Contacts of the helix formed by residues 155 - 177 (chain B) in PDB entry 1JUO
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 THR 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109B PHE* 4.5 0.4 - - - -
118B GLY 4.5 0.9 - - - -
119B THR* 3.8 21.1 - - + -
150B THR* 3.2 29.2 + - + +
153B LYS 4.0 0.9 + - - +
154B ILE* 1.3 79.2 - - - +
156B PHE* 1.3 63.4 + - - +
157B ASP* 3.6 10.6 + - - +
158B ASP* 3.1 26.9 + - - +
159B TYR* 3.0 21.7 + - - +
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Residues in contact with PHE 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ILE* 3.9 5.8 - - + -
64B ALA* 3.7 34.1 - - + -
65B GLY* 4.0 10.8 - - - +
70B PHE* 3.8 22.7 - + - -
102B LEU* 5.0 2.0 - - + -
106B ARG* 3.7 43.7 - - + -
109B PHE* 3.6 39.4 - + + -
118B GLY* 3.4 13.4 + - - +
155B THR* 1.3 73.8 - - - +
157B ASP* 1.3 56.1 + - - +
159B TYR* 3.2 9.0 + + - +
160B ILE* 3.0 57.6 + - + +
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Residues in contact with ASP 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LYS* 5.8 2.7 - - + +
69B PRO 4.4 6.1 - - - +
70B PHE* 3.3 25.9 - - + -
71B ASN* 2.6 41.7 + - - +
74B THR* 2.7 27.5 + - - +
155B THR* 3.6 9.5 + - - +
156B PHE* 1.3 79.8 - - - +
158B ASP* 1.3 64.6 + - - +
160B ILE* 3.4 4.7 + - - +
161B ALA* 3.2 20.1 + - - +
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Residues in contact with ASP 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ARG* 3.0 41.5 + - - -
71B ASN* 3.7 16.8 + - - -
148B TYR* 3.3 29.5 - - + +
150B THR* 3.9 6.2 + - - +
154B ILE* 3.8 17.5 - - + -
155B THR* 3.1 17.2 + - - +
157B ASP* 1.3 78.4 - - - +
159B TYR* 1.3 61.4 + - - +
161B ALA* 3.4 6.0 + - - +
162B CYS* 2.8 31.4 + - - +
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Residues in contact with TYR 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B TRP 3.0 33.4 + - - -
108B HIS* 3.8 8.7 - - - +
109B PHE* 3.4 38.1 + + + -
120B VAL* 5.3 0.9 - - + -
125B LEU* 3.8 20.9 - - + -
128B ALA* 4.1 10.6 - - + +
129B LEU* 4.0 17.5 - - + -
132B MET* 3.7 19.4 - - - -
154B ILE* 3.9 9.1 - - + +
155B THR 3.0 14.0 + - - +
156B PHE* 3.2 13.0 + + - +
158B ASP* 1.3 78.6 - - - +
160B ILE* 1.3 69.1 + - + +
162B CYS* 3.4 8.3 - - - +
163B CYS* 2.9 51.9 + - - -
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Residues in contact with ILE 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B PHE* 3.8 21.3 - - + -
74B THR* 4.3 5.8 - - - +
78B MET* 4.3 14.8 - - - -
102B LEU* 4.0 26.2 - - + +
105B TRP* 4.1 22.4 - - + -
156B PHE* 3.0 45.9 + - + +
157B ASP 3.6 7.0 - - - +
158B ASP 3.2 0.2 - - - -
159B TYR* 1.3 84.7 - - + +
161B ALA* 1.3 60.7 + - - +
162B CYS 3.0 1.1 - - - -
163B CYS* 2.7 24.8 + - - +
164B VAL* 2.8 22.6 + - + +
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Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ASN* 5.5 1.1 - - - +
73B GLU* 5.8 1.6 - - + -
74B THR* 3.7 22.4 + - - +
77B LEU* 3.6 23.9 - - + +
148B TYR* 4.3 13.9 - - + -
157B ASP 3.2 6.6 + - - +
158B ASP* 3.7 12.6 - - - +
160B ILE* 1.3 79.0 - - - +
162B CYS* 1.3 62.9 + - - +
164B VAL* 3.3 6.6 + - - +
165B LYS* 3.1 28.2 + - - +
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Residues in contact with CYS 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A MET* 3.7 12.3 - - - +
