Contacts of the helix formed by residues 47 - 76 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PRO* 3.2 45.7 - - - +
47A GLN* 6.1 0.2 - - - +
45D GLY 3.1 0.4 + - - -
46D PRO* 1.4 100.9 - - - +
48D PHE* 1.3 66.7 - - - +
49D ILE* 3.2 2.5 + - - -
50D ALA* 3.3 5.9 + - + +
51D VAL* 3.1 30.1 + - + +
103D ILE* 3.6 27.8 - - + +
47F GLN* 3.7 25.5 + - - +
157F HIS* 4.7 0.2 - - - -
161F LYS 5.7 0.6 + - - -
162F SER* 4.6 5.9 - - - +
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Residues in contact with PHE 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D TRP 5.1 0.4 - - - -
43D LEU* 3.2 47.2 - - + +
45D GLY 3.0 17.8 + - - +
46D PRO 3.3 2.8 + - - -
47D GLN* 1.3 76.4 - - - +
49D ILE* 1.3 67.3 + - + +
51D VAL* 4.2 0.5 - - - +
52D HIS* 2.8 58.2 + + + +
103D ILE* 3.4 8.2 - - - +
152F TRP* 3.9 15.9 - + - -
153F PHE* 3.5 44.0 - + - -
156F ALA* 3.7 17.7 - - + +
157F HIS* 3.8 22.6 - + + +
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Residues in contact with ILE 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D GLN 3.4 0.6 - - - -
48D PHE* 1.3 86.5 - - + +
50D ALA* 1.3 61.0 + - - +
52D HIS* 4.1 3.1 - - - +
53D GLU* 2.9 57.9 + - + +
50F ALA* 3.8 35.4 - - + +
51F VAL 4.8 0.2 - - - +
54F LEU* 4.1 17.9 - - + -
153F PHE* 3.6 40.6 - - + -
157F HIS* 3.3 25.1 + - + +
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Residues in contact with ALA 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 3.5 26.7 - - + +
50A ALA* 4.3 12.8 - - + -
47D GLN* 3.3 7.0 + - + +
48D PHE 3.2 0.6 - - - -
49D ILE* 1.3 83.4 - - - +
51D VAL* 1.3 58.9 + - + +
53D GLU* 3.5 5.6 + - - +
54D LEU* 3.0 28.8 + - - +
47F GLN* 4.3 17.9 - - - +
50F ALA* 4.4 5.2 - - + -
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Residues in contact with VAL 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 5.0 0.9 - - - -
43D LEU* 3.5 24.7 - - + -
47D GLN* 3.1 28.8 + - + +
50D ALA* 1.3 73.3 - - + +
52D HIS* 1.3 66.2 + - - +
54D LEU* 3.3 10.0 + - + +
55D LEU* 3.0 39.3 + - + +
103D ILE* 4.3 11.4 - - + -
106D HIS* 6.5 0.9 - - + -
107D LEU* 4.5 18.2 - - + -
110D LEU* 5.7 1.1 - - + -
154D LEU* 5.9 0.7 - - + -
157D HIS* 4.1 26.5 - - + +
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Residues in contact with HIS 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D HIS* 2.8 85.8 + + - -
43D LEU* 4.1 8.1 - - + +
48D PHE* 2.8 41.6 + + + +
49D ILE* 3.6 10.0 - - - +
51D VAL* 1.3 79.5 - - - +
53D GLU* 1.3 67.1 + - - +
55D LEU* 3.5 6.3 + - - +
56D ASP* 3.6 1.7 + - - -
149F LYS* 5.5 2.2 - - - -
152F TRP* 3.9 16.3 - + - -
153F PHE* 3.7 32.2 - + - -
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Residues in contact with GLU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D ILE* 2.9 48.2 + - + +
50D ALA* 4.1 4.9 - - - +
52D HIS* 1.3 78.2 - - - +
54D LEU* 1.3 66.6 + - - +
56D ASP* 3.1 19.9 + - - +
57D THR* 3.4 12.4 + - - -
54F LEU* 5.4 2.3 - - - +
153F PHE* 5.5 1.6 - - - -
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Residues in contact with LEU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 4.1 31.9 - - + -
