Contacts of the helix formed by residues 165 - 192 (chain B) in PDB entry 3H8E
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 GLY 165 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B HIS* 3.5 33.6 + - - -
161B ALA* 4.7 0.4 - - - -
162B ASP* 3.1 15.0 + - - -
164B ALA* 1.3 77.2 - - - +
166B GLN* 1.3 64.0 + - - +
167B ALA 3.3 2.0 - - - -
168B GLU* 3.1 9.4 + - - +
169B VAL* 2.9 26.3 + - - +
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Residues in contact with GLN 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 3.4 42.2 + - + -
6B LYS* 4.1 3.8 - - - +
7B SER* 3.3 26.3 - - - +
161B ALA* 4.7 2.0 - - + -
162B ASP 3.3 9.0 + - - +
163B LYS* 3.3 18.6 + - - +
164B ALA 3.4 0.2 - - - -
165B GLY* 1.3 76.3 - - - +
167B ALA* 1.3 63.1 + - - +
169B VAL* 3.3 4.5 + - - +
170B GLU* 2.9 45.3 + - - +
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Residues in contact with ALA 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LYS 4.8 0.6 + - - -
164B ALA 4.9 2.8 + - - +
165B GLY 3.3 0.8 + - - -
166B GLN* 1.3 80.1 - - - +
168B GLU* 1.3 64.9 + - + +
170B GLU* 3.3 13.7 + - - +
171B ARG* 2.9 27.7 + - - +
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Residues in contact with GLU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ASP* 5.9 0.7 - - - +
123B HIS* 3.6 26.6 - - + +
124B TYR* 3.7 14.5 - - + +
164B ALA 5.4 2.7 - - - +
165B GLY* 3.1 7.9 + - - +
167B ALA* 1.3 80.2 - - + +
169B VAL* 1.3 62.0 + - - +
171B ARG* 3.3 40.0 + - - +
172B ALA* 2.9 27.0 + - - +
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 3.6 27.8 - - + -
123B HIS* 3.5 26.9 - - + +
127B TYR* 3.7 31.9 - - + -
159B LEU* 4.1 13.7 - - + -
161B ALA* 3.9 20.2 - - + -
165B GLY 2.9 15.5 + - - +
166B GLN 3.8 6.1 - - - +
168B GLU* 1.3 76.5 - - - +
170B GLU* 1.3 55.5 + - - +
172B ALA* 3.2 3.2 + - - +
173B VAL* 2.9 26.9 + - - +
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Residues in contact with GLU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 3.7 31.3 + - + +
166B GLN* 2.9 44.3 + - - +
167B ALA* 3.6 11.9 - - - +
169B VAL* 1.3 74.7 - - - +
171B ARG* 1.3 59.6 - - - +
173B VAL* 3.3 5.0 + - - +
174B LYS* 2.9 27.4 + - - +
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Residues in contact with ARG 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B TYR* 3.5 34.3 + - - +
167B ALA 2.9 15.8 + - - +
168B GLU* 3.3 33.0 + - - +
170B GLU* 1.3 76.8 - - - +
172B ALA* 1.3 62.3 + - - +
174B LYS* 3.3 10.3 + - + +
175B HIS* 3.0 48.5 + - + +
497B ALA 3.0 28.1 + - - -
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Residues in contact with ALA 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B TYR* 3.4 39.8 - - + +
127B TYR* 3.8 10.5 - - + -
128B ARG* 3.5 18.8 - - - +
168B GLU 2.9 14.1 + - - +
169B VAL 3.2 7.6 + - - +
171B ARG* 1.3 75.7 - - - +
173B VAL* 1.3 56.8 + - - +
175B HIS 3.4 0.2 + - - -
176B ALA* 2.8 33.5 + - - +
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Residues in contact with VAL 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 2.9 56.1 - - + +
5B VAL* 4.1 10.8 - - + -
127B TYR* 5.4 0.7 - - + -
131B ALA* 4.3 6.7 - - + -
159B LEU* 3.8 23.3 - - + -
169B VAL* 2.9 23.9 + - + +
170B GLU* 3.7 7.2 - - - +
172B ALA* 1.3 72.9 - - + +
174B LYS* 1.4 57.3 + - - +
177B SER* 2.8 40.6 + - - +
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Residues in contact with LYS 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B GLU 2.9 14.3 + - - +
171B ARG* 3.3 15.0 + - + +
173B VAL* 1.4 77.5 - - - +
175B HIS* 1.3 73.7 + - + +
177B SER* 3.4 4.8 + - - -
178B ALA* 3.2 22.9 + - - +
306B GLU* 4.9 9.7 + - - +
307B LEU* 4.0 29.8 + - + +
