Contacts of the helix formed by residues 28 - 53 (chain B) in PDB entry 2OKC
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 GLY 28 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ALA* 5.3 2.7 - - - -
26B GLY 3.6 5.3 + - - -
27B ILE* 1.3 78.3 - - - +
29B PHE* 1.3 59.9 + - - -
30B THR* 3.4 2.7 - - - -
31B ASP* 3.4 11.6 + - - +
32B TYR* 3.0 25.0 + - - +
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Residues in contact with PHE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TRP* 5.2 8.5 - + + -
19B ALA* 3.6 31.4 - - + -
23B ALA* 5.9 1.9 - - - +
28B GLY* 1.3 72.4 - - - -
30B THR* 1.3 57.4 + - - +
32B TYR* 3.1 12.4 + + - +
33B ILE* 2.9 59.7 + - + +
137B ILE* 3.4 33.2 - - + -
140B LYS* 5.4 5.2 - - + -
141B ASN* 3.1 32.5 - - + +
144B ASP* 5.7 3.6 - - - +
147B SER* 4.7 7.9 + - - +
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Residues in contact with THR 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLY 5.2 0.2 - - - -
29B PHE* 1.3 78.9 - - - +
31B ASP* 1.3 57.4 + - - +
33B ILE* 3.6 5.0 + - - +
34B THR* 2.7 33.3 + - - -
141B ASN* 3.2 19.8 + - - +
147B SER* 4.4 7.9 + - - -
149B ALA* 3.4 17.0 - - - +
152B TYR* 4.6 13.4 - - + -
218B LEU* 3.5 37.0 - - + -
222B LEU* 5.2 4.9 - - + +
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Residues in contact with ASP 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE* 4.3 9.8 - - + -
28B GLY* 3.4 14.6 + - - +
29B PHE 3.4 0.4 - - - -
30B THR* 1.3 77.4 - - - +
32B TYR* 1.3 64.6 + - - +
34B THR* 3.4 6.2 + - - -
35B GLN* 3.0 30.3 + - - +
103B LYS* 3.6 43.6 - - + +
218B LEU* 4.3 15.9 - - - +
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Residues in contact with TYR 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 2.8 36.3 + - + +
18B LEU* 3.5 26.2 - - + +
19B ALA* 3.6 34.1 - - + +
22B LEU* 3.7 23.1 - - + -
27B ILE* 4.1 13.4 - - + +
28B GLY 3.0 14.1 + - - +
29B PHE* 3.1 18.8 + + - +
31B ASP* 1.3 76.7 - - - +
33B ILE* 1.3 55.6 + - - +
35B GLN* 3.3 6.4 + - + +
36B LEU* 2.8 52.2 + - + +
104B ILE* 5.5 0.4 - - + -
113B VAL* 4.3 11.9 - - + -
116B MSE 3.5 16.3 - - - +
137B ILE* 4.7 4.9 - - + -
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Residues in contact with ILE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PHE* 2.9 55.7 + - + +
30B THR* 4.0 5.4 - - - +
32B TYR* 1.3 76.0 - - + +
34B THR* 1.4 54.0 + - - +
36B LEU* 3.6 10.9 - - + +
37B THR* 2.8 39.8 + - - +
134B TYR* 4.6 8.3 - - + +
137B ILE* 4.2 19.5 - - + +
138B LEU* 4.4 17.3 - - + -
141B ASN* 3.4 23.3 - - + +
222B LEU* 3.5 26.0 - - + -
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Residues in contact with THR 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B THR 2.7 21.8 + - - -
31B ASP* 3.6 8.8 - - - -
33B ILE* 1.4 75.4 - - - +
35B GLN* 1.3 69.4 + - - +
37B THR* 3.2 4.5 + - - -
38B TYR* 3.0 56.7 + - + +
101B GLN 5.3 0.2 - - - +
218B LEU* 3.6 39.0 - - + +
221B THR* 4.5 4.7 - - + -
222B LEU* 4.1 11.3 - - - +
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Residues in contact with GLN 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ASP* 3.0 19.4 + - - +
32B TYR 3.8 3.6 - - - +
34B THR* 1.3 76.3 - - - +
36B LEU* 1.3 65.5 + - - +
38B TYR* 3.4 16.3 + - - +
39B LEU* 3.0 34.7 + - + +
79B TYR* 2.6 39.9 + - + +
101B GLN 2.9 24.2 + - - -
102B ASN* 3.5 4.7 - - - +
103B LYS* 3.4 22.2 - - + +
104B ILE* 3.9 33.2 - - + -
113B VAL* 5.6 2.0 - - + -
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Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 3.8 31.0 - - + -
32B TYR* 2.8 31.2 + - + +
33B ILE* 3.6 11.9 - - + +
