLU* 4.0 6.1 + - - +
45B LYS* 3.4 26.7 + - - +
38F ASN* 5.7 0.9 - - - +
41F THR* 3.7 26.2 + - + +
40J PHE* 3.9 20.4 - - - +
41J THR* 3.8 27.5 - - + +
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B MET* 4.1 12.8 - - + -
38B ASN* 3.0 18.4 + - + +
41B THR* 1.3 78.2 + - - +
43B GLY* 1.3 56.7 + - - +
44B GLU 3.3 1.1 - - - -
45B LYS* 3.0 10.9 + - + +
46B MET* 2.8 38.5 + - + +
95B MET* 3.5 34.3 - - + -
99B MET* 4.0 22.0 - - + -
146B PHE* 4.6 3.1 - - + -
149B PHE* 3.5 26.9 - - + -
40J PHE* 3.7 35.7 - - + -
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Residues in contact with GLY 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B HIS* 3.2 30.1 + - - -
34B MET* 3.5 13.6 - - - -
39B PHE* 3.0 21.8 + - - -
40B PHE* 4.1 0.7 - - - -
42B LEU* 1.3 75.8 - - - +
44B GLU* 1.3 56.5 + - - +
46B MET 3.3 0.5 + - - -
47B ASP* 3.1 23.2 + - - -
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Residues in contact with GLU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE* 2.7 44.0 + - - +
41B THR* 4.0 7.6 - - - +
42B LEU 3.3 0.2 - - - -
43B GLY* 1.3 74.4 - - - +
45B LYS* 1.3 65.8 + - + +
47B ASP* 3.5 15.7 + - - +
48B ASP* 3.3 28.7 + - - +
45F LYS* 5.3 7.8 - - - +
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Residues in contact with LYS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B THR 3.4 20.0 + - - +
42B LEU* 3.0 17.6 + - + +
44B GLU* 1.3 82.9 - - + +
46B MET* 1.3 69.4 + - + +
48B ASP* 3.3 19.1 + - - +
49B LEU* 3.1 28.5 + - - +
142B HIS* 5.4 4.4 + - - -
145B MET* 4.2 12.9 - - - +
146B PHE* 3.9 21.9 - - + -
40J PHE* 3.6 43.2 - - + -
44J GLU* 4.9 11.0 - - - +
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Residues in contact with MET 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE* 3.3 24.7 - - + +
30B ILE* 4.0 22.7 - - + -
31B HIS* 3.7 21.8 - - + +
34B MET* 3.8 19.1 - - + -
42B LEU* 2.8 23.0 + - + +
43B GLY 3.3 5.6 + - - +
45B LYS* 1.3 82.1 - - + +
47B ASP* 1.3 61.4 + - - +
49B LEU* 3.7 23.6 - - + -
50B TYR* 2.8 27.5 + - - +
99B MET* 4.3 9.6 - - + -
102B LEU* 3.9 20.2 - - + -
146B PHE* 4.0 6.5 - - + -
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Residues in contact with ASP 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B HIS* 3.0 25.2 + - - -
43B GLY 3.1 13.3 + - - +
44B GLU* 3.5 20.2 - - + +
46B MET* 1.3 73.7 - - - +
48B ASP* 1.3 70.1 + - - +
50B TYR* 3.5 6.1 + - - +
51B SER* 3.1 26.3 + - - -
58D ASP* 5.2 4.5 - - - +
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Residues in contact with ASP 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B GLU* 3.3 15.8 + - - +
45B LYS* 3.3 22.5 + - - +
47B ASP* 1.3 84.4 - - - +
49B LEU* 1.3 61.3 + - + +
51B SER* 3.5 6.0 + - - -
52B GLU* 2.9 28.5 + - - +
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Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 5.6 0.2 - - + -
27B ILE* 4.0 12.3 - - + -
45B LYS* 3.1 15.3 + - - +
46B MET* 3.7 22.7 - - + +
48B ASP* 1.3 76.9 - - + +
50B TYR* 1.3 60.9 + - - +
52B GLU* 4.0 6.3 - - - +
53B PHE* 2.8 48.1 + - + +
102B LEU* 4.1 14.1 - - + -
106B LEU* 5.6 1.8 - - + -
142B HIS* 3.4 42.0 - - + +
146B PHE* 3.6 32.8 - - + -
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Residues in contact with TYR 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 3.5 51.6 + - + +
25B VAL* 5.4 0.2 - - - -
27B ILE* 3.9 12.9 - - + +
28B HIS* 3.5 45.4 + + + +
46B MET 2.8 19.8 + - - +
47B ASP* 3.6 7.6 - - - +
49B LEU* 1.3 74.9 - - - +
