Contacts of the helix formed by residues 133 - 157 (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 ASP 133 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LEU* 3.4 33.4 - - + +
14D ALA* 5.6 0.2 - - + -
18D VAL* 3.6 19.1 - - + +
72D ARG* 3.0 14.7 + - - -
76D LEU* 3.8 2.1 - - - +
128D SER 3.1 18.0 + - - +
129D ASP* 3.8 1.4 + - - -
131D ALA 5.0 0.7 - - - -
132D GLY* 1.3 78.6 - - - +
134D PRO* 1.3 58.8 - - - +
135D THR* 3.4 4.2 + - - -
136D THR* 2.5 41.2 + - - -
137D ALA* 3.0 22.7 + - - +
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Residues in contact with PRO 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D ASP* 3.6 23.3 - - - +
132D GLY* 3.3 11.0 - - - +
133D ASP* 1.3 89.9 - - - +
135D THR* 1.3 60.1 + - - +
137D ALA* 3.6 6.1 - - + +
138D ASP* 2.9 28.1 + - - +
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Residues in contact with THR 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ARG* 3.5 34.1 - - - +
133D ASP* 3.1 3.0 + - - -
134D PRO* 1.3 78.8 - - - +
136D THR* 1.4 65.3 + - - +
138D ASP* 3.2 16.2 + - - +
139D ILE* 3.3 18.0 + - + +
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Residues in contact with THR 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D VAL* 3.3 25.0 - - + +
22D LEU* 3.9 13.0 - - + -
72D ARG* 2.8 25.5 + - + +
76D LEU* 4.1 0.2 - - - +
128D SER* 3.6 13.2 - - - +
133D ASP* 2.5 35.2 + - - -
135D THR* 1.4 72.5 - - - +
137D ALA* 1.3 66.6 + - - +
139D ILE* 3.0 17.7 + - + +
140D PHE* 3.1 25.3 + - + -
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Residues in contact with ALA 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D ILE* 3.6 29.1 - - + +
128D SER* 3.9 7.5 - - - -
129D ASP* 3.9 15.3 - - + +
133D ASP 3.0 14.4 + - - +
134D PRO* 3.3 13.2 + - + +
136D THR* 1.3 76.2 - - - +
138D ASP* 1.3 57.2 + - - +
140D PHE* 3.2 7.4 + - - +
141D THR* 2.8 31.7 + - - +
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Residues in contact with ASP 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ASP* 4.1 3.3 - - - +
1164B TRS 2.6 50.0 + - - -
134D PRO 2.9 13.2 + - - +
135D THR* 3.4 12.1 - - - +
136D THR 3.1 0.4 - - - -
137D ALA* 1.3 75.3 - - - +
139D ILE* 1.3 67.3 + - - +
141D THR* 3.1 7.1 + - - -
142D ALA* 2.9 24.9 + - - +
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Residues in contact with ILE 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LEU* 5.1 4.5 - - + -
65D HIS* 4.7 3.0 + - - +
68D THR* 3.6 34.3 - - + +
69D ILE* 4.0 27.6 - - + +
72D ARG* 3.8 41.3 - - + +
75D GLN* 5.5 1.6 - - - +
135D THR* 3.3 16.3 + - + +
136D THR* 3.0 8.4 + - + +
138D ASP* 1.3 80.2 - - + +
140D PHE* 1.4 63.2 + - + +
142D ALA* 3.4 6.5 + - - +
143D ALA* 3.1 20.8 + - + +
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Residues in contact with PHE 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ILE* 3.8 13.5 - - + -
22D LEU* 3.5 25.4 - - + -
25D SER* 3.6 26.0 - - - -
69D ILE* 4.1 16.2 - - + -
121D ILE* 3.3 25.8 - - + +
124D ALA* 3.7 24.9 - - + -
125D ILE* 3.6 19.7 - - + +
128D SER* 3.3 28.7 - - - -
136D THR* 3.1 32.2 + - + -
137D ALA 3.6 3.4 - - - +
139D ILE* 1.4 76.0 - - + +
141D THR* 1.3 52.7 + - - +
143D ALA* 3.3 3.0 + - - -
144D SER* 2.8 30.3 + - - -
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Residues in contact with THR 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B PRO* 4.0 12.3 - - + +
135B THR* 4.3 9.2 - - - +
138B ASP* 3.4 40.6 - - + +
125D ILE* 3.5 25.7 - - - +
137D ALA 2.8 18.7 + - - -
138D ASP* 3.1 10.8 + - - +
140D PHE* 1.3 73.3 - - - +
142D ALA* 1.3 60.9 + - - +
144D SER* 3.2 2.4 + - - -
145D ARG* 2.9 30.7 + - - +
