Contacts of the helix formed by residues 47 - 76 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E GLY 3.1 0.6 + - - -
46E PRO* 1.3 99.2 - - - +
48E PHE* 1.3 66.1 + - - +
49E ILE* 3.2 3.7 + - - -
50E ALA* 3.3 9.2 + - + +
51E VAL* 3.2 29.3 + - + +
103E ILE* 3.5 26.1 - - + +
157E HIS* 5.7 6.7 - - + -
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Residues in contact with PHE 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E HIS 4.6 4.0 - - - -
41E TRP 5.2 4.9 - - - -
43E LEU* 3.2 35.7 - - + +
44E LYS* 4.5 2.0 - - + -
45E GLY 3.0 21.3 + - - +
46E PRO 3.3 2.4 + - - -
47E GLN* 1.3 76.2 - - - +
49E ILE* 1.3 78.8 + - + +
51E VAL* 4.2 0.3 - - - +
52E HIS* 2.8 72.9 + + + +
103E ILE* 3.5 8.0 - - - +
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Residues in contact with ILE 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E GLN 3.4 1.0 - - - -
48E PHE* 1.3 100.0 - - + +
50E ALA* 1.3 68.8 + - + +
52E HIS* 3.7 9.4 - - + +
53E GLU* 3.0 54.1 + - + +
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Residues in contact with ALA 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E GLN* 3.3 10.8 + - + +
48E PHE 3.3 0.8 - - - -
49E ILE* 1.3 87.1 - - + +
51E VAL* 1.3 60.6 + - + +
53E GLU* 3.9 4.8 - - - +
54E LEU* 3.0 29.5 + - - +
157E HIS* 6.0 2.9 - - - +
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Residues in contact with VAL 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E LEU* 3.3 28.3 - - + -
47E GLN* 3.2 26.0 + - + +
50E ALA* 1.3 75.7 - - + +
52E HIS* 1.3 67.1 + - - +
54E LEU* 3.2 10.1 + - + +
55E LEU* 3.0 36.5 + - + +
103E ILE* 4.3 13.2 - - + -
107E LEU* 4.4 19.3 - - + -
110E LEU* 5.8 0.4 - - + -
154E LEU* 5.8 0.9 - - + -
157E HIS* 4.2 26.9 - - + +
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Residues in contact with HIS 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E HIS* 2.8 85.3 + + - +
41E TRP* 4.8 5.2 - + - -
43E LEU* 3.9 6.4 - - + +
48E PHE* 2.8 49.3 + + + +
49E ILE* 3.7 17.3 - - + +
51E VAL* 1.3 77.5 - - - +
53E GLU* 1.4 68.2 + - + +
55E LEU* 3.4 8.6 + - - +
56E ASP* 3.5 2.0 + - - -
71F GLU* 4.8 7.8 + - + -
1163F FE 4.1 7.5 - - - -
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Residues in contact with GLU 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E ILE* 3.0 48.0 + - + +
50E ALA* 4.2 4.0 - - - +
52E HIS* 1.4 80.2 - - + +
54E LEU* 1.3 66.5 + - - +
56E ASP* 3.1 20.1 + - - +
57E THR* 3.4 11.5 + - - -
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Residues in contact with LEU 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E ALA 3.0 19.6 + - - +
51E VAL* 3.2 10.3 + - + +
53E GLU* 1.3 76.3 - - - +
55E LEU* 1.3 66.4 + - + +
57E THR* 2.9 25.0 + - + +
58E PHE* 3.1 49.2 + - + -
153E PHE* 3.9 25.8 - - + +
154E LEU* 5.3 4.5 - - + -
157E HIS* 4.2 25.4 - - + -
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Residues in contact with LEU 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E THR* 3.2 27.5 - - + +
39E ALA* 4.0 7.6 - - + -
40E HIS* 3.7 36.1 - - + +
43E LEU* 4.0 19.3 - - + -
51E VAL* 3.0 27.6 + - + +