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Residues in contact with HIS 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B TYR* 2.5 27.8 + - - +
128B ARG* 3.7 17.7 - - - +
171B ARG* 3.0 30.7 + - + +
174B LYS* 1.3 83.5 - - + +
176B ALA* 1.4 66.9 + - - +
178B ALA* 3.3 3.5 + - - +
179B ILE* 3.0 29.1 + - - +
307B LEU* 3.8 24.7 - - + +
492B LEU* 3.8 31.4 - - + +
497B ALA* 3.6 26.0 + - - +
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ARG* 3.8 13.3 - - - +
131B ALA* 3.4 30.1 - - + -
132B GLU* 3.5 18.2 - - - +
135B LEU* 4.3 1.3 - - - +
172B ALA 2.8 23.9 + - - +
173B VAL 4.0 0.7 - - - +
175B HIS* 1.4 74.1 - - - +
177B SER* 1.3 56.9 + - - +
179B ILE* 3.7 8.8 - - - +
180B ALA* 2.7 32.1 + - - +
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Residues in contact with SER 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 4.3 1.7 - - - +
135B LEU* 3.2 24.9 - - - +
173B VAL* 2.8 34.0 + - - +
174B LYS* 3.8 5.8 - - - -
175B HIS 3.2 0.2 - - - -
176B ALA* 1.3 77.2 - - - +
178B ALA* 1.3 58.5 + - - +
180B ALA* 3.8 0.9 - - - +
181B THR* 2.9 35.3 + - - -
306B GLU* 3.9 10.3 - - - -
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Residues in contact with ALA 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LYS 3.2 7.0 + - - +
175B HIS 3.7 6.3 - - - +
177B SER* 1.3 76.7 - - - +
179B ILE* 1.3 57.3 + - + +
181B THR 3.3 0.5 + - - -
182B GLY 2.9 24.9 + - - -
303B ALA* 3.4 22.5 - - + +
306B GLU* 2.7 27.5 + - - +
307B LEU* 3.5 37.9 - - + -
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Residues in contact with ILE 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ARG* 3.5 35.4 - - - +
132B GLU* 3.3 30.5 - - - +
175B HIS* 3.0 24.5 + - + +
176B ALA* 3.7 6.3 - - - +
178B ALA* 1.3 75.9 - - - +
180B ALA* 1.4 57.8 + - - +
182B GLY* 3.2 2.4 + - - -
183B MET* 2.7 36.5 + - + +
303B ALA* 4.4 4.5 - - - -
484B VAL* 3.8 3.5 - - + +
485B PRO* 3.8 27.1 - - + +
488B THR* 3.7 33.2 - - + -
489B GLN 5.2 0.7 - - - +
492B LEU* 5.0 2.9 - - + -
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Residues in contact with ALA 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLU* 4.7 5.8 - - + +
135B LEU* 3.6 30.5 - - + -
136B ASP* 4.0 18.3 - - + +
176B ALA 2.7 22.0 + - - +
177B SER 4.0 2.7 - - - +
179B ILE* 1.4 74.4 - - - +
181B THR* 1.3 56.0 + - - +
183B MET* 3.3 11.7 + - - +
184B ALA* 2.9 28.4 + - - +
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Residues in contact with THR 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B SER* 2.9 19.6 + - - -
180B ALA* 1.3 74.4 - - - +
182B GLY* 1.3 64.1 + - - +
184B ALA* 3.3 14.6 + - - +
185B PHE* 3.3 13.3 + - - +
302B ARG* 3.6 27.5 + - + +
306B GLU* 3.7 19.8 + - + +
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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
----------------------------------------------------------
178B ALA 2.9 15.0 + - - -
179B ILE 3.6 3.1 - - - -
181B THR* 1.3 76.9 - - - +
183B MET* 1.3 61.6 + - - +
185B PHE* 3.2 2.8 + - - +
186B THR* 3.0 24.7 + - - -
299B GLY* 3.2 34.3 - - - -
302B ARG* 4.2 8.9 - - - +
484B VAL* 4.3 2.5 - - - -
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Residues in contact with MET 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLU* 3.3 32.5 - - + +
136B ASP* 3.7 31.2 - - - +
179B ILE* 2.7 27.8 + - - +
180B ALA* 3.6 6.5 - - - +
181B THR 3.3 0.2 - - - -
182B GLY* 1.3 72.7 - - - +
184B ALA* 1.3 58.6 + - - +
186B THR* 3.3 2.2 + - - -
187B ARG* 2.8 35.9 + - - +
481B GLY* 2.9 48.2 - - - +
482B ARG* 5.2 0.4 - - - -
484B VAL* 3.7 14.6 - - + +
485B PRO* 3.7 9.0 - - + -
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Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ASP* 5.1 1.1 + - - +
139B TYR* 3.7 24.6 - - + -
180B ALA 2.9 17.0 + - - +
