Contacts of the helix formed by residues 47 - 76 (chain F) in PDB entry 1O9R
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 GLN 47 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PRO 5.2 0.2 + - - -
47A GLN* 3.4 37.5 - - - +
50A ALA* 4.6 8.6 - - - +
157A HIS* 4.6 1.3 - - - -
46D PRO* 3.3 29.8 + - + +
47D GLN* 3.7 31.2 + - + +
49D ILE* 6.0 0.2 - - - +
50D ALA* 4.3 10.7 - - - +
45F GLY 3.1 1.0 + - - -
46F PRO* 1.3 79.9 - - + +
48F PHE* 1.3 66.8 + - - +
49F ILE 3.3 2.1 + - - -
50F ALA* 3.3 22.9 + - + +
51F VAL* 3.1 30.1 + - + +
103F ILE* 3.5 11.9 - - + +
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Residues in contact with PHE 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A TRP* 4.0 15.0 - + - -
153A PHE* 3.5 44.2 - + - -
156A ALA* 3.6 22.0 - - + +
157A HIS* 3.7 21.4 - + + +
40F HIS 4.6 0.4 - - - -
41F TRP 5.2 0.2 - - - -
43F LEU* 3.2 46.5 - - + +
44F LYS* 4.5 0.2 - - - -
45F GLY 3.0 17.9 + - - +
46F PRO 3.3 2.4 + - - -
47F GLN* 1.3 77.7 - - - +
49F ILE* 1.3 81.2 + - + +
51F VAL* 4.0 0.3 - - - +
52F HIS* 2.8 52.9 + + - +
103F ILE* 3.5 8.9 - - - +
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Residues in contact with ILE 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ALA* 3.7 35.4 - - + +
51A VAL 4.7 0.2 - - - +
54A LEU* 4.1 18.6 - - + -
153A PHE* 3.7 37.7 - - + -
157A HIS* 3.4 24.4 + - + +
47F GLN 3.3 0.6 + - - -
48F PHE* 1.3 86.3 - - + +
50F ALA* 1.3 66.9 + - - +
52F HIS* 4.2 5.8 - - + -
53F GLU* 2.9 54.3 + - + +
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Residues in contact with ALA 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ALA* 4.2 12.8 - - + -
49D ILE* 3.8 23.9 - - + +
50D ALA* 4.4 6.1 - - + -
47F GLN* 3.3 26.8 + - - +
48F PHE 3.3 0.4 - - - -
49F ILE* 1.3 82.5 - - - +
51F VAL* 1.4 60.7 + - + +
53F GLU* 4.1 4.8 - - - +
54F LEU* 3.0 28.6 + - - +
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Residues in contact with VAL 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D ILE* 5.2 0.2 - - - -
43F LEU* 3.5 25.6 - - + -
47F GLN* 3.1 27.2 + - + +
50F ALA* 1.4 74.4 - - + +
52F HIS* 1.3 66.9 + - - +
54F LEU* 3.3 9.1 + - + +
55F LEU* 3.0 37.0 + - + +
103F ILE* 4.3 13.7 - - + -
107F LEU* 4.4 20.6 - - + -
110F LEU* 5.9 0.2 - - + -
154F LEU* 5.9 0.7 - - + -
157F HIS* 4.1 27.6 - - + +
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Residues in contact with HIS 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A TRP* 3.8 24.2 - + - -
153A PHE* 3.8 27.0 - + - -
1163E FE 4.1 6.3 - - - -
40F HIS* 2.7 84.0 + + - -
41F TRP* 4.8 0.7 - + - -
43F LEU* 4.1 9.2 - - + +
48F PHE* 2.8 38.0 + + + +
49F ILE* 3.6 12.1 - - + +
51F VAL* 1.3 79.1 - - - +
53F GLU* 1.4 67.3 + - + +
55F LEU* 3.4 8.5 + - - +
56F ASP 3.5 1.4 + - - -
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Residues in contact with GLU 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 5.3 3.1 - - - +
153A PHE* 5.4 1.7 - - - -
49F ILE* 2.9 48.8 + - + +
50F ALA* 4.1 4.5 - - - +
52F HIS* 1.4 80.9 - - + +
54F LEU* 1.3 67.3 + - - +
56F ASP* 3.0 18.9 + - - +
57F THR* 3.4 11.6 + - - -
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Residues in contact with LEU 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D ILE* 4.1 22.9 - - + -