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Residues in contact with ALA 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1164B TRS 4.4 22.6 + - - +
65D HIS* 3.5 19.4 + - + +
138D ASP* 2.9 16.3 + - - +
139D ILE* 3.8 6.5 - - - +
141D THR* 1.3 79.6 - - - +
143D ALA* 1.3 60.8 + - - +
145D ARG* 3.3 15.8 + - - +
146D ASP* 3.4 11.4 + - - +
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Residues in contact with ALA 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D VAL* 6.6 0.2 - - + -
65D HIS* 3.5 35.9 - - + +
69D ILE* 5.0 5.8 - - + -
121D ILE* 4.0 15.7 - - + -
139D ILE* 3.1 13.5 + - + +
140D PHE* 3.6 9.2 - - - +
142D ALA* 1.3 75.3 - - - +
144D SER* 1.3 58.2 + - - +
146D ASP* 3.2 4.3 + - - +
147D LEU* 2.8 37.8 + - + +
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Residues in contact with SER 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B THR* 2.7 28.4 + - - +
118D ALA 5.1 1.6 + - - -
121D ILE* 3.7 13.9 - - - +
122D ARG* 4.2 10.8 + - - +
125D ILE* 3.9 10.9 - - - +
140D PHE 2.8 20.2 + - - -
141D THR 3.2 5.8 + - - -
143D ALA* 1.3 72.2 - - - +
145D ARG* 1.3 64.9 + - - +
147D LEU* 4.3 5.2 - - - -
148D ASP* 2.8 34.8 + - - +
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Residues in contact with ARG 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B THR* 3.6 25.5 + - - +
75B GLN* 4.6 3.0 + - - +
135B THR* 3.6 22.7 - - + +
138B ASP* 2.9 41.5 + - - -
139B ILE* 3.6 25.7 - - + +
142B ALA* 4.4 9.5 - - - +
1164B TRS 3.8 14.3 + - - -
141D THR 2.9 16.4 + - - +
142D ALA* 3.5 9.9 - - - +
143D ALA 3.2 0.2 - - - -
144D SER* 1.3 77.8 - - - +
146D ASP* 1.3 66.3 + - - +
148D ASP* 4.1 1.9 - - - +
149D LYS* 3.1 24.1 + - - +
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Residues in contact with ASP 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D GLN* 3.7 31.9 + - + +
65D HIS* 2.8 38.1 + - + +
142D ALA 3.4 3.7 + - - +
143D ALA 3.2 3.7 + - - +
145D ARG* 1.3 79.8 - - - +
147D LEU* 1.4 63.0 + - + +
149D LYS* 3.4 8.0 + - - +
150D SER* 2.9 34.9 + - - -
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Residues in contact with LEU 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D VAL* 5.6 2.5 - - + -
32D LEU* 4.1 16.8 - - + -
62D LEU* 4.2 15.9 - - + -
65D HIS* 6.0 2.9 - - + -
114D TYR* 4.3 14.1 - - + +
117D VAL* 3.9 23.6 - - + -
118D ALA* 4.0 20.4 - - + +
121D ILE* 3.5 38.4 - - + -
143D ALA* 2.8 30.1 + - + +
144D SER* 4.0 3.4 - - - +
146D ASP* 1.4 74.0 - - + +
148D ASP* 1.4 57.8 + - - +
150D SER* 3.3 4.3 + - - -
151D LEU* 2.9 30.3 + - - +
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Residues in contact with ASP 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ASN* 3.1 15.2 - - - +
72B ARG* 2.7 34.0 + - - +
75B GLN* 3.7 10.0 - - + +
135B THR* 4.3 0.2 - - - +
118D ALA* 3.5 11.4 - - - +
122D ARG* 2.8 40.9 + - - -
144D SER* 2.8 28.5 + - - +
145D ARG 4.2 0.9 - - - +
147D LEU* 1.4 73.2 - - - +
149D LYS* 1.3 62.9 + - - +
151D LEU* 3.5 7.4 + - - +
152D TRP* 3.1 22.9 + - - +
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Residues in contact with LYS 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLU* 3.0 38.0 + - - +
75B GLN* 3.9 16.9 + - - +
1163B FE 4.1 3.6 - - - -
145D ARG 3.1 19.0 + - - +
146D ASP* 3.7 10.3 - - - +
148D ASP* 1.3 78.1 - - - +
150D SER* 1.3 58.4 + - - +
152D TRP* 3.2 13.5 + - + +
153D PHE* 2.9 59.7 + - + -
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Residues in contact with SER 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D PHE* 3.4 38.0 - - - +
61D GLN* 3.5 10.9 + - - -
114D TYR* 3.9 21.4 - - - -
146D ASP 2.9 24.3 + - - -