125B LEU* 5.1 4.7 - - - -
129B LEU* 5.1 11.0 - - - -
144B ILE* 3.6 28.3 - - + -
148B TYR* 3.7 23.3 - - + -
154B ILE* 6.2 0.4 - - + -
158B ASP 2.8 19.8 + - - +
159B TYR* 3.4 10.8 - - - +
161B ALA* 1.3 77.6 - - - +
163B CYS* 1.3 56.8 + - - +
166B LEU* 2.9 44.4 + - - +
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Residues in contact with CYS 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B TRP* 3.7 38.6 - - + +
129B LEU* 5.1 4.9 - - - -
132B MET* 4.3 15.5 - - + +
134B PHE* 5.8 0.5 - - - -
159B TYR* 2.9 57.2 + - - -
160B ILE* 2.7 16.2 + - - +
162B CYS* 1.3 73.6 - - - +
164B VAL* 1.3 57.9 + - - +
166B LEU* 3.5 8.0 + - - +
167B ARG* 3.1 23.7 + - - +
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Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B LEU* 3.6 38.8 - - + +
78B MET* 4.2 20.6 - - + -
81B MET* 3.9 21.4 - - + +
105B TRP* 3.6 24.5 - - + -
160B ILE* 2.8 22.1 + - + +
161B ALA* 3.7 8.1 - - - +
162B CYS 3.3 0.2 - - - -
163B CYS* 1.3 76.1 - - - +
165B LYS* 1.3 61.8 + - - +
167B ARG* 3.3 4.9 + - - +
168B ALA* 3.1 22.8 + - + +
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Residues in contact with LYS 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLU* 5.5 1.2 + - - -
165A LYS* 5.1 6.1 - - - +
195A VAL 4.7 4.6 + - - -
196A MET* 4.1 24.8 + - + -
198A VAL* 3.9 26.5 + - - -
73B GLU* 5.7 1.6 - - - +
76B ARG* 5.8 0.4 - - - +
77B LEU* 4.0 19.7 - - + -
147B ARG* 4.7 6.5 - - - +
148B TYR* 3.1 24.5 + - - +
161B ALA 3.1 17.3 + - - +
162B CYS 4.0 2.9 - - - +
164B VAL* 1.3 73.4 - - - +
166B LEU* 1.3 62.9 + - - +
168B ALA* 3.1 1.7 + - - +
169B LEU* 2.8 39.8 + - + +
198B VAL* 3.6 32.5 - - + +
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Residues in contact with LEU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ILE* 4.1 22.2 - - + -
196A MET* 3.6 32.8 - - + -
129B LEU* 4.1 29.2 - - + -
132B MET* 5.9 0.7 - - + -
134B PHE* 3.8 37.5 - - + -
136B LEU* 4.2 6.7 - - + -
144B ILE* 4.4 4.3 - - + -
162B CYS* 2.9 25.9 + - - +
163B CYS* 3.7 7.6 - - - +
165B LYS* 1.3 75.5 - - - +
167B ARG* 1.3 57.8 + - - +
169B LEU* 4.8 1.6 - - - -
170B THR* 2.7 35.7 + - - -
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Residues in contact with ARG 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B MET* 4.3 21.0 - - + -
101B VAL* 3.6 31.3 - - - +
105B TRP* 3.7 26.9 - - + +
132B MET* 5.9 0.8 - - - +
134B PHE* 4.9 5.7 - - + -
163B CYS 3.1 18.7 + - - +
164B VAL* 3.6 6.7 - - - +
165B LYS 3.1 0.2 - - - -
166B LEU* 1.3 77.9 - - - +
168B ALA* 1.3 62.2 + - - +
170B THR* 4.0 3.1 - - - -
171B ASP* 3.0 43.3 + - - +
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Residues in contact with ALA 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B VAL* 3.1 17.4 + - + +
165B LYS* 3.7 5.2 - - - +
167B ARG* 1.3 78.6 - - - +
169B LEU* 1.3 57.4 + - - +
171B ASP* 3.2 8.3 + - - +
172B SER* 3.0 30.9 + - - -
198B VAL* 4.1 23.1 - - + -
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A PHE* 3.8 27.0 - - + -
192A ILE* 4.4 8.1 - - + -
195A VAL* 3.3 37.9 - - + +
196A MET* 3.7 23.1 - - + -
165B LYS* 2.8 30.4 + - + +
166B LEU 4.2 2.0 - - - +
168B ALA* 1.3 72.1 - - - +
170B THR* 1.3 56.6 + - - +
172B SER* 3.3 5.1 + - - -
173B PHE* 3.0 28.4 + - - +
194B CYS* 4.7 4.9 - - - +
