Contacts of the helix formed by residues 136 - 160 (chain B) in PDB entry 1O9I
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 ASN 136 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B SER* 3.0 10.3 + - - -
135B GLY* 1.3 77.7 - - - +
137B LEU* 1.3 60.6 - - - +
138B VAL* 2.9 27.6 + - - +
139B ALA* 3.0 15.1 + - + -
140B ASP* 2.9 23.3 + - - -
200B VAL* 4.2 5.9 - - - +
201B PRO* 4.3 16.8 - - - +
153C LEU* 3.7 38.7 - - + +
157C ARG* 4.7 1.1 - - - +
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLN* 4.3 12.6 - - + +
49B SER* 4.1 21.5 - - - +
51B GLY* 6.2 1.8 - - - -
52B ALA 6.3 0.7 - - - +
55B TYR* 4.2 26.9 - - + -
59B LEU* 4.1 24.7 - - + -
135B GLY* 4.0 6.1 + - - +
136B ASN* 1.3 72.7 + - - +
138B VAL* 1.3 61.0 + - - +
139B ALA 3.3 0.2 - - - -
140B ASP* 3.6 20.9 - - + +
141B MET* 2.8 37.6 + - + +
192B LEU* 3.7 19.6 - - + +
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ASN* 2.9 14.0 + - - +
137B LEU* 1.3 81.4 - - - +
139B ALA* 1.3 63.2 + - - +
141B MET* 4.3 2.4 - - - +
142B ARG* 3.3 29.7 + - + +
189B GLN* 4.6 3.0 - - + +
192B LEU* 3.9 26.2 - - + +
193B GLU* 3.9 28.3 - - + +
196B TYR* 4.0 27.4 - - + -
197B GLY 4.3 7.0 - - - +
200B VAL* 3.4 22.2 - - + -
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Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B SER* 4.4 1.8 - - - +
136B ASN* 3.0 20.2 + - + +
138B VAL* 1.3 77.7 - - - +
140B ASP* 1.3 59.2 + - - +
142B ARG* 3.2 10.8 + - - +
143B PHE* 3.0 21.5 + - - +
200B VAL* 4.0 22.7 - - + +
146C VAL* 4.6 2.4 - - - +
149C SER* 4.3 10.8 - - - +
150C GLU* 3.4 28.1 - - - +
153C LEU* 4.8 1.6 - - + -
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Residues in contact with ASP 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLN* 3.8 26.8 - - - +
132B THR* 3.6 5.3 - - - +
133B SER* 3.4 7.8 + - - -
134B SER* 2.7 43.8 + - - -
135B GLY 3.9 2.9 + - - -
136B ASN 2.9 19.5 + - - +
137B LEU* 4.1 11.5 - - + +
138B VAL 3.3 0.4 - - - -
139B ALA* 1.3 73.5 - - - +
141B MET* 1.3 60.2 + - - +
143B PHE* 3.1 5.6 + - - +
144B ASN* 2.8 35.0 + - - +
150C GLU* 2.8 17.5 - - - +
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Residues in contact with MET 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TYR* 3.9 23.6 - - + -
58B LEU* 4.3 9.2 - - + -
59B LEU* 4.0 26.7 - - + -
137B LEU* 2.8 33.0 + - + +
138B VAL 4.3 0.7 - - - +
140B ASP* 1.3 68.5 - - - +
142B ARG* 1.3 65.9 + - - +
144B ASN* 3.2 10.3 + - - +
145B VAL* 3.0 27.9 + - - +
185B PHE* 3.6 28.1 - - - +
188B ALA* 3.9 23.1 - - + -
189B GLN* 4.0 20.9 - - + -
192B LEU* 3.9 12.3 - - + -
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Residues in contact with ARG 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B VAL* 3.3 20.7 + - - +
139B ALA 3.2 7.3 + - - +
140B ASP 3.2 0.2 - - - -
141B MET* 1.3 78.0 - - - +
143B PHE* 1.3 63.1 + - - +
145B VAL* 3.3 5.1 + - - +