52E HIS 3.8 4.9 - - - +
53E GLU 3.2 0.4 - - - -
54E LEU* 1.3 79.8 - - + +
56E ASP* 1.3 57.9 + - - +
58E PHE* 3.3 25.9 + - + -
59E ARG* 3.0 23.2 + - - +
110E LEU* 3.9 23.3 - - + -
114E TYR* 5.0 0.7 - - + +
154E LEU* 4.5 6.1 - - + -
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Residues in contact with ASP 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E LYS* 2.6 35.0 + - - -
40E HIS* 3.1 30.3 + - - -
52E HIS* 3.5 2.0 + - - -
53E GLU* 3.1 13.8 + - - +
55E LEU* 1.3 76.6 - - - +
57E THR* 1.3 64.9 + - - +
59E ARG* 3.3 5.5 + - - +
60E THR* 3.0 26.3 + - - -
1163F FE 4.1 4.9 - - - -
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Residues in contact with THR 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E GLU 3.4 7.9 + - - -
54E LEU* 2.9 17.1 + - + +
56E ASP* 1.3 77.0 - - - +
58E PHE* 1.4 68.3 + - + +
60E THR* 3.3 8.5 + - - -
61E GLN* 3.1 41.3 + - + +
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Residues in contact with PHE 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E THR* 4.1 0.7 - - + -
54E LEU* 3.1 47.5 + - + -
55E LEU* 3.5 22.0 - - + +
57E THR* 1.4 83.3 - - + +
59E ARG* 1.4 57.5 + - - +
61E GLN* 3.2 11.9 + - - +
62E LEU* 2.9 34.0 + - + +
114E TYR* 3.2 32.3 - + + +
150E SER* 3.5 43.5 - - - +
153E PHE* 4.0 11.9 - + + -
154E LEU* 3.8 29.4 - - + -
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Residues in contact with ARG 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E ALA* 3.0 46.6 + - - +
34E LEU* 4.1 15.4 - - - +
36E THR* 4.0 11.2 - - + +
37E LYS* 3.3 41.7 - - + +
55E LEU 3.0 17.1 + - - +
56E ASP* 3.7 7.9 - - - +
57E THR 3.3 0.2 - - - -
58E PHE* 1.4 75.5 - - - +
60E THR* 1.3 64.0 + - - +
62E LEU* 3.2 4.2 + - - +
63E ASP* 2.8 50.3 + - - +
33F ALA* 6.2 0.4 - - - +
59F ARG* 3.4 24.7 - - - +
63F ASP* 4.0 13.9 + - - -
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Residues in contact with THR 60 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E ASP 3.0 14.4 + - - -
57E THR* 3.5 11.3 - - - -
59E ARG* 1.3 76.0 - - - +
61E GLN* 1.3 65.9 + - + +
63E ASP* 3.3 12.5 + - + +
64E ASN* 3.0 37.5 + - - +
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Residues in contact with GLN 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E THR* 3.1 34.5 + - + +
58E PHE* 3.2 11.0 + - - +
60E THR* 1.3 80.2 - - + +
62E LEU* 1.4 59.0 + - + +
64E ASN* 3.2 8.5 + - - +
65E HIS* 3.0 46.4 + - + -
146E ASP* 3.8 28.1 + - + +
150E SER* 3.5 20.6 + - - -
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Residues in contact with LEU 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E VAL* 3.6 25.0 - - + +
32E LEU* 3.9 22.7 - - + -
33E ALA* 3.8 31.9 - - + +
36E THR* 3.7 13.7 - - - +
58E PHE 2.9 18.0 + - - +
59E ARG* 3.2 4.7 + - - +
61E GLN* 1.4 77.2 - - + +
63E ASP* 1.3 56.7 + - - +
65E HIS* 4.6 7.2 - - + +
66E GLY* 2.8 28.4 + - - -
114E TYR* 3.5 26.2 - - + +
147E LEU* 4.1 19.7 - - + -
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Residues in contact with ASP 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E ALA* 4.4 3.7 - - - +
