Contacts of the helix formed by residues 172 - 198 (chain B) in PDB entry 3REO
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 172 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B VAL* 4.1 7.8 - - - +
168B TYR* 2.9 49.7 + - + +
169B HIS 3.4 9.7 - - - +
171B THR* 1.3 77.9 - - - +
173B HIS* 1.3 58.3 + - - +
174B ARG* 3.3 15.8 + - - +
175B ILE* 3.1 28.1 + - + +
176B ASN 3.0 23.2 + - - -
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Residues in contact with HIS 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B HIS 5.0 0.7 - - - -
170B GLY 4.4 12.6 + - - -
171B THR* 3.9 19.6 + - - -
172B ASP* 1.3 71.3 + - - +
174B ARG* 1.3 64.0 + - - +
176B ASN* 3.5 11.8 + - - +
177B LYS* 3.2 22.7 + - - +
241B ASP* 5.2 1.0 - - - +
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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
----------------------------------------------------------
136B ASP* 2.8 42.4 + - - -
137B LYS* 5.7 1.8 - - - +
138B VAL* 3.8 18.0 - - - +
172B ASP* 3.3 11.0 + - - +
173B HIS* 1.3 78.3 - - - +
175B ILE* 1.3 66.5 + - - +
177B LYS* 3.2 20.4 + - - +
178B VAL* 3.0 42.1 + - + +
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Residues in contact with ILE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 5.5 2.7 - - + +
136B ASP* 3.6 38.8 - - + +
138B VAL* 4.2 17.0 - - + -
139B LEU* 5.3 8.3 - - + -
168B TYR* 3.8 11.9 - - + -
169B HIS* 3.8 23.1 - - + +
172B ASP* 3.1 35.1 + - + +
174B ARG* 1.3 80.7 - - - +
176B ASN* 1.3 64.0 + - - +
178B VAL* 4.1 15.3 - - + -
179B PHE* 2.8 33.5 + - + +
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Residues in contact with ASN 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B HIS* 3.3 35.6 + - - +
172B ASP 3.0 11.2 + - - +
173B HIS* 3.6 12.7 + - + +
175B ILE* 1.3 79.1 - - - +
177B LYS* 1.3 55.2 + - - +
179B PHE* 3.5 1.1 + - - +
180B ASN* 2.9 54.3 + - - +
237B HIS* 3.3 41.6 + - - +
238B VAL* 4.0 4.0 - - - +
241B ASP* 3.6 21.4 + - - -
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Residues in contact with LYS 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B HIS 3.2 8.8 + - - +
174B ARG* 3.2 23.3 + - - +
176B ASN* 1.3 74.4 - - - +
178B VAL* 1.3 84.9 + - - +
180B ASN* 3.9 5.0 - - - +
181B LYS* 3.0 42.2 + - + +
241B ASP* 4.5 15.3 - - - +
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Residues in contact with VAL 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PRO* 4.6 2.3 - - - +
132B LEU* 4.6 4.9 - - + -
133B LEU* 3.7 32.2 - - + +
136B ASP* 4.3 6.3 - - - +
174B ARG* 3.0 39.5 + - + +
175B ILE* 3.7 20.6 - - + +
177B LYS* 1.3 94.9 - - - +
179B PHE* 1.3 58.0 + - - +
181B LYS* 3.6 3.8 + - - +
182B GLY* 3.0 26.5 + - - -
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Residues in contact with PHE 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 3.5 25.0 - - + +
139B LEU* 6.0 1.3 - - + -
165B ILE* 5.5 1.6 - - + -
166B PHE* 4.1 11.0 - + - -
169B HIS* 3.3 31.6 - + + +
175B ILE* 2.8 20.2 + - + +
176B ASN 3.8 2.2 - - - +
178B VAL* 1.3 78.4 - - - +
180B ASN* 1.3 72.3 + - - +
182B GLY 3.3 0.5 + - - -
183B MET* 3.0 56.6 + - + +
238B VAL* 6.2 0.2 - - + -
369B EUG 3.8 37.2 - + + -
370B SAH 3.7 35.0 - - - -
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Residues in contact with ASN 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ASN* 2.9 44.2 + - - +
177B LYS* 3.9 5.1 - - - +
179B PHE* 1.3 91.8 - - - +
181B LYS* 1.3 58.6 + - - +
183B MET* 3.5 4.1 + - - +
184B SER* 2.9 30.9 + - - -
213B GLY* 5.3 2.2 - - - -
214B THR* 3.7 25.0 + - + +
238B VAL* 3.8 38.9 - - - +
241B ASP* 4.5 4.8 - - + +
370B SAH 4.8 2.2 + - - -
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Residues in contact with LYS 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PRO* 3.9 28.2 - - + +
