Contacts of the helix formed by residues 171 - 196 (chain u) in PDB entry 6QY3
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 u).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169u SER* 3.6 9.8 + - - +
170u ASP* 1.3 76.8 - - - +
172u ASP* 1.3 62.1 + - - +
173u ILE* 3.1 10.1 - - + +
174u ASN* 3.1 7.8 + - + +
175u ALA* 3.0 28.1 + - - +
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Residues in contact with ASP 172 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171u ASN* 1.3 74.0 - - - +
173u ILE* 1.3 58.0 + - - +
175u ALA* 3.9 7.5 - - - +
176u ALA* 2.9 29.1 + - - +
234u ARG 6.0 1.6 - - - +
236u ASN 5.2 6.1 - - - +
237u ASN* 5.2 0.7 - - - -
238u PHE* 4.2 31.7 - - + +
241u ILE* 5.5 0.7 - - - +
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Residues in contact with ILE 173 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161u PHE* 5.8 8.5 - - + -
171u ASN* 3.1 7.8 - - + +
172u ASP* 1.3 76.0 - - - +
174u ASN* 1.3 59.8 + - - +
176u ALA* 3.3 6.3 + - - +
177u LEU* 2.9 27.5 + - - +
230u VAL* 5.4 8.3 - - + +
234u ARG* 5.6 13.9 - - + +
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Residues in contact with ASN 174 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166u THR 5.0 5.8 - - - +
167u ARG* 4.3 14.1 - - - +
169u SER 3.6 23.8 - - - +
170u ASP* 5.2 0.4 - - - -
171u ASN* 3.1 12.3 + - + +
173u ILE* 1.3 78.9 - - - +
175u ALA* 1.3 57.1 + - - +
177u LEU* 3.2 7.5 + - - +
178u ASP* 2.9 28.4 + - - +
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Residues in contact with ALA 175 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171u ASN 3.0 15.7 + - - +
172u ASP* 4.0 8.1 - - - +
174u ASN* 1.3 76.4 - - - +
176u ALA* 1.3 56.3 + - - +
178u ASP* 3.4 7.5