53D GLU* 5.4 2.5 - - - +
50F ALA 3.0 18.6 + - - +
51F VAL* 3.3 10.5 + - + +
53F GLU* 1.3 76.7 - - - +
55F LEU* 1.3 65.1 + - + +
57F THR* 3.0 24.0 + - + +
58F PHE* 3.1 48.1 + - + -
153F PHE* 3.9 22.7 - - + +
154F LEU* 5.3 4.3 - - + -
157F HIS* 4.0 26.7 - - + -
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Residues in contact with LEU 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F THR* 3.2 24.8 - - + +
39F ALA* 4.0 14.1 - - + +
40F HIS* 3.7 35.2 - - + +
43F LEU* 4.6 4.5 - - + -
51F VAL* 3.0 31.7 + - + +
52F HIS 3.8 5.2 - - - +
53F GLU 3.2 0.2 - - - -
54F LEU* 1.3 79.7 - - + +
56F ASP* 1.3 57.7 + - - +
58F PHE* 3.3 26.3 + - + -
59F ARG* 2.9 24.1 + - - +
106F HIS* 6.1 0.4 - - + -
110F LEU* 3.9 24.0 - - + -
114F TYR* 5.2 0.4 - - + +
154F LEU* 4.4 6.1 - - + -
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Residues in contact with ASP 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1163E FE 4.0 4.7 - - - -
37F LYS* 2.7 33.7 + - - +
40F HIS* 3.1 31.3 + - - -
52F HIS* 3.5 2.2 + - - +
53F GLU* 3.0 14.4 + - - +
55F LEU* 1.3 75.6 - - - +
57F THR* 1.3 67.3 + - - +
59F ARG* 3.2 5.2 + - - +
60F THR* 3.1 26.0 + - - -
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Residues in contact with THR 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F GLU 3.4 8.4 + - - -
54F LEU* 3.0 17.6 + - + +
56F ASP* 1.3 79.3 - - - +
58F PHE* 1.3 67.4 + - + +
60F THR* 3.3 8.5 + - - -
61F GLN* 3.1 42.3 + - + +
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Residues in contact with PHE 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F THR* 4.2 0.2 - - + -
54F LEU* 3.1 46.7 + - + -
55F LEU* 3.6 22.9 - - + +
56F ASP 3.2 0.2 - - - -
57F THR* 1.3 80.7 - - + +
59F ARG* 1.4 56.5 + - - +
61F GLN* 3.2 12.6 + - - +
62F LEU* 2.9 32.9 + - - +
114F TYR* 3.3 30.5 - + + +
150F SER* 3.5 42.4 - - - +
153F PHE* 3.9 12.8 - + + -
154F LEU* 3.8 29.4 - - + -
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Residues in contact with ARG 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E ALA* 6.2 0.2 - - - +
59E ARG* 3.4 25.1 - - - +
63E ASP* 4.1 13.3 + - - -
33F ALA* 2.9 53.7 + - - +
34F LEU* 4.0 15.3 - - - +
36F THR* 4.0 10.7 - - + +
37F LYS* 3.4 41.4 - - + +
55F LEU 2.9 17.0 + - - +
56F ASP* 3.2 8.7 + - - +
58F PHE* 1.4 76.6 - - - +
60F THR* 1.3 57.7 + - - +
62F LEU* 3.2 4.5 + - - -
63F ASP* 2.9 54.2 + - - +
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Residues in contact with THR 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F ASP 3.1 13.9 + - - -
57F THR* 3.6 12.2 - - - -
59F ARG* 1.3 76.2 - - - +
61F GLN* 1.3 65.7 + - + +
63F ASP* 3.2 12.3 + - + +
64F ASN* 3.0 39.3 + - - +
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Residues in contact with GLN 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F THR* 3.1 34.3 + - + +
58F PHE* 3.6 10.5 - - - +
60F THR* 1.3 79.9 - - + +
62F LEU* 1.4 59.0 + - + +
64F ASN* 3.2 8.9 + - - +
65F HIS* 2.9 45.2 + - + -
146F ASP* 3.8 28.4 + - + +
150F SER* 3.5 20.8 + - - -
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Residues in contact with LEU 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F VAL* 3.6 25.0 - - + +