59E ARG* 2.8 49.7 + - - +
60E THR* 3.4 14.0 - - + +
62E LEU* 1.3 75.5 - - - +
64E ASN* 1.3 62.3 + - - +
66E GLY* 3.9 0.6 - - - -
67E ASP* 3.0 39.4 + - - +
59F ARG* 4.1 12.4 + - - -
63F ASP* 4.4 11.5 - - - +
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Residues in contact with ASN 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E THR* 3.0 33.4 + - - +
61E GLN* 3.2 11.0 + - - +
63E ASP* 1.3 80.8 - - - +
65E HIS* 1.3 62.7 + - + +
67E ASP* 3.3 11.1 + - - +
68E THR* 2.9 31.3 + - - -
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Residues in contact with HIS 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E VAL* 5.2 4.3 - - + -
61E GLN* 3.0 31.1 + - + +
62E LEU* 4.3 7.9 - - + +
64E ASN* 1.3 76.9 - - + +
66E GLY* 1.3 66.8 + - - +
68E THR* 3.3 9.2 + - - +
69E ILE* 2.9 34.7 + - + +
139E ILE* 4.7 3.6 + - + +
142E ALA* 3.5 17.6 - - + +
143E ALA* 3.5 43.6 + - + +
146E ASP* 2.7 37.3 + - + +
147E LEU* 6.1 2.7 - - + -
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Residues in contact with GLY 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E LEU* 3.4 19.3 - - - +
29E VAL* 3.8 16.2 - - - +
30E ILE* 5.7 1.8 - - - -
62E LEU 2.8 22.6 + - - -
63E ASP 3.9 0.7 - - - -
65E HIS* 1.3 72.8 - - - +
67E ASP* 1.3 62.7 + - - +
69E ILE* 4.5 2.7 - - - -
70E ALA* 2.9 25.7 + - - +
41F TRP* 4.7 3.1 - - - -
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Residues in contact with ASP 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E ASP* 3.0 27.5 + - - +
64E ASN* 3.5 11.2 - - - +
66E GLY* 1.3 78.0 - - - +
68E THR* 1.3 56.7 + - - +
70E ALA* 3.3 1.2 + - - +
71E GLU* 2.9 38.3 + - - +
1163E FE 4.4 10.1 - - - -
37F LYS* 3.0 46.5 + - - +
41F TRP* 3.4 15.3 + - - +
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Residues in contact with THR 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ARG* 3.6 28.0 + - - +
64E ASN 2.9 17.6 + - - -
65E HIS* 3.3 10.5 + - - +
67E ASP* 1.3 76.1 - - - +
69E ILE* 1.3 57.4 + - - +
71E GLU* 3.5 13.4 + - - +
72E ARG* 3.0 27.7 + - - +
75E GLN* 5.2 0.5 + - - -
139E ILE* 3.7 26.3 - - + +
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Residues in contact with ILE 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E LEU* 3.3 44.5 - - + +
25E SER* 4.5 2.7 - - - -
26E LEU* 4.0 14.1 - - + +
29E VAL* 4.4 14.6 - - + -
65E HIS* 2.9 30.0 + - + +
66E GLY* 3.7 4.5 - - - +
68E THR* 1.3 75.5 - - - +
70E ALA* 1.3 64.1 + - - +
72E ARG* 3.2 12.6 + - - +
73E VAL* 3.2 13.4 + - + +
121E ILE* 4.3 13.7 - - + -
139E ILE* 4.1 17.7 - - + -
140E PHE* 4.1 22.9 - - + -
143E ALA* 5.0 4.7 - - + -
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Residues in contact with ALA 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E LEU* 3.8 19.5 - - + -
66E GLY 2.9 16.0 + - - +
69E ILE* 1.3 77.2 - - - +
71E GLU* 1.4 63.6 + - - +
73E VAL* 3.1 16.4 + - - +
74E VAL* 3.3 10.4 + - - +
80E ALA* 3.7 13.2 - - + +
41F TRP* 3.3 44.2 - - + +
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Residues in contact with GLU 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LYS* 2.9 41.1 + - - +