195B VAL* 4.6 15.0 - - + -
198B VAL* 3.9 25.1 - - + -
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Residues in contact with THR 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A TYR* 2.7 40.3 + - + +
192A ILE* 4.1 4.2 - - - +
134B PHE* 3.6 14.7 - - + -
166B LEU* 2.7 23.6 + - - -
167B ARG* 4.1 4.0 - - - -
169B LEU* 1.3 73.5 - - - +
171B ASP* 1.3 67.5 + - - +
173B PHE* 3.4 0.7 + - - +
174B ARG* 3.1 54.6 + - + +
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Residues in contact with ASP 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B ARG* 3.0 40.9 + - - +
168B ALA* 3.2 7.0 + - - +
170B THR* 1.3 80.7 - - - +
172B SER* 1.3 57.6 + - - +
174B ARG* 4.1 7.5 - - - +
175B ARG* 3.0 32.5 + - - +
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Residues in contact with SER 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A PHE* 5.4 0.2 - - - -
168B ALA 3.0 13.7 + - - -
169B LEU* 3.6 10.3 - - - +
170B THR 3.2 0.2 - - - -
171B ASP* 1.3 75.5 - - - +
173B PHE* 1.3 64.7 + - - +
175B ARG* 3.5 12.7 + - - +
176B ARG* 2.9 35.1 + - - +
186B PHE* 5.4 0.4 - - - -
194B CYS* 3.5 33.9 + - - -
198B VAL* 5.9 1.4 - - - +
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Residues in contact with PHE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A PHE* 3.3 22.2 - - + -
187A PRO 4.1 0.7 - - - -
188A TYR* 3.4 44.0 - + + -
191A PHE* 4.0 30.7 - + + -
169B LEU 3.0 16.3 + - - +
170B THR 3.9 3.8 - - - +
171B ASP 3.3 0.2 - - - -
172B SER* 1.3 73.8 - - - +
174B ARG* 1.3 75.6 + - + +
176B ARG* 2.9 13.7 + - - -
177B ASP* 3.2 14.1 + - - -
182B GLY* 3.1 37.5 - - - -
184B VAL* 3.4 36.1 - - + +
186B PHE* 4.5 7.2 - + - -
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Residues in contact with ARG 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A TYR* 5.7 3.4 + - + -
134B PHE* 6.0 2.8 - - - -
170B THR* 3.1 39.8 + - + +
171B ASP* 4.1 7.8 + - - +
173B PHE* 1.3 86.4 - - + +
175B ARG* 1.3 63.3 + - - +
177B ASP* 2.9 23.3 + - - +
180B GLN* 4.8 3.1 - - - +
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Residues in contact with ARG 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B ASP 3.0 20.1 + - - +
172B SER* 3.5 11.7 + - - +
173B PHE 3.2 0.2 - - - -
174B ARG* 1.3 76.7 - - - +
176B ARG* 1.3 102.2 + - - +
177B ASP 3.9 0.3 + - - -
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Residues in contact with ARG 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B SER* 2.9 36.0 + - - +
173B PHE 2.9 8.7 + - - +
175B ARG* 1.3 118.2 - - - +
177B ASP* 1.3 57.6 + - - +
178B THR* 2.8 18.9 + - - -
184B VAL* 3.6 22.4 - - + +
185B ASN 5.4 1.6 + - - -
186B PHE* 3.3 30.5 - - - -
190B ASP* 2.8 39.0 + - - -
193B GLN* 6.1 0.4 - - - +
194B CYS* 3.6 21.1 - - - +
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Residues in contact with ASP 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B PHE* 3.2 8.9 + - + +
174B ARG* 2.9 19.1 + - - +
175B ARG 3.6 0.4 - - - -
176B ARG* 1.3 72.5 - - - +
178B THR* 1.3 60.6 + - - +
179B ALA* 3.8 1.7 + - - -
180B GLN* 2.7 51.9 + - - +
181B GLN 3.5 5.4 + - - -
182B GLY* 2.7 33.8 + - - -
183B VAL 3.2 20.1 - - - +
184B VAL* 3.9 11.2 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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