53A GLU* 5.1 3.4 - - - +
50D ALA 3.0 18.8 + - - +
51D VAL* 3.7 9.2 - - + +
53D GLU* 1.3 76.0 - - - +
55D LEU* 1.3 64.7 + - + +
57D THR* 3.0 24.7 + - + +
58D PHE* 3.1 48.4 + - + -
153D PHE* 3.8 24.0 - - + -
154D LEU* 5.3 4.0 - - + -
157D HIS* 4.3 16.2 - - + -
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Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D THR* 3.2 27.1 - - + +
39D ALA* 4.0 12.3 - - + +
40D HIS* 3.6 36.3 - - + +
43D LEU* 4.8 2.7 - - + -
51D VAL* 3.0 36.7 + - + +
52D HIS 3.8 4.7 - - - +
53D GLU 3.2 0.4 - - - -
54D LEU* 1.3 78.5 - - + +
56D ASP* 1.3 57.6 + - - +
58D PHE* 3.3 26.8 + - + -
59D ARG* 3.0 23.2 + - - +
106D HIS* 6.1 0.4 - - + -
110D LEU* 3.9 23.6 - - + -
114D TYR* 5.1 0.4 - - - +
154D LEU* 4.4 5.8 - - + -
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Residues in contact with ASP 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LYS* 2.6 34.2 + - - +
40D HIS* 3.0 31.5 + - - -
52D HIS* 3.6 2.7 + - - -
53D GLU* 3.1 15.1 + - - +
55D LEU* 1.3 72.9 - - - +
57D THR* 1.3 65.5 + - - +
59D ARG* 3.2 6.4 + - - +
60D THR* 3.0 25.7 + - - -
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Residues in contact with THR 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D GLU 3.4 8.7 + - - -
54D LEU* 3.0 18.5 + - + +
56D ASP* 1.3 77.5 - - - +
58D PHE* 1.4 67.0 + - + +
60D THR* 3.3 8.0 + - - -
61D GLN* 3.1 42.6 + - - +
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Residues in contact with PHE 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D THR* 4.2 0.7 - - + -
54D LEU* 3.1 46.2 + - + -
55D LEU* 3.6 24.5 - - + +
56D ASP 3.2 0.2 - - - -
57D THR* 1.4 81.7 - - + +
59D ARG* 1.3 62.0 + - - +
61D GLN* 3.1 12.4 + - - +
62D LEU* 2.9 27.6 + - + +
114D TYR* 3.2 32.3 - + + +
150D SER* 3.4 45.5 - - - +
153D PHE* 4.0 11.7 - + + -
154D LEU* 3.8 30.3 - - + -
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Residues in contact with ARG 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ALA* 2.9 54.2 + - - +
34D LEU* 4.1 15.9 - - - +
36D THR* 4.0 10.9 - - + +
37D LYS* 3.3 41.0 - - + +
55D LEU 3.0 15.0 + - - +
56D ASP* 3.2 10.7 + - - +
58D PHE* 1.3 77.1 - - - +
60D THR* 1.3 64.5 + - - +
62D LEU* 3.2 3.3 + - - +
63D ASP* 2.8 52.1 + - - +
1164D EDO 4.4 4.6 + - - -
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Residues in contact with THR 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D ASP 3.0 14.2 + - - -
57D THR* 3.6 11.6 - - - -
58D PHE 3.3 0.2 - - - -
59D ARG* 1.3 78.3 - - - +
61D GLN* 1.3 63.3 + - + +
63D ASP* 3.3 13.0 + - + +
64D ASN* 3.0 38.2 + - - +
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Residues in contact with GLN 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D THR* 3.1 34.0 + - + +
58D PHE* 3.1 11.4 + - - +
60D THR* 1.3 78.2 - - + +
62D LEU* 1.3 59.8 + - + +
64D ASN* 3.2 8.4 + - - +
65D HIS* 2.9 45.7 + - + -
146D ASP* 3.7 28.3 + - + +
150D SER* 3.5 20.6 + - - -
