Contacts of the helix formed by residues 171 - 196 (chain l) in PDB entry 6QXT
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 171 (chain l).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169l SER* 3.6 9.6 + - - +
170l ASP* 1.3 75.9 - - - +
172l ASP* 1.3 61.6 + - - +
173l ILE* 3.1 11.2 - - + +
174l ASN* 3.1 7.6 + - + +
175l ALA* 3.0 27.7 + - - +
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Residues in contact with ASP 172 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171l ASN* 1.3 73.4 - - - +
173l ILE* 1.3 57.9 + - - +
175l ALA* 3.9 8.1 - - - +
176l ALA* 2.9 29.5 + - - +
234l ARG 6.0 1.6 - - - +
236l ASN 5.2 6.1 - - - +
237l ASN* 5.6 0.4 - - - -
238l PHE* 4.2 31.4 - - + +
241l ILE* 5.5 0.5 - - - +
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Residues in contact with ILE 173 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161l PHE* 5.8 8.3 - - + -
171l ASN* 3.1 7.9 - - + +
172l ASP* 1.3 76.8 - - - +
174l ASN* 1.3 60.6 + - - +
176l ALA* 3.3 5.9 + - - +
177l LEU* 2.9 28.4 + - - +
230l VAL* 5.4 8.1 - - + +
234l ARG* 5.6 14.4 - - + +
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Residues in contact with ASN 174 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166l THR 5.0 5.4 - - - +
167l ARG* 4.3 14.1 - - - +
169l SER 3.6 23.8 - - - +
170l ASP* 5.2 0.4 - - - -
171l ASN* 3.1 12.7 + - + +
173l ILE* 1.3 76.2 - - - +
175l ALA* 1.3 60.2 + - - +
177l LEU* 3.2 8.2 + - - +
178l ASP* 2.9 28.8 + - - +
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Residues in contact with ALA 175 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171l ASN 3.0 15.9 + - - +
172l ASP* 4.0 7.2 - - - +
174l ASN* 1.3 76.3 - - - +
176l ALA* 1.3 57.9 + - - +
178l ASP* 3.4 7.2 + - - +
179l TYR* 2.9 28.1 + - - +
238l PHE* 5.8 5.4 - - + -
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Residues in contact with ALA 176 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172l ASP 2.9 20.5 + - - +
173l ILE* 3.6 7.6 - - - +
174l ASN 3.2 0.2 - - - -
175l ALA* 1.3 74.2 - - - +
177l LEU* 1.3 60.1 + - - +
179l TYR* 3.2 7.1 + - - +
180l GLY* 2.9 26.0 + - - -
226l ILE* 6.1 0.2 - - - +
230l VAL* 5.0 13.7 - - + -
238l PHE* 6.0 1.9 - - + +
241l ILE* 4.2 24.7 - - + -
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Residues in contact with LEU 177 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173l ILE 2.9 14.5 + - - +
174l ASN* 3.5 10.8 - - - +
176l ALA* 1.3 77.4 - - - +
178l ASP* 1.3 58.1 + - - +
180l GLY* 3.5 1.4 + - - +
181l TYR* 2.9 30.4 + - - +
226l ILE* 5.8 4.3 - - - +
230l VAL* 5.5 4.2 - - - +
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Residues in contact with ASP 178 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174l ASN 2.9 16.7 + - - +
175l ALA* 3.8 7.6 - - - +
177l LEU* 1.3 76.5 - - - +
179l TYR* 1.3 56.9 + - - +
181l TYR* 3.8 6.4 - - - +
182l THR* 2.9 28.1 + - - -
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Residues in contact with TYR 179 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175l ALA 2.9 17.4 + - - +
176l ALA* 3.2 10.0 + - - +
178l ASP* 1.3 75.2 - - - +
180l GLY* 1.3 61.7 + - - +
182l THR* 3.0 8.8 + - - -
183l LEU* 2.9 27.0 + - - +
242l LYS* 6.1 6.1 - - + -