146B VAL* 3.0 24.8 + - - +
189B GLN* 3.5 28.0 + - - +
193B GLU* 2.7 32.9 + - - +
198B ILE* 2.7 25.6 + - - +
200B VAL* 3.6 12.4 - - - +
145C VAL* 3.8 12.2 - - + +
146C VAL* 3.4 15.0 - - + +
149C SER* 2.9 30.4 + - - -
182C GLN* 3.3 17.4 + - - -
186C MET* 3.4 19.0 - - - +
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Residues in contact with PHE 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TRP* 3.8 33.0 - + - -
37B THR* 4.7 0.4 - - + -
41B SER* 3.5 24.7 - - - -
45B GLN* 4.0 7.2 - - - -
130B TYR 3.8 20.6 - - - -
132B THR* 3.7 32.3 - - + -
139B ALA 3.0 12.4 + - - +
140B ASP* 3.1 11.4 + - - +
142B ARG* 1.3 76.8 - - - +
144B ASN* 1.3 69.6 + - - +
146B VAL* 3.1 5.1 + - + +
147B ARG* 2.8 36.7 + - + +
33C TRP* 3.9 16.4 - + - -
143C PHE* 6.4 0.2 - + - -
146C VAL* 3.4 18.7 - - + +
150C GLU* 4.4 4.3 - - - +
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Residues in contact with ASN 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PHE* 3.2 24.4 - - + -
45B GLN* 2.8 41.5 + - - -
59B LEU* 3.4 18.6 - - - +
140B ASP 2.8 16.2 + - - +
141B MET* 3.6 16.8 - - - +
142B ARG 3.2 0.2 - - - -
143B PHE* 1.3 76.9 - - - +
145B VAL* 1.3 67.1 + - - +
147B ARG* 3.2 3.4 + - - +
148B GLU* 3.0 27.9 + - - +
185B PHE* 3.5 23.3 - - + -
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Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B MET 3.0 19.3 + - - +
142B ARG* 3.6 7.6 - - - +
144B ASN* 1.3 77.8 - - - +
146B VAL* 1.3 52.8 + - - +
148B GLU* 3.3 5.6 + - - +
149B SER* 2.7 45.5 + - - +
182B GLN* 4.0 6.4 - - + +
185B PHE* 3.6 22.0 - - + -
186B MET* 3.6 31.4 - - + +
189B GLN* 3.8 13.9 - - - +
142C ARG* 3.8 24.5 - - + +
189C GLN* 6.1 0.2 - - - +
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TRP* 3.7 24.5 - - + -
142B ARG 3.0 15.3 + - - +
143B PHE* 3.3 9.4 - - + +
145B VAL* 1.3 73.9 - - - +
147B ARG* 1.3 67.1 + - - +
149B SER* 3.0 6.4 + - - -
150B GLU* 2.8 37.0 + - + +
139C ALA 4.8 1.1 - - - +
142C ARG* 3.4 43.1 - - + +
143C PHE* 3.5 18.4 - - + +
146C VAL* 3.6 8.1 - - + -
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Residues in contact with ARG 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TRP* 2.9 61.7 + - + +
34B GLY 3.0 15.6 + - - -
35B GLU* 3.0 18.4 + - - -
37B THR* 4.0 12.8 - - + -
38B GLY* 3.6 23.5 - - - +
42B PHE* 4.1 5.3 - - + -
66B GLU* 3.2 24.7 + - - -
143B PHE* 2.8 25.9 + - + +
144B ASN* 3.5 12.8 - - - +
146B VAL* 1.3 72.5 - - - +
148B GLU* 1.3 86.5 + - - +
150B GLU* 4.1 1.4 - - - +
151B ALA* 2.9 39.7 + - - +
178B GLU* 5.6 1.0 + - - +
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Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PHE* 3.2 13.5 - - + -
66B GLU* 2.9 22.7 - - - +
144B ASN 3.0 17.2 + - - +
145B VAL 3.8 0.7 - - - +
147B ARG* 1.3 91.9 + - - +
149B SER* 1.3 58.2 + - - +
151B ALA* 3.9 3.2 - - - +
152B ARG* 3.0 30.1 + - - +