181B THR* 3.6 8.7 - - - +
182B GLY 3.3 0.4 - - - -
183B MET* 1.3 76.5 - - - +
185B PHE* 1.3 55.5 + - - +
187B ARG* 3.4 1.1 + - - +
188B ASP* 2.9 38.5 + - - +
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Residues in contact with PHE 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B THR 3.3 8.3 + - - +
182B GLY 3.2 7.8 + - - +
184B ALA* 1.3 75.2 - - - +
186B THR* 1.3 64.4 + - - +
188B ASP* 3.3 8.8 + - + +
189B LEU* 3.1 40.5 + - + +
205B GLN* 4.0 25.8 - - + -
209B LEU* 4.9 8.1 - - + -
298B PHE* 2.5 77.6 - + + -
299B GLY* 3.6 4.3 - - - -
302B ARG* 3.3 47.3 - - + +
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Residues in contact with THR 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B GLY 3.0 13.0 + - - -
183B MET* 3.5 8.1 - - - -
185B PHE* 1.3 76.6 - - - +
187B ARG* 1.4 59.2 + - - +
189B LEU* 3.3 1.3 + - - -
190B GLY* 2.9 25.1 + - - -
292B CYS* 4.7 6.6 - - + +
295B ALA* 2.8 39.5 + - + +
296B SER* 3.8 17.7 - - - +
299B GLY* 3.3 8.7 - - - -
479B ALA* 4.7 2.0 - - + +
480B THR 4.2 14.8 - - - +
481B GLY* 5.2 2.0 - - - -
483B PRO* 5.4 2.0 - - + -
484B VAL* 3.4 15.2 - - + +
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Residues in contact with ARG 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ASP* 2.8 50.1 + - - -
139B TYR* 3.3 59.3 + - + +
183B MET 2.8 25.4 + - - +
186B THR* 1.4 71.7 - - - +
188B ASP* 1.3 61.6 + - - +
190B GLY* 3.3 0.5 + - - -
191B ASN* 2.8 36.4 + - - +
479B ALA* 3.2 29.5 + - + +
480B THR* 3.4 29.2 - - - +
481B GLY* 4.1 2.0 - - - +
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Residues in contact with ASP 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TYR* 2.6 35.4 + - - -
140B VAL 4.7 2.3 - - - +
141B PHE* 3.6 12.4 - - - -
143B ARG* 3.4 26.6 + - - +
184B ALA* 2.9 21.8 + - - +
185B PHE* 3.6 8.3 - - + +
187B ARG* 1.3 77.9 - - - +
189B LEU* 1.4 64.5 + - + +
192B LEU* 3.0 31.5 + - + +
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Residues in contact with LEU 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B PHE* 3.1 50.3 + - + +
186B THR 3.8 3.6 - - - +
188B ASP* 1.4 81.9 - - + +
190B GLY* 1.3 64.2 + - - +
192B LEU* 3.5 13.8 + - + +
197B CYS* 3.7 19.3 - - - -
201B PHE* 3.9 27.8 - - + -
202B LEU* 4.1 10.1 - - + -
205B GLN* 4.1 18.2 - - + +
291B MET* 4.4 10.6 - - + +
295B ALA* 4.1 15.3 - - + -
298B PHE* 3.5 23.8 - - + -
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Residues in contact with GLY 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B THR 2.9 15.0 + - - -
187B ARG 3.8 1.6 - - - -
189B LEU* 1.3 79.1 - - - +
191B ASN* 1.3 65.2 + - - +
192B LEU 3.4 6.4 + - - +
291B MET* 5.3 7.1 - - - +
292B CYS* 4.3 22.8 - - - -
295B ALA* 4.5 2.6 - - - +
479B ALA* 4.5 5.4 - - - -
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Residues in contact with ASN 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TYR* 3.1 28.5 + - - -
141B PHE* 3.7 34.6 - - + +
144B PHE* 5.3 0.2 - - - -
187B ARG* 2.8 27.2 + - - +
190B GLY* 1.3 73.7 - - - +
192B LEU* 1.4 64.8 + - - +
193B PRO* 3.4 3.3 - - - +
478B GLY* 3.5 10.4 - - - -
479B ALA* 3.0 29.8 + - - +
----------------------------------------------------------
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Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B PHE* 3.8 9.2 - - + -
143B ARG* 3.7 27.1 - - - +
144B PHE* 3.9 23.6 - - + -
188B ASP* 3.0 26.4 + - + +
189B LEU* 3.7 15.0 - - + +
190B GLY 3.3 8.8 - - - +
191B ASN* 1.4 77.5 - - - +
193B PRO* 1.3 74.8 - - + +
194B PRO* 3.8 1.6 - - - +
196B LEU* 4.9 6.5 - - + -
197B CYS* 3.7 17.7 - - + +
201B PHE* 3.6 38.6 - - + -
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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