32F LEU* 3.9 24.5 - - + -
33F ALA* 3.8 32.3 - - + +
36F THR* 3.6 13.2 - - - +
58F PHE 2.9 16.4 + - - +
59F ARG* 3.7 5.8 - - - +
61F GLN* 1.4 77.4 - - + +
63F ASP* 1.3 58.4 + - - +
65F HIS* 4.8 6.5 - - + -
66F GLY* 2.8 28.1 + - - -
114F TYR* 3.5 25.8 - - + +
147F LEU* 3.9 20.2 - - + -
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Residues in contact with ASP 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E ARG* 4.0 13.1 + - - +
63E ASP* 4.4 11.7 - - - +
33F ALA* 4.4 4.0 - - - +
59F ARG* 2.9 50.9 + - - +
60F THR* 3.4 14.1 + - - +
61F GLN 3.2 0.2 - - - -
62F LEU* 1.3 77.2 - - - +
64F ASN* 1.3 62.4 - - - +
66F GLY* 3.9 0.4 - - - -
67F ASP* 3.0 38.1 + - - +
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Residues in contact with ASN 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F THR* 3.0 33.9 + - - +
61F GLN* 3.6 9.3 - - - +
63F ASP* 1.3 80.6 - - - +
65F HIS* 1.4 62.6 + - + +
67F ASP* 3.4 10.1 + - - +
68F THR* 2.9 32.4 + - - -
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Residues in contact with HIS 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F VAL* 5.3 4.7 - - + -
61F GLN* 2.9 30.1 + - + +
62F LEU* 4.2 7.6 - - + +
64F ASN* 1.4 77.1 - - + +
66F GLY* 1.3 66.8 + - - +
68F THR* 3.2 9.0 + - - +
69F ILE* 2.9 33.6 + - + +
139F ILE* 4.7 3.0 + - - +
142F ALA* 3.5 15.1 - - + +
143F ALA* 3.4 47.2 + - + +
146F ASP* 2.8 36.2 + - + +
147F LEU* 6.0 2.9 - - + -
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Residues in contact with GLY 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E TRP* 4.7 2.0 - - - -
26F LEU* 3.4 22.8 - - - +
29F VAL* 3.9 16.4 - - - +
30F ILE* 5.8 1.8 - - - -
62F LEU 2.8 22.4 + - - -
63F ASP* 3.9 0.9 - - - -
65F HIS* 1.3 72.0 - - - +
67F ASP* 1.3 55.2 + - - +
69F ILE* 3.3 3.2 + - - -
70F ALA* 2.9 27.5 + - - +
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Residues in contact with ASP 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E LYS* 2.9 36.5 + - - +
41E TRP* 3.4 24.5 + - - +
63F ASP* 3.0 24.9 + - - +
64F ASN* 3.5 11.2 - - - +
66F GLY* 1.3 75.8 - - - +
68F THR* 1.4 58.9 + - - +
70F ALA* 3.3 1.0 + - - +
71F GLU* 2.9 37.3 + - - +
1163F FE 4.5 9.9 - - - -
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Residues in contact with THR 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F ASN* 2.9 18.6 + - - +
65F HIS* 3.2 10.7 + - - +
67F ASP* 1.4 77.0 - - - +
69F ILE* 1.3 62.8 - - - +
71F GLU* 3.5 12.1 + - - +
72F ARG* 3.1 22.3 + - - +
75F GLN* 5.2 0.9 + - - -
139F ILE* 3.6 35.7 - - + +
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Residues in contact with ILE 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F LEU* 3.3 44.0 - - + +
25F SER* 4.6 2.7 - - - -
26F LEU* 3.9 15.5 - - + +
29F VAL* 4.5 20.9 - - + -
65F HIS* 2.9 29.2 + - + +
66F GLY* 3.7 4.5 - - - +
68F THR* 1.3 76.0 - - - +
70F ALA* 1.4 63.3 + - - +
72F ARG* 3.2 4.9 + - - +
73F VAL* 3.1 21.2 + - + +
121F ILE* 4.5 5.8 - - + -
139F ILE* 4.1 17.3 - - + -
140F PHE* 4.0 24.5 - - + -
143F ALA* 5.0 5.6 - - + -
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Residues in contact with ALA 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E TRP* 3.2 46.7 - - + +
26F LEU* 3.9 17.0 - - + -