35B GLN* 1.3 78.8 - - - +
37B THR* 1.3 57.7 + - - +
39B LEU* 3.5 1.9 + - - +
40B LEU* 2.9 37.1 + - + +
113B VAL* 4.0 21.9 - - + +
116B MSE 4.0 11.7 - - + -
117B ILE* 3.4 32.5 - - + -
122B TRP* 5.8 0.9 - - + -
134B TYR* 6.2 4.9 - - + -
137B ILE* 5.2 4.5 - - + -
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Residues in contact with THR 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE 2.8 21.6 + - - -
34B THR* 3.5 6.1 - - - -
36B LEU* 1.3 74.0 - - - +
38B TYR* 1.3 66.3 + - - +
40B LEU* 4.3 5.8 - - - -
41B PHE* 3.0 24.6 + - - +
96B ILE* 4.7 5.4 - - + -
134B TYR* 2.6 30.3 + - - +
221B THR* 3.7 23.6 - - + -
222B LEU* 3.7 1.4 - - - +
225B MSE 3.5 35.9 - - + +
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Residues in contact with TYR 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B THR* 3.0 30.3 + - + +
35B GLN* 3.5 30.5 - - - +
37B THR* 1.3 76.4 - - - +
39B LEU* 1.3 63.1 + - - +
42B LEU* 3.2 8.0 + - - +
79B TYR* 3.5 9.0 - - + +
83B LEU* 3.7 15.7 - - + -
96B ILE* 3.6 22.9 - - + -
97B TYR* 2.6 48.6 + + + -
98B THR 4.5 2.3 + - - -
99B LYS 4.5 1.0 + - - -
100B ALA* 3.4 19.1 - - + -
101B GLN* 3.2 41.6 + - - +
217B PRO* 6.1 0.3 - - - +
218B LEU* 5.2 3.5 - - - +
221B THR* 3.7 17.2 + - + -
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLN* 3.0 20.7 + - + +
36B LEU 3.9 2.7 - - - +
38B TYR* 1.3 81.2 - - - +
40B LEU* 1.3 57.3 + - - +
42B LEU* 3.1 9.1 + - + +
43B LYS* 2.9 23.9 + - - +
64B TRP* 3.4 17.1 - - + -
67B LEU* 3.4 33.4 - - + -
79B TYR* 3.5 26.5 - - + +
110B LEU* 4.6 6.7 - - + -
113B VAL* 3.8 27.8 - - + -
114B ILE* 3.8 22.2 - - + +
117B ILE* 4.3 9.4 - - + -
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 2.9 25.4 + - + +
37B THR* 3.8 2.5 - - - +
39B LEU* 1.3 73.3 - - - +
41B PHE* 1.3 65.9 + - - +
43B LYS* 4.4 3.4 - - - -
44B MSE 3.0 37.5 + - + +
117B ILE* 4.2 12.0 - - + +
122B TRP* 3.3 63.9 - - + +
134B TYR* 5.4 11.0 - - + -
225B MSE 3.7 23.3 - - + -
229B LEU* 5.5 4.3 - - + -
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Residues in contact with PHE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B THR 3.0 18.1 + - - +
40B LEU* 1.3 76.0 - - - +
42B LEU* 1.3 62.5 + - - +
44B MSE 3.5 6.2 + - + +
45B ASP* 3.1 26.1 + - + +
58B ILE* 5.1 6.5 - - + -
92B LEU* 4.0 20.0 - - + -
93B ILE* 3.7 30.7 - - + -
96B ILE* 3.9 34.5 - - + -
97B TYR* 3.6 25.1 - + - +
225B MSE 3.9 11.9 - - + +
228B TYR* 3.8 36.8 - + - -
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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
----------------------------------------------------------
38B TYR 3.2 12.0 + - - +
39B LEU* 3.1 12.0 + - + +
41B PHE* 1.3 74.4 - - - +
43B LYS* 1.3 63.9 + - - +
45B ASP* 3.4 4.9 + - - +
46B ALA* 3.3 15.6 + - - +
58B ILE* 3.6 31.9 - - + -
62B TYR 3.8 17.5 - - - +
63B GLN* 4.3 3.4 - - - +
64B TRP* 3.9 40.1 + - + +
67B LEU* 4.0 20.6 - - + -
79B TYR* 5.9 1.8 - - + -
82B THR* 4.1 16.6 - - + -
86B LEU* 4.1 11.4 - - + -
97B TYR* 3.5 4.9 + - - +
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Residues in contact with LYS 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU 2.9 9.7 + - - +
40B LEU* 3.8 3.8 - - - +
42B LEU* 1.3 74.8 - - - +
44B MSE 1.3 64.3 + - - +
46B ALA* 3.0 8.3 + - + +
47B GLU* 3.0 58.3 + - - +
64B TRP* 3.4 36.0 - - + +
117B ILE* 3.4 31.2 - - + -
118B ASP* 3.6 31.6 - - - -
120B GLU 3.6 11.9 + - - -
121B GLN* 4.9 2.0 - - - +
122B TRP* 3.8 6.1 - - + -
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Residues in contact with MSE 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 3.0 37.9 + - + +
41B PHE* 3.9 5.8 - - + +