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Residues in contact with LEU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D VAL* 3.6 23.8 - - + +
32D LEU* 3.8 24.2 - - + +
33D ALA* 3.7 30.7 - - + +
36D THR* 3.7 13.0 - - - +
58D PHE 2.9 19.8 + - - +
59D ARG* 3.7 4.3 - - - +
61D GLN* 1.3 74.9 - - + +
63D ASP* 1.3 61.0 - - - +
65D HIS* 4.5 7.2 - - + +
66D GLY* 2.8 28.9 + - - -
114D TYR* 3.5 25.8 - - + +
147D LEU* 4.2 19.1 - - + -
1164D EDO 4.0 3.0 - - - -
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Residues in contact with ASP 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D ARG* 2.8 47.7 + - - +
60D THR* 3.4 14.2 - - + +
62D LEU* 1.3 78.2 - - - +
64D ASN* 1.3 61.6 + - - +
66D GLY 3.9 0.3 - - - -
67D ASP* 3.0 38.0 + - - +
1164D EDO 2.5 32.7 + - - +
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Residues in contact with ASN 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D THR* 3.0 31.7 + - - +
61D GLN* 3.2 10.6 + - - +
63D ASP* 1.3 79.8 - - - +
65D HIS* 1.3 66.4 + - + +
67D ASP* 3.3 9.0 + - - +
68D THR* 2.9 29.4 + - - +
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Residues in contact with HIS 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D VAL* 5.2 4.7 - - + -
61D GLN* 2.9 32.0 + - + +
62D LEU* 4.3 7.9 - - + +
64D ASN* 1.3 77.7 - - + +
66D GLY* 1.3 67.6 + - - +
68D THR* 3.2 9.1 + - - +
69D ILE* 2.9 33.8 + - + +
139D ILE* 4.7 3.0 + - - +
142D ALA* 3.5 18.3 - - + +
143D ALA* 3.5 44.4 + - + +
146D ASP* 2.8 36.7 + - + +
147D LEU* 6.0 2.9 - - + -
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Residues in contact with GLY 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LEU* 3.4 14.3 - - - +
29D VAL* 3.9 14.0 - - - +
62D LEU 2.8 23.0 + - - -
65D HIS* 1.3 72.0 - - - +
67D ASP* 1.3 63.0 + - - +
69D ILE* 3.3 3.4 + - - -
70D ALA* 2.9 26.2 + - - +
1164D EDO 3.9 14.8 - - - -
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Residues in contact with ASP 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ASP* 3.0 23.9 + - - +
64D ASN* 3.6 8.4 - - - +
66D GLY* 1.3 76.0 - - - +
68D THR* 1.3 57.1 + - - +
70D ALA* 3.3 5.5 + - - +
71D GLU* 2.9 38.0 + - - +
1163D FE 4.3 16.9 - - - -
1164D EDO 3.5 14.4 + - - -
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Residues in contact with THR 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D ASN 2.9 18.2 + - - -
65D HIS* 3.8 10.8 + - - +
67D ASP* 1.3 74.8 - - - +
69D ILE* 1.3 59.0 + - - +
71D GLU* 3.9 13.1 + - - +
72D ARG* 3.0 28.4 + - - +
75D GLN* 5.2 0.5 + - - -
139D ILE* 3.6 34.3 - - + +
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Residues in contact with ILE 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LEU* 3.3 43.7 - - + +
25D SER* 4.6 2.0 - - - -
26D LEU* 3.9 14.8 - - + +
29D VAL* 4.5 15.0 - - + -
65D HIS* 2.9 30.0 + - + +
66D GLY* 3.7 4.9 - - - +
68D THR* 1.3 73.9 - - - +
70D ALA* 1.3 66.2 + - - +
72D ARG* 3.2 5.7 + - - +
73D VAL* 3.2 20.3 + - + +
121D ILE* 4.4 13.7 - - + -
139D ILE* 4.0 17.9 - - + -
140D PHE* 4.1 22.9 - - + -
143D ALA* 5.0 4.9 - - + -