132B LEU* 6.3 1.2 - - - +
177B LYS* 3.0 31.5 + - + +
178B VAL* 3.9 4.7 - - - +
180B ASN* 1.3 74.0 - - - +
182B GLY* 1.3 65.1 + - - +
184B SER* 3.6 6.4 - - - -
185B SER* 2.9 34.3 + - - +
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Residues in contact with GLY 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PRO* 3.7 28.6 - - - +
130B PHE* 3.6 15.1 - - - +
133B LEU* 4.4 4.3 - - - -
178B VAL 3.0 16.5 + - - -
179B PHE 3.8 1.1 - - - -
181B LYS* 1.3 75.6 - - - +
183B MET* 1.3 62.2 + - - +
185B SER* 3.7 2.3 - - - -
186B ASN* 3.3 24.1 + - - +
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Residues in contact with MET 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B PHE* 3.7 21.8 - - + -
133B LEU* 3.9 16.4 - - + -
179B PHE* 3.0 41.5 + - + +
180B ASN* 3.9 4.0 - - - +
182B GLY* 1.3 75.5 - - - +
184B SER* 1.3 58.9 + - - +
186B ASN* 3.5 4.5 + - - +
187B SER* 2.9 34.1 + - - -
269B TRP* 4.3 11.7 - - - -
369B EUG 3.3 38.4 - - + -
370B SAH 3.9 40.2 - - + +
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Residues in contact with SER 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ASN 2.9 19.3 + - - -
181B LYS* 3.6 9.2 - - - -
183B MET* 1.3 77.5 - - - +
185B SER* 1.3 52.4 + - - +
187B SER* 3.8 4.0 - - - -
188B THR* 2.7 42.8 + - - -
214B THR* 4.0 14.4 + - - +
216B ALA* 3.3 26.4 - - - +
370B SAH 4.9 0.9 - - - -
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Residues in contact with SER 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B VAL* 3.7 12.1 - - - +
126B SER 3.2 23.2 + - - -
127B LEU* 5.0 0.9 - - - -
129B PRO* 3.4 23.4 - - - +
130B PHE 4.8 2.0 - - - -
181B LYS* 2.9 20.1 + - - +
182B GLY* 3.7 4.9 - - - -
184B SER* 1.3 73.5 - - - +
186B ASN* 1.3 67.1 + - - +
188B THR* 3.2 4.2 + - - -
189B ILE* 3.1 26.0 + - - +
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Residues in contact with ASN 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 3.2 26.5 - - + +
130B PHE* 4.0 15.6 - - + +
182B GLY 3.3 15.2 + - - +
183B MET* 3.8 5.4 + - - +
185B SER* 1.3 79.1 - - - +
187B SER* 1.3 63.1 + - - +
189B ILE* 3.3 3.5 + - - +
190B THR* 3.1 29.2 + - - -
268B LYS* 4.4 5.1 - - - +
269B TRP* 3.2 43.0 - - - -
22D ASN* 5.4 1.7 + - - +
26D MET* 3.5 15.1 - - - +
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Residues in contact with SER 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B MET* 2.9 13.6 + - - -
184B SER* 3.9 4.5 - - - -
186B ASN* 1.3 77.9 + - - +
188B THR* 1.3 57.4 + - - +
190B THR* 4.0 0.3 - - - -
191B MET* 2.9 37.1 + - - +
216B ALA* 5.8 0.9 - - - -
217B VAL* 3.7 22.2 - - - -
268B LYS* 3.2 17.9 + - - +
370B SAH 2.3 39.6 + - - -
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Residues in contact with THR 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B VAL* 4.1 29.1 - - + +
184B SER* 2.7 26.0 + - - -
185B SER 3.2 4.7 + - - -
187B SER* 1.3 73.9 - - - +
189B ILE* 1.3 67.2 + - + +
192B LYS* 3.1 28.5 + - + +
216B ALA* 3.5 19.3 - - - +
217B VAL* 5.7 0.2 - - - -
220B MET* 3.7 26.1 - - + +
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Residues in contact with ILE 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PHE* 3.9 17.7 - - + -
121B ASN* 3.4 29.8 - - - +
125B VAL* 3.8 19.1 - - + +
126B SER* 4.8 5.2 - - - -
127B LEU* 4.1 15.0 - - + -
185B SER 3.1 14.9 + - - +
186B ASN 3.7 6.1 - - - +
188B THR* 1.3 79.6 - - + +
190B THR* 1.3 62.1 + - - +
192B LYS* 3.6 12.0 + - + +
193B LYS* 3.6 7.3 + - - +
357B PHE* 3.7 15.7 - - + -
22D ASN* 3.5 28.3 - - - +
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Residues in contact with THR 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ASN* 3.1 20.5 + - - -
187B SER 4.0 2.2 - - - -