43B LYS* 1.3 78.1 - - - +
45B ASP* 1.3 61.4 + - - +
47B GLU* 3.3 8.1 + - - +
48B ASN* 3.1 23.0 + - - +
122B TRP* 3.9 24.9 - - + -
123B LEU* 3.5 32.9 - - + +
130B LYS* 4.0 19.1 - - - +
225B MSE 4.4 7.0 - - - -
228B TYR* 3.9 31.0 - - + +
229B LEU* 4.2 18.2 - - + -
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Residues in contact with ASP 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 3.1 23.0 + - + +
42B LEU 3.7 6.3 - - - +
43B LYS 3.2 0.4 - - - -
44B MSE 1.3 76.5 - - - +
46B ALA* 1.3 63.0 + - - +
48B ASN* 3.3 10.3 + - - +
49B VAL* 3.2 20.3 + - - +
56B SER* 2.6 48.7 + - - +
58B ILE* 3.8 21.1 - - + +
63B GLN* 5.8 1.2 - - - +
93B ILE* 4.9 4.7 - - - +
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Residues in contact with ALA 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU 3.3 2.6 + - - +
43B LYS* 3.0 11.4 + - + +
45B ASP* 1.3 80.3 + - - +
47B GLU* 1.3 59.6 + - + +
48B ASN 3.1 0.2 - - - -
49B VAL* 3.5 7.6 + - - +
50B GLU* 3.0 29.8 + - - +
63B GLN* 6.1 1.8 - - + -
64B TRP* 3.8 31.6 - - + +
65B ALA 5.4 1.1 - - - +
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Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LYS* 3.0 43.8 + - - +
44B MSE 3.3 10.8 + - - +
46B ALA* 1.3 76.1 - - + +
48B ASN* 1.3 56.9 + - - +
50B GLU* 3.7 7.2 - - - +
51B MSE 2.9 38.9 + - + +
121B GLN* 3.2 12.5 - - - +
122B TRP* 2.9 50.2 + - - +
123B LEU* 3.3 23.6 + - + +
124B ILE* 4.5 2.4 + - - +
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Residues in contact with ASN 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B MSE 3.1 13.1 + - - +
45B ASP* 3.5 14.5 + - - +
46B ALA 3.1 0.2 - - - -
47B GLU* 1.3 75.0 - - - +
49B VAL* 1.3 60.8 + - - +
51B MSE 4.4 1.6 - - - +
52B PHE* 2.9 61.7 + - - +
54B GLU* 3.2 35.7 + - - +
55B GLU 5.0 2.8 + - - -
123B LEU* 3.4 11.2 - - + +
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Residues in contact with VAL 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASP* 3.2 16.1 + - - +
46B ALA* 3.7 8.5 - - - +
48B ASN* 1.3 78.3 - - - +
50B GLU* 1.3 58.1 + - - +
53B GLY* 3.0 30.6 + - - -
54B GLU 3.6 26.0 - - - +
55B GLU* 3.8 12.1 - - - +
56B SER* 3.8 19.7 - - - -
63B GLN* 5.9 0.7 - - - +
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Residues in contact with GLU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ALA 3.0 16.4 + - - +
47B GLU* 3.7 8.0 - - - +
48B ASN 3.3 0.2 - - - -
49B VAL* 1.3 82.9 - - - +
51B MSE 1.3 63.2 + - + +
53B GLY 4.7 0.2 - - - -
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Residues in contact with MSE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP* 6.2 2.9 - - + -
20A THR* 5.2 9.6 - - + -
47B GLU* 2.9 25.9 + - + +
48B ASN 4.3 0.4 - - - +
49B VAL 3.3 0.2 - - - -
50B GLU* 1.3 85.4 - - + +
52B PHE* 1.3 100.6 + - + +
53B GLY 3.5 1.2 + - - -
123B LEU* 4.1 21.5 - - - +
124B ILE* 4.0 29.6 - - + -
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Residues in contact with PHE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LYS* 4.3 30.7 - - + -
16A TRP* 5.2 12.1 - - + -
17A ASN* 6.1 4.0 - - + -
48B ASN* 2.9 34.9 + - - +
51B MSE 1.3 119.0 - - + +
53B GLY* 1.3 56.9 + - - +
54B GLU* 2.8 34.1 + - - +
123B LEU* 4.6 10.8 - - + -
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Residues in contact with GLY 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 3.0 17.3 + - - -
50B GLU 4.7 0.4 + - - -
51B MSE 3.5 2.6 + - - -
52B PHE* 1.3 74.6 - - - +
54B GLU* 1.3 64.0 + - - +
55B GLU 3.9 0.3 + - - -
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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