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Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LEU* 3.9 18.4 - - + -
66D GLY 2.9 17.2 + - - +
67D ASP* 3.7 6.5 - - - +
69D ILE* 1.3 76.6 - - - +
71D GLU* 1.3 63.6 + - + +
73D VAL* 3.1 17.9 + - - +
74D VAL* 3.3 10.9 + - - +
80D ALA* 3.7 27.5 - - + +
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Residues in contact with GLU 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D ASP* 2.9 24.8 + - - +
68D THR* 3.9 12.0 + - - +
70D ALA* 1.3 77.1 - - + +
72D ARG* 1.4 58.5 + - - +
74D VAL* 3.2 9.4 + - - +
75D GLN* 2.9 45.4 + - - +
1163D FE 2.2 35.6 - - - -
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Residues in contact with ARG 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ASN* 4.4 10.1 + - - +
10D LEU* 5.0 2.0 - - - +
22D LEU* 3.7 17.3 - - + -
68D THR 3.0 17.8 + - - +
69D ILE 3.5 5.6 - - - +
70D ALA 3.1 0.4 - - - -
71D GLU* 1.4 75.0 - - - +
73D VAL* 1.3 65.4 + - - +
75D GLN* 3.0 32.1 + - - +
76D LEU* 3.1 43.3 + - + +
133D ASP* 3.0 28.5 + - - -
135D THR* 3.5 26.5 - - - +
136D THR* 2.8 26.1 + - - +
139D ILE* 3.8 22.4 - - + -
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Residues in contact with VAL 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ILE* 4.0 12.4 - - + +
22D LEU* 3.5 35.6 - - + +
23D ASN* 3.7 24.0 - - - +
26D LEU* 5.6 0.2 - - + -
69D ILE* 3.2 10.7 + - + +
70D ALA* 3.1 13.1 + - - +
72D ARG* 1.3 76.7 - - - +
74D VAL* 1.3 62.7 - - - +
76D LEU* 3.2 10.9 + - - +
77D GLY 3.4 0.2 + - - -
78D GLY* 3.0 25.2 + - - -
79D THR 3.4 41.1 - - - +
80D ALA* 4.2 1.6 - - - -
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Residues in contact with VAL 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D HIS* 5.8 0.7 - - + +
70D ALA 3.3 12.3 + - - +
71D GLU* 3.2 10.4 + - - +
72D ARG 3.2 0.4 - - - -
73D VAL* 1.3 73.9 - - - +
75D GLN* 1.3 65.4 + - - +
77D GLY* 2.9 15.1 + - - -
78D GLY 3.6 17.9 - - - +
79D THR* 4.9 0.4 - - - -
80D ALA* 4.0 19.7 - - + +
----------------------------------------------------------
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Residues in contact with GLN 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D THR* 4.3 16.8 + - - +
8D ASN* 4.2 12.6 - - - +
68D THR 5.2 0.4 + - - -
71D GLU* 2.9 43.6 + - + +
72D ARG* 3.0 43.1 + - - +
74D VAL* 1.3 77.9 - - - +
76D LEU* 1.3 59.8 - - - +
77D GLY 3.4 2.6 + - - -
----------------------------------------------------------
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Residues in contact with LEU 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D THR* 5.1 1.1 - - - -
8D ASN* 4.1 17.7 - - - +
10D LEU* 3.9 19.1 - - + -
15D LYS* 3.3 39.8 - - + +
18D VAL* 4.0 22.4 - - + -
19D ILE* 3.6 17.2 - - + +
22D LEU* 4.2 7.0 - - + -
72D ARG* 3.1 43.0 + - - +
73D VAL 3.8 4.7 - - - +
74D VAL 3.1 0.6 - - - -
75D GLN* 1.3 75.6 - - - +
77D GLY* 1.3 58.8 + - - +
78D GLY 3.5 1.6 - - - -
133D ASP* 3.8 17.3 - - - +
136D 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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il