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Residues in contact with GLY 180 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176l ALA 2.9 15.0 + - - -
177l LEU 3.9 0.9 - - - -
179l TYR* 1.3 75.0 - - - +
181l TYR* 1.3 57.7 + - - +
183l LEU* 3.2 7.4 + - - +
184l LEU* 2.9 30.7 + - - +
226l ILE* 4.7 20.3 - - - +
245l LEU* 5.3 12.4 - - - +
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Residues in contact with TYR 181 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177l LEU 2.9 18.8 + - - +
178l ASP* 3.9 7.2 - - - +
180l GLY* 1.3 75.3 - - - +
182l THR* 1.3 56.9 + - - +
184l LEU* 4.3 5.7 - - - +
185l LEU* 2.9 29.1 + - - +
226l ILE* 5.4 1.2 - - - +
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Residues in contact with THR 182 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178l ASP 2.9 19.3 + - - -
179l TYR* 3.0 9.8 + - - -
181l TYR* 1.3 76.7 - - - +
183l LEU* 1.3 59.5 + - - +
185l LEU* 3.7 5.5 - - - +
186l SER* 2.9 27.5 + - - -
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Residues in contact with LEU 183 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179l TYR 2.9 12.2 + - - +
180l GLY* 3.7 9.2 - - - +
182l THR* 1.3 74.1 - - - +
184l LEU* 1.3 60.5 + - - +
186l SER* 3.0 8.8 + - - -
187l MET* 2.9 27.8 + - - +
245l LEU 6.0 1.3 - - - +
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Residues in contact with LEU 184 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180l GLY 2.9 17.2 + - - +
181l TYR* 4.3 6.1 - - - +
183l LEU* 1.3 76.5 - - - +
185l LEU* 1.3 57.8 + - - +
187l MET* 3.9 6.6 - - - +
188l PHE* 2.9 33.5 + - - +
219l MET* 4.3 17.2 - - + +
222l PHE* 6.0 7.6 - - + +
223l ARG* 6.4 1.8 - - - -
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Residues in contact with LEU 185 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181l TYR 2.9 22.3 + - - +
182l THR* 3.7 7.0 - - - +
184l LEU* 1.3 76.6 - - - +
186l SER* 1.3 57.8 + - - +
188l PHE* 4.8 2.9 - - - -
189l ALA* 2.8 33.9 + - - +
212l PHE* 5.7 9.4 - - + +
215l ALA* 4.5 4.8 - - + +
216l SER* 5.7 9.2 - - - +
219l MET* 5.0 5.3 - - + +
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Residues in contact with SER 186 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71l LYS 4.1 20.2 - - - -
72l ARG* 4.6 17.3 - - - +
73l LEU* 4.8 9.2 - - - +
182l THR 2.9 14.3 + - - -
183l LEU* 3.0 11.9 + - - -
185l LEU* 1.3 75.4 - - - +
187l MET* 1.3 60.2 + - - +
189l ALA* 3.9 3.2 - - - +
190l ARG* 2.9 29.8 + - - +
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Residues in contact with MET 187 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183l LEU 2.9 14.2 + - - +
184l LEU* 3.9 6.3 - - - +
186l SER* 1.3 76.8 - - - +
188l PHE* 1.3 57.9 + - - +
190l ARG* 3.1 8.2 + - - +
191l GLU* 2.9 27.1 + - - +
263l SER* 6.4 1.8 - - - -
266l VAL* 5.4 10.3 - - + -
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Residues in contact with PHE 188 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184l LEU 2.9 18.3 + - - +
185l LEU* 4.5 0.7 - - - +
187l MET* 1.3 76.9 - - - +
189l ALA* 1.3 57.7 + - - +
191l GLU* 3.2 8.8 + - - +
192l VAL* 2.9 28.2 + - - +
215l ALA* 3.9 25.5 - - + +
218l ILE* 5.1 5.6 - - + -
219l MET* 4.1 14.1 - - + +
266l VAL* 5.5 8.0 - - + +
270l THR* 5.6 0.7 - - - -