178B GLU* 3.4 26.5 - - - +
181B HIS* 3.3 34.3 + - + +
182B GLN* 3.3 24.5 + - + +
185B PHE* 4.0 8.3 - - + -
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Residues in contact with SER 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B VAL 2.7 23.6 + - - -
146B VAL* 3.0 7.8 + - - -
148B GLU* 1.3 76.4 - - - +
150B GLU* 1.3 66.2 + - - +
152B ARG* 3.4 0.9 + - - +
153B LEU* 3.0 24.1 + - - +
182B GLN* 3.6 11.4 - - - +
139C ALA* 4.4 10.1 - - - -
142C ARG* 2.9 30.4 + - - -
200C VAL* 3.6 22.8 - - - +
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TRP* 3.5 41.7 + - + +
146B VAL* 2.8 26.9 + - + +
147B ARG 4.1 0.2 - - - +
149B SER* 1.3 73.7 - - - +
151B ALA* 1.3 63.0 + - - +
153B LEU* 3.3 9.3 + - - +
154B GLN* 3.1 30.5 + - - +
132C THR* 3.4 16.3 - - - +
134C SER* 3.2 24.1 + - - -
139C ALA* 3.4 21.8 - - + +
140C ASP* 2.7 24.0 - - - +
143C PHE* 4.4 2.8 - - - +
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Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TRP* 3.6 10.0 - - - +
34B GLY* 5.6 0.4 - - - -
35B GLU* 4.5 2.0 - - - +
147B ARG* 2.9 44.7 + - - +
148B GLU* 3.9 4.5 - - - +
150B GLU* 1.3 77.0 - - - +
152B ARG* 1.3 58.1 + - - +
154B GLN* 3.1 9.8 + - - +
155B VAL* 2.8 31.8 + - + +
178B GLU* 3.9 16.6 - - - +
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Residues in contact with ARG 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B GLU 3.0 20.4 + - - +
149B SER 4.0 0.2 - - - +
150B GLU 3.3 0.2 - - - -
151B ALA* 1.3 73.3 - - - +
153B LEU* 1.3 60.1 + - - +
155B VAL* 3.8 0.9 - - - +
156B SER* 2.8 34.6 + - - -
175B LEU* 2.9 38.1 + - + +
178B GLU* 3.2 24.8 + - + +
179B THR* 3.1 11.9 + - - +
182B GLN* 3.6 10.3 - - - +
199C ILE* 3.4 10.1 - - - +
200C VAL 3.1 20.8 + - - +
201C PRO* 2.9 33.8 + - - +
204C MET* 3.8 23.4 + - - +
205C LYS* 4.6 1.4 - - - +
208C GLU* 2.8 27.1 + - - -
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Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B SER 3.0 17.5 + - - +
150B GLU* 3.5 11.4 - - - +
152B ARG* 1.3 77.9 - - - +
154B GLN* 1.3 60.0 + - + +
156B SER* 3.2 3.5 + - - -
157B ARG* 2.9 50.0 + - - +
134C SER* 3.5 35.0 - - - +
136C ASN* 3.7 19.1 - - + +
139C ALA* 4.7 2.9 - - + -
200C VAL* 4.5 4.7 - - + -
201C PRO* 4.0 11.1 - - + +
261D LEU 3.8 10.3 - - - +
262D HIS* 3.8 35.2 - - + +
111E VAL 5.2 0.2 - - - +
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Residues in contact with GLN 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLU* 3.5 30.7 + - + +
28B SER* 5.2 4.3 + - - +
32B GLN* 5.5 0.6 + - - +
33B TRP* 4.2 35.7 - - - +
34B GLY* 5.4 0.3 - - - -
150B GLU* 3.1 17.1 + - - +
151B ALA* 3.5 8.2 - - - +
153B LEU* 1.3 80.2 - - + +
155B VAL* 1.3 57.6 + - + +
157B ARG* 3.2 2.1 + - - +
158B LEU* 2.8 37.2 + - + +
110E LEU* 3.5 32.0 - - + +
111E VAL* 4.0 26.8 + - - +
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Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B SER* 4.7 14.4 - - - +