152A TRP* 3.7 25.2 - - + -
67E ASP* 2.9 27.8 + - - +
68E THR* 3.8 11.7 + - - +
70E ALA* 1.4 76.3 - - - +
72E ARG* 1.4 57.4 + - - +
74E VAL* 3.2 6.6 + - - +
75E GLN* 2.9 41.6 + - - +
1163E FE 2.2 34.2 - - - -
41F TRP* 4.1 10.8 - - + -
52F HIS* 4.9 1.0 + - + -
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Residues in contact with ARG 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ARG* 4.3 4.9 - - - +
145A ARG* 5.7 0.4 - - - +
148A ASP* 2.8 34.2 + - - +
10E LEU* 5.0 1.2 - - - +
22E LEU* 3.7 17.9 - - + -
68E THR 3.0 14.8 + - - +
69E ILE 3.2 9.2 + - - +
71E GLU* 1.4 75.6 - - - +
73E VAL* 1.3 67.1 + - - +
75E GLN* 3.1 29.8 + - - +
76E LEU* 3.1 44.4 + - + +
133E ASP* 3.0 28.7 + - - -
135E THR* 3.5 19.3 - - - +
136E THR* 2.8 24.3 + - - +
139E ILE* 3.7 22.8 - - + +
----------------------------------------------------------
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Residues in contact with VAL 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E ILE* 4.0 12.6 - - + +
22E LEU* 3.4 35.4 - - + +
23E ASN* 3.7 25.4 - - - +
69E ILE* 3.2 10.7 + - + +
70E ALA* 3.1 12.2 + - - +
72E ARG* 1.3 76.7 - - - +
74E VAL* 1.3 61.4 + - - +
76E LEU* 3.2 10.6 + - - +
78E GLY* 2.9 24.6 + - - -
79E THR 3.5 40.4 - - - +
80E ALA* 4.3 1.6 - - - -
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Residues in contact with VAL 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A TRP* 3.2 34.1 - - + +
4E HIS* 5.2 1.7 - - - +
70E ALA 3.3 11.0 + - - +
71E GLU* 3.2 7.9 + - - +
72E ARG 3.2 0.4 - - - -
73E VAL* 1.3 72.4 - - - +
75E GLN* 1.3 66.5 + - - +
77E GLY* 2.9 14.9 + - - -
78E GLY 3.6 11.0 - - - +
80E ALA* 4.0 10.1 - - + +
41F TRP* 3.5 21.8 - - + +
42F ASN* 3.6 19.1 - - - +
44F LYS* 3.5 23.3 - - - +
----------------------------------------------------------
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Residues in contact with GLN 75 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ARG* 4.6 3.0 + - - +
148A ASP* 3.7 14.7 - - + +
149A LYS* 3.8 26.0 + - - +
152A TRP* 3.7 34.6 - - + +
6E THR* 4.4 16.5 + - - +
8E ASN* 4.3 10.3 - - - +
68E THR 5.2 0.8 + - - -
71E GLU* 2.9 40.3 + - - +
72E ARG* 3.1 43.7 + - - +
74E VAL* 1.3 76.2 - - - +
76E LEU* 1.3 62.6 + - + +
77E GLY 3.4 0.9 + - - -
139E ILE* 5.4 0.7 - - - +
----------------------------------------------------------
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Residues in contact with LEU 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E THR* 5.7 1.2 - - - +
6E THR* 5.0 1.7 - - - +
8E ASN* 4.2 13.9 - - - +
10E LEU* 3.9 19.5 - - + -
15E LYS* 3.3 35.8 - - + +
18E VAL* 3.9 23.3 - - + -
19E ILE* 3.6 20.3 - - + +
22E LEU* 4.2 7.4 - - + -
72E ARG* 3.1 45.3 + - - +
73E VAL 3.2 4.7 + - - +
74E VAL 3.1 0.8 - - - -
75E GLN* 1.3 78.5 - - - +
77E GLY* 1.3 57.7 + - - +
78E GLY 3.5 1.3 - - - -
133E ASP* 3.6 18.6 - - - +
136E THR* 4.1 4.5 - - - +
----------------------------------------------------------
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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