51B SER* 1.3 61.4 + - - +
53B PHE* 3.8 0.3 - - - -
54B GLY* 2.9 29.6 + - - -
21D ASN* 5.7 0.2 + - - -
24D THR* 5.5 4.5 - - - +
50D TYR* 4.6 15.0 + + - -
54D GLY* 5.8 4.7 - - - -
57D MET* 4.6 7.6 - - - +
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Residues in contact with SER 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ASP 3.1 13.1 + - - -
48B ASP* 3.6 9.3 - - - -
50B TYR* 1.3 81.0 - - - +
52B GLU* 1.3 67.7 + - - +
54B GLY* 3.3 1.7 + - - -
55B GLU* 3.0 34.6 + - - +
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Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASP 2.9 20.5 + - - +
49B LEU* 4.0 6.9 - - - +
51B SER* 1.3 73.4 - - - +
53B PHE* 1.3 67.7 - - + +
55B GLU* 3.1 13.6 + - - +
56B GLN* 3.0 37.2 + - + +
138B SER* 2.2 33.5 + - - -
142B HIS* 2.8 30.8 + - - -
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Residues in contact with PHE 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LEU* 4.2 15.5 - - + +
23B PHE* 3.8 35.7 - + + -
24B THR* 4.2 9.5 + - - +
27B ILE* 4.4 6.5 - - + -
49B LEU* 2.8 45.0 + - + +
50B TYR 4.4 0.9 - - - +
52B GLU* 1.3 81.2 - - + +
54B GLY* 1.3 59.2 + - - +
56B GLN* 3.5 35.7 + - - +
57B MET* 3.1 22.5 + - - +
106B LEU* 3.5 25.6 - - + -
109B LEU* 4.2 8.5 - - + -
139B ILE* 3.9 17.7 - - + -
142B HIS* 4.1 20.0 - + - -
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Residues in contact with GLY 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 4.0 9.1 + - - -
50B TYR* 2.9 19.9 + - - -
51B SER* 3.8 2.0 - - - -
53B PHE* 1.3 75.5 - - - +
55B GLU* 1.3 56.8 + - - +
57B MET* 3.5 12.9 - - - +
58B ASP* 3.2 33.4 + - - +
50D TYR* 6.0 3.4 - - - -
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Residues in contact with GLU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B SER* 3.0 23.0 + - - +
52B GLU* 3.1 13.1 + - - +
54B GLY* 1.3 74.2 - - - +
56B GLN* 1.4 61.4 + - - +
58B ASP* 3.5 11.2 + - + +
59B GLU* 3.0 42.6 + - - +
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Residues in contact with GLN 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 4.4 7.5 - - + +
52B GLU* 3.0 34.8 + - + +
53B PHE* 3.6 35.3 - - + +
55B GLU* 1.4 71.3 - - - +
57B MET* 1.3 67.2 + - - +
59B GLU* 3.2 2.4 + - - +
60B VAL* 2.9 29.6 + - - +
113B TYR* 3.1 28.2 + - - -
135B PHE* 3.4 61.7 + - + +
138B SER* 4.8 1.4 - - - -
139B ILE* 4.7 0.6 - - - +
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Residues in contact with MET 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 4.2 8.3 - - + +
20B LEU* 3.6 28.7 - - + +
21B ASN* 3.2 42.6 - - - +
24B THR* 5.9 6.3 - - + +
53B PHE 3.1 15.1 + - - +
54B GLY* 3.5 11.2 - - - +
56B GLN* 1.3 79.7 - - - +
58B ASP* 1.3 59.7 + - - +
60B VAL* 3.2 4.4 + - - +
61B ALA* 3.0 29.3 + - - +
28D HIS* 3.7 28.9 - - + +
32D TRP* 3.8 23.6 - - + -
50D TYR* 4.3 7.0 - - - +
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Residues in contact with ASP 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLY 3.2 15.9 + - - +
55B GLU* 3.6 12.9 - - - +
57B MET* 1.3 82.0 - - - +
59B GLU* 1.3 57.1 + - + +
61B ALA* 3.3 6.0 + - - +
62B GLU* 2.8 45.5 + - - +
28D HIS* 3.1 34.1 + - - -
31D HIS* 6.5 0.9 - - - -
32D TRP* 4.5 6.7 + - - +
47D ASP* 5.8 0.2 - - - +
50D TYR* 5.6 2.9 - - - -
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Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLU* 3.0 33.4 + - - +
56B GLN 3.8 3.8 + - - +
58B ASP* 1.3 77.4 - - + +
60B VAL* 1.3 56.5 + - - +