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Residues in contact with ALA 189 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73l LEU* 5.8 7.9 - - + -
74l PRO* 5.3 3.9 - - - +
185l LEU 2.8 24.1 + - - +
186l SER* 3.9 5.2 - - - +
188l PHE* 1.3 76.1 - - - +
190l ARG* 1.3 58.2 + - - +
192l VAL* 3.4 4.1 + - - +
193l VAL* 2.9 28.9 + - - +
199l THR* 6.0 5.4 - - - -
212l PHE* 5.6 6.1 - - + -
215l ALA* 3.6 18.0 - - + +
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Residues in contact with ARG 190 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72l ARG 4.9 9.9 - - - +
74l PRO* 5.3 6.9 - - + -
186l SER 2.9 19.3 + - - +
187l MET* 3.1 7.4 + - - +
189l ALA* 1.3 76.5 - - - +
191l GLU* 1.3 56.5 + - - +
193l VAL* 3.3 7.7 + - - +
194l VAL* 2.9 27.4 + - - +
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Residues in contact with GLU 191 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187l MET 2.9 13.3 + - - +
188l PHE* 3.2 11.4 + - - +
190l ARG* 1.3 75.0 - - - +
192l VAL* 1.3 60.8 + - - +
194l VAL* 3.1 9.9 + - - +
195l CYS* 2.9 26.9 + - - +
266l VAL* 4.4 11.2 - - + +
267l SER* 4.8 8.5 - - - -
270l THR* 3.9 25.1 - - - -
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Residues in contact with VAL 192 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188l PHE 2.9 16.1 + - - +
189l ALA* 3.8 7.4 - - - +
190l ARG 3.3 0.2 - - - -
191l GLU* 1.3 75.3 - - - +
193l VAL* 1.3 61.8 + - - +
195l CYS* 3.2 10.3 + - - +
196l GLY 3.0 16.5 + - - -
197l CYS* 3.6 20.3 + - + +
199l THR* 5.2 10.5 - - - -
214l LEU* 5.6 4.3 - - + -
215l ALA* 4.8 12.6 - - + +
270l THR* 5.1 3.3 - - - -
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Residues in contact with VAL 193 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74l PRO* 4.0 24.7 - - + -
189l ALA 2.9 17.0 + - - +
190l ARG* 3.7 5.4 - - - +
191l GLU 3.2 0.2 - - - -
192l VAL* 1.3 76.9 - - - +
194l VAL* 1.3 62.7 + - - +
196l GLY* 3.2 14.1 + - - +
197l CYS 5.0 3.1 - - - -
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Residues in contact with VAL 194 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87l SER* 5.8 1.6 - - - -
190l ARG 2.9 13.8 + - - +
191l GLU* 3.1 12.5 + - - +
193l VAL* 1.3 78.8 - - - +
195l CYS* 1.3 60.3 + - - +
196l GLY* 3.4 1.0 + - - -
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Residues in contact with CYS 195 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87l SER* 4.5 9.1 - - - -
90l GLN* 5.1 7.1 - - - +
191l GLU 2.9 13.1 + - - +
192l VAL* 3.2 12.3 + - - +
194l VAL* 1.3 76.1 - - - +
196l GLY* 1.3 56.3 + - - +
197l CYS* 3.3 12.1 + - + +
270l THR* 5.5 5.2 - - - +
271l LYS* 6.1 1.8 - - - -
274l ILE* 4.5 21.5 - - + -
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Residues in contact with GLY 196 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87l SER* 4.2 23.1 - - - +
90l GLN* 6.3 0.7 - - - -
91l ILE* 4.6 11.1 - - - +
192l VAL 3.0 5.3 + - - -
193l VAL* 3.2 14.7 + - - -
194l VAL 3.2 0.8 - - - -
195l CYS* 1.3 77.2 - - - +
197l CYS* 1.3 64.6 + - - +
198l MET* 3.6 1.7 + - - -
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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) + - + + + + + -
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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