35B GLU* 6.4 0.4 - - - -
151B ALA* 2.8 20.0 + - + +
152B ARG 3.9 1.8 - - - +
154B GLN* 1.3 75.3 - - + +
156B SER* 1.3 62.0 + - - +
158B LEU* 3.2 11.0 + - + +
159B TYR* 3.0 22.2 + - - +
171B LEU* 3.7 37.0 - - + +
174B LEU* 4.4 10.1 - - + -
175B LEU* 3.6 21.1 - - + +
178B GLU* 3.6 26.7 - - - +
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Residues in contact with SER 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ARG 2.8 23.3 + - - -
153B LEU 3.4 4.7 - - - -
154B GLN 3.2 0.2 - - - -
155B VAL* 1.3 76.9 - - - +
157B ARG* 1.3 62.5 + - - +
159B TYR* 3.3 16.6 + - - +
160B SER* 3.6 5.7 + - - -
175B LEU* 3.4 13.7 - - - +
201C PRO* 3.3 28.7 - - - +
204C MET* 3.4 25.7 - - - +
262D HIS* 4.0 16.5 + - - -
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Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU* 2.9 41.8 + - + +
154B GLN* 3.2 7.1 + - - +
156B SER* 1.3 77.0 - - - +
158B LEU* 1.3 64.0 + - - +
160B SER* 2.9 15.4 + - - -
161B MET* 3.3 24.5 + - + +
134C SER 2.7 30.7 + - - -
135C GLY* 4.3 1.8 - - - -
260D ARG 4.1 15.0 - - - +
261D LEU* 2.8 29.1 + - + +
262D HIS* 4.5 2.0 + - + -
263D ASN* 2.8 24.4 + - - -
86E PHE* 5.7 1.0 - - + -
109E SER 3.7 9.5 + - - -
110E LEU* 3.0 35.6 + - + -
111E VAL 3.2 13.3 + - - -
113E GLY* 3.5 9.6 - - - +
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B MET* 3.6 19.8 - - + +
24B ARG* 3.7 32.8 - - + +
25B LEU* 3.9 16.6 - - + +
27B GLU* 5.9 0.2 - - + -
28B SER* 3.6 24.2 - - - +
154B GLN* 2.8 25.1 + - + +
155B VAL* 3.2 15.9 + - + +
157B ARG* 1.3 72.2 - - - +
159B TYR* 1.3 58.0 + - - +
161B MET* 2.8 29.0 + - - +
162B THR* 3.6 5.5 + - - +
171B LEU* 3.8 17.3 - - + -
110E LEU* 3.8 22.2 - - + -
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Residues in contact with TYR 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B VAL 3.0 11.9 + - - +
156B SER 3.3 11.9 - - - +
157B ARG 3.1 0.2 - - - -
158B LEU* 1.3 77.2 - - - +
160B SER* 1.3 63.2 + - - +
161B MET 3.3 0.2 - - - -
162B THR* 3.2 6.9 - - - +
165B GLU* 5.0 0.9 + - - -
168B ARG* 2.9 91.6 + - + +
171B LEU* 3.6 15.7 - - + +
172B LYS* 3.8 23.5 - - + -
175B LEU* 5.1 2.9 - - + -
204C MET* 4.3 16.8 - - + -
207C ILE* 3.5 38.5 - - + +
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Residues in contact with SER 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B SER 3.6 5.1 + - - -
157B ARG 2.9 10.6 + - - -
159B TYR* 1.3 80.5 - - - +
161B MET* 1.3 60.1 + - - +
162B THR 3.5 2.5 - - - -
168B ARG* 4.4 5.7 + - - +
260D ARG* 3.7 50.8 + - - +
262D HIS* 5.0 2.8 + - - -
86E PHE* 4.8 3.3 - - - -
87E GLY* 3.7 6.9 - - - -
88E PRO* 3.4 14.4 - - - +
89E GLU 5.4 0.2 + - - -
----------------------------------------------------------
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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