62B GLU* 4.0 8.9 - - - +
63B ARG* 3.0 29.1 + - - +
131B MET* 3.6 13.9 - - - +
135B PHE* 3.3 31.5 - - + -
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Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.4 39.6 - - + +
16B GLN* 4.5 7.6 - - + -
17B VAL* 3.7 16.6 - - + +
20B LEU* 4.4 10.8 - - + -
56B GLN 2.9 21.4 + - - +
57B MET* 3.5 5.2 - - - +
59B GLU* 1.3 75.8 - - - +
61B ALA* 1.3 61.3 + - - +
63B ARG* 3.3 2.4 + - - +
64B LEU* 3.0 27.7 + - - +
113B TYR* 4.9 2.2 - - + +
131B MET* 4.1 12.6 - - + -
132B LEU* 5.2 3.1 - - + -
135B PHE* 3.6 23.3 - - + -
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 4.2 15.7 - - + -
57B MET 3.0 12.2 + - - +
58B ASP 3.9 1.3 - - - +
60B VAL* 1.3 75.1 - - - +
62B GLU* 1.3 58.7 + - - +
64B LEU* 3.8 5.3 - - - +
65B LEU* 3.1 34.4 + - - +
71B PRO* 4.4 7.4 - - + +
32D TRP* 3.5 46.0 - - + +
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASP* 2.8 29.6 + - - +
59B GLU* 4.1 9.4 - - - +
61B ALA* 1.3 76.4 - - - +
63B ARG* 1.3 59.1 + - - +
65B LEU* 3.5 10.3 + - + +
66B ALA* 3.0 27.7 + - - +
31D HIS* 4.4 17.3 + - - -
32D TRP* 5.0 8.6 + - + +
141G LYS* 2.6 37.5 + - + +
144G TRP* 3.6 31.5 - - + -
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Residues in contact with ARG 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 4.3 5.2 - - + -
59B GLU 3.0 20.6 + - - +
60B VAL 3.7 4.3 - - - +
62B GLU* 1.3 77.8 - - - +
64B LEU* 1.3 62.9 + - - +
66B ALA* 3.1 15.9 + - - +
67B ILE* 3.1 37.9 + - - +
125B ASP* 2.8 27.1 + - - -
127B VAL* 3.4 32.2 - - - +
128B THR* 3.1 20.9 + - - +
131B MET* 3.9 23.8 - - + -
136G LYS* 4.7 4.8 - - - +
137G ALA 4.9 1.4 + - - -
140G ASP* 2.8 42.4 + - - +
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Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LYS* 3.6 38.6 - - + +
13B LEU* 4.2 13.5 - - + +
14B ASN* 3.9 22.0 - - + +
17B VAL* 5.0 2.9 - - + -
60B VAL 3.0 16.5 + - - +
61B ALA* 3.8 3.8 - - - +
63B ARG* 1.3 72.7 - - - +
65B LEU* 1.3 59.1 + - - +
67B ILE* 3.3 9.4 + - + +
68B GLY 3.2 5.4 + - - -
69B GLY* 2.8 45.8 + - - -
70B SER 3.7 4.3 - - - +
71B PRO* 3.4 41.5 - - + -
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ALA 3.1 26.1 + - - +
62B GLU* 3.5 9.4 - - - +
64B LEU* 1.3 77.9 - - - +
66B ALA* 1.3 58.0 + - - +
68B GLY* 3.1 16.1 + - - -
69B GLY 3.5 11.6 - - - +
70B SER* 4.9 0.2 - - - -
71B PRO* 3.4 27.8 - - + -
32D TRP* 3.8 45.1 - - + +
33D TYR* 5.1 5.8 - - + -
144G TRP* 3.9 33.4 - - + +
154G PRO* 3.2 19.0 - - - +
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLU 3.0 18.1 + - - +
63B ARG* 3.1 20.7 + - - +
65B LEU* 1.3 78.0 - - - +
67B ILE* 1.3 58.3 + - - +
68B GLY 3.4 0.7 - - - -
140G ASP* 3.7 32.9 - - + +
141G LYS* 4.4 5.8 - - + +
144G TRP* 4.0 15.0 - - + -
154G PRO* 4.1 5.0 - - - +
155G LEU* 4.1 16.5 - - - +
----------------------------------------------------------
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Residues in contact with ILE 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR* 3.8 19.7 - - + -
10B LYS* 3.3 40.4 + - + -
13B LEU* 3.8 28.0 - - + -
63B ARG* 3.1 41.2 + - - +
64B LEU* 3.5 13.2 - - - +
65B LEU 3.3 0.2 - - - -
66B ALA* 1.3 75.0 - - - +
68B GLY* 1.3 56.0 + - - +
125B ASP* 4.2 8.1 - - - +
128B THR* 4.6 0.2 - - - +
140G ASP* 6.2 0.2 - - - -
155G LEU* 3.6 17.6 - - + +
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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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