66F GLY 2.9 15.7 + - - +
69F ILE* 1.4 80.0 - - - +
71F GLU* 1.4 61.9 + - - +
73F VAL* 3.1 20.5 + - - +
74F VAL* 3.3 12.0 + - - +
80F ALA* 3.7 6.5 - - + +
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Residues in contact with GLU 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E TRP* 4.1 13.2 - - + -
52E HIS* 4.8 8.4 + - + -
67F ASP* 2.9 24.2 + - - +
68F THR* 3.9 12.0 + - - +
70F ALA* 1.4 77.3 - - - +
72F ARG* 1.3 57.2 + - - +
74F VAL* 2.9 29.7 - - + +
75F GLN* 2.9 30.6 + - - +
1163F FE 2.2 34.4 - - - -
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Residues in contact with ARG 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F ASN* 4.3 10.9 + - - +
10F LEU* 5.1 1.6 - - - +
22F LEU* 3.7 17.9 - - + -
68F THR 3.1 14.5 + - - +
69F ILE 3.2 9.4 + - - +
71F GLU* 1.3 75.4 - - - +
73F VAL* 1.4 66.5 + - - +
75F GLN* 3.1 33.9 + - - +
76F LEU* 3.1 40.8 + - + +
133F ASP* 3.0 28.5 + - - -
135F THR* 3.5 28.1 - - - +
136F THR* 2.8 25.0 + - - +
139F ILE* 3.8 22.2 - - + -
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Residues in contact with VAL 73 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ILE* 4.0 12.9 - - + +
22F LEU* 3.5 36.0 - - + +
23F ASN* 3.7 25.4 - - - +
26F LEU* 5.5 0.2 - - + -
69F ILE* 3.1 10.1 + - + +
70F ALA* 3.1 12.8 + - - +
72F ARG* 1.4 76.7 - - - +
74F VAL* 1.4 60.6 + - - +
76F LEU* 3.2 10.2 + - - +
77F GLY 3.5 0.2 + - - -
78F GLY* 2.9 25.3 + - - -
79F THR 3.5 39.3 - - - +
80F ALA* 4.3 1.8 - - - -
----------------------------------------------------------
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Residues in contact with VAL 74 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E TRP* 3.5 29.6 - - + +
42E ASN* 3.7 19.7 - - - +
44E LYS* 4.7 12.9 + - - +
4F HIS* 5.2 1.4 - - - +
70F ALA 3.6 9.6 - - - +
71F GLU* 2.9 32.3 - - + +
72F ARG 3.1 0.4 - - - -
73F VAL* 1.4 72.8 - - - +
75F GLN* 1.3 66.4 + - + +
77F GLY* 2.9 14.9 + - - -
78F GLY 3.6 14.3 - - - +
80F ALA* 3.9 10.1 - - + +
----------------------------------------------------------
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Residues in contact with GLN 75 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F THR* 4.2 17.5 + - - +
8F ASN* 4.2 11.5 - - - +
68F THR 5.2 0.4 + - - -
71F GLU* 2.9 44.5 + - - +
72F ARG* 3.1 44.0 + - - +
74F VAL* 1.3 77.4 - - + +
76F LEU* 1.3 59.3 + - - +
77F GLY 3.1 2.8 + - - -
139F ILE* 5.4 0.7 - - - +
----------------------------------------------------------
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Residues in contact with LEU 76 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F THR* 4.8 1.1 - - - +
8F ASN* 4.2 14.4 - - - +
10F LEU* 4.0 18.6 - - + -
15F LYS* 3.4 35.5 - - + +
18F VAL* 4.0 22.7 - - + -
19F ILE* 3.6 21.4 - - + +
22F LEU* 4.1 7.9 - - + -
72F ARG* 3.1 40.5 + - - +
73F VAL 3.7 7.2 - - - +
74F VAL 3.1 0.8 - - - -
75F GLN* 1.3 76.8 - - - +
77F GLY* 1.3 59.3 + - - +
78F GLY 3.4 1.3 - - - -
133F ASP* 3.7 18.2 - - - +
136F THR* 4.1 5.4 - - - +
----------------------------------------------------------
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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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