189B ILE* 1.3 76.1 - - - +
191B MET* 1.3 63.0 + - - +
193B LYS* 3.1 6.1 + - - +
194B ILE* 2.9 45.9 + - + +
268B LYS* 4.3 13.7 - - - -
269B TRP* 6.0 1.0 - - - -
356B ALA* 3.8 10.3 - - + +
357B PHE* 3.6 24.6 + - - +
359B THR* 3.8 29.1 + - + +
22D ASN* 5.2 1.2 + - - -
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Residues in contact with MET 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B SER 2.9 24.7 + - - +
190B THR* 1.3 75.1 - - - +
192B LYS* 1.3 63.3 + - - +
194B ILE* 3.8 22.1 - - + +
195B LEU* 2.8 65.7 + - + +
201B PHE* 4.3 13.5 - - + -
217B VAL* 3.2 37.0 - - + +
220B MET* 4.0 16.8 - - + -
221B ILE* 4.5 1.6 - - + -
266B PHE* 3.8 24.5 - - + -
268B LYS* 4.5 7.2 - - + -
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Residues in contact with LYS 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ASN* 4.9 11.8 - - - +
122B GLU* 5.1 10.3 - - - +
123B ASP* 3.3 30.8 + - + +
188B THR* 3.1 21.7 + - + +
189B ILE* 3.7 8.7 - - + +
191B MET* 1.3 79.8 - - - +
193B LYS* 1.3 62.9 + - - +
195B LEU* 3.5 5.0 + - - +
196B GLU* 3.4 39.5 + - - +
220B MET* 3.6 17.2 - - + +
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Residues in contact with LYS 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ILE 3.6 2.0 + - - +
190B THR 3.1 9.0 + - - +
192B LYS* 1.3 77.9 - - - +
194B ILE* 1.3 65.9 + - - +
196B GLU* 3.0 25.5 + - + +
197B MET* 3.6 27.6 + - - +
355B CYS 4.9 1.1 - - - -
356B ALA* 3.7 21.3 - - + +
357B PHE* 3.9 32.5 - - + -
15D HIS* 3.9 44.0 + - + +
18D ASP* 5.6 1.0 - - - +
19D GLU* 2.9 25.3 + - - +
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Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B THR* 2.9 37.3 + - + +
191B MET* 3.8 31.2 - - + +
193B LYS* 1.3 75.9 - - - +
195B LEU* 1.3 58.5 + - + +
197B MET* 3.0 12.1 + - - +
198B TYR* 2.8 53.0 + - + +
201B PHE* 5.2 0.9 - - + -
266B PHE* 5.4 2.0 - - + -
268B LYS* 5.5 0.7 - - - -
299B ALA* 4.8 4.9 - - + -
354B SER* 4.7 2.9 - - - +
356B ALA* 3.7 16.8 - - + +
359B THR* 4.5 9.9 - - + +
361B VAL* 3.7 31.6 - - + -
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Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B MET* 2.8 40.5 + - + +
192B LYS* 3.9 5.4 - - - +
193B LYS 3.2 0.4 - - - -
194B ILE* 1.3 75.9 - - + +
196B GLU* 1.3 57.8 + - + +
197B MET 3.3 0.4 + - - -
198B TYR 4.0 11.4 - - - +
201B PHE* 3.5 39.3 - - + -
220B MET* 3.9 38.6 - - + +
221B ILE* 4.4 4.5 - - + +
224B LYS* 2.7 53.4 + - + -
225B TYR* 4.7 4.0 - - + -
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Residues in contact with GLU 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B LYS* 3.4 36.2 + - - +
193B LYS* 3.0 15.4 + - + +
195B LEU* 1.3 78.4 - - + +
197B MET* 1.3 63.0 + - + +
199B ASN* 5.7 0.3 - - - +
224B LYS* 4.4 6.7 + - - +
15D HIS* 5.6 6.1 - - - -
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Residues in contact with MET 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LYS* 3.9 34.1 - - - +
194B ILE* 3.0 10.2 + - + +
196B GLU* 1.3 84.8 - - + +
198B TYR* 1.3 62.0 + - - +
199B ASN* 3.8 13.1 + - - -
354B SER* 3.6 29.1 + - - +
355B CYS 3.3 28.5 - - - +
356B ALA* 4.5 2.0 - - + -
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Residues in contact with TYR 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ILE* 2.8 26.8 + - + +
195B LEU* 4.0 16.5 - - + +
197B MET* 1.3 77.7 - - - +
199B ASN* 1.3 64.6 + - - +
200B GLY* 3.2 27.7 - - - -
201B PHE* 3.8 37.2 + + - -
224B LYS* 5.3 0.3 - - - -
225B TYR* 4.3 6.9 + - - -
297B ILE* 3.5 25.7 - - + +
351B LYS* 6.2 0.4 - - - -
353B ALA* 3.6 29.4 - - + -
354B SER* 3.8 14.8 - - - +
361B VAL* 3.9 14.6 - - + -
363B GLU* 2.3 35.8 + - - -
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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