147D LEU* 3.7 4.7 - - - -
149D LYS* 1.3 75.1 - - - +
151D LEU* 1.3 64.1 + - - +
153D PHE* 3.2 3.7 + - - +
154D LEU* 3.0 29.0 + - - +
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Residues in contact with LEU 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B THR* 4.1 2.9 - - - +
7B LYS* 4.4 0.7 - - + -
8B ASN* 3.7 39.7 - - + +
111D ILE* 4.0 13.0 - - + +
114D TYR* 4.3 10.5 - - + -
115D GLY* 3.9 33.0 - - - +
118D ALA* 4.4 11.4 - - + -
147D LEU 2.9 17.5 + - - +
148D ASP* 3.7 6.7 - - - +
150D SER* 1.3 76.3 - - - +
152D TRP* 1.3 56.4 + - - +
154D LEU* 3.2 8.8 + - + +
155D GLU* 2.8 58.0 + - + +
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Residues in contact with TRP 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A TRP* 3.7 21.2 + - - -
43A LEU 5.2 0.2 + - - -
44A LYS* 4.3 4.6 - - - +
48A PHE* 3.9 18.4 - + - -
52A HIS* 3.7 22.7 - + - -
71B GLU* 3.6 39.5 - - + -
74B VAL* 3.1 32.6 - - + +
75B GLN* 3.6 35.4 - - + +
148D ASP 3.1 14.6 + - - +
149D LYS* 3.2 11.0 + - + +
151D LEU* 1.3 77.2 - - - +
153D PHE* 1.3 75.2 + + - +
155D GLU* 3.2 8.6 + - - +
156D ALA* 2.7 49.5 + - + +
159D GLN* 4.9 3.6 - - - +
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Residues in contact with PHE 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 3.5 20.5 - + + -
49A ILE* 3.6 16.4 - - + -
52A HIS* 3.8 23.8 - + - -
53A GLU* 5.2 2.2 - - - -
54D LEU* 3.8 27.8 - - + -
58D PHE* 4.0 16.2 - + + -
149D LYS* 2.9 37.8 + - + +
150D SER 3.2 7.4 + - - +
152D TRP* 1.3 113.9 - + - +
154D LEU* 1.3 61.9 + - - +
156D ALA* 3.6 5.4 + - - +
157D HIS* 2.8 25.8 + - - -
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Residues in contact with LEU 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D VAL* 5.9 1.1 - - + -
54D LEU* 5.3 4.5 - - + -
55D LEU* 4.4 5.4 - - + -
58D PHE* 3.8 19.7 - - + -
107D LEU* 3.8 23.3 - - + +
110D LEU* 4.0 28.9 - - + +
111D ILE* 3.6 23.1 - - + +
114D TYR* 3.7 44.4 - - + -
150D SER 3.0 17.6 + - - +
151D LEU* 3.6 6.3 - - - +
153D PHE* 1.3 76.7 - - - +
155D GLU* 1.4 63.0 + - - +
157D HIS* 3.1 23.4 + - + +
158D VAL* 3.9 1.9 + - - +
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Residues in contact with GLU 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LYS 4.3 2.0 - - - +
6B THR* 2.6 32.7 + - - -
7B LYS* 2.7 38.6 + - - +
75B GLN 5.2 0.7 - - - +
111D ILE* 3.9 26.1 - - + +
151D LEU* 2.8 37.9 + - + +
152D TRP* 4.0 6.0 - - - +
154D LEU* 1.4 68.0 - - - +
156D ALA* 1.3 67.7 + - - +
158D VAL* 2.9 17.1 + - + +
159D GLN* 3.0 32.4 + - + +
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Residues in contact with ALA 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU 4.1 5.8 - - - +
44A LYS* 3.4 5.2 - - + +
45A GLY 2.8 26.0 + - - -
48A PHE* 3.6 34.7 - - + +
152D TRP* 2.7 33.2 + - + +
153D PHE 3.9 2.5 - - - +
154D LEU 3.2 0.2 - - - -
155D GLU* 1.3 73.3 - - - +
157D HIS* 1.3 56.0 + - - +
158D VAL 3.2 0.4 + - - -
159D GLN* 3.5 18.2 + - - +
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Residues in contact with HIS 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLY* 3.3 24.2 - - - -
46A PRO* 3.4 35.5 + - + +
48A PHE* 3.9 20.6 - + + -
49A ILE* 3.6 31.3 + - + +
47D GLN* 5.7 0.4 - - + +
51D VAL* 4.1 19.1 - - + +
54D LEU* 4.3 13.2 - - + -
103D ILE* 6.3 0.2 - - + -
107D LEU* 3.7 26.8 - - + +
153D PHE 2.8 27.0 + - - -
154D LEU* 3.1 13.0 + - + +
155D GLU 3.1 1.0 + - - -
156D ALA* 1.3 76.9 - - - +
158D VAL* 1.3 60.9 + - - +
159D GLN 3.6 0.2 - - - -
160D GLU 4.0 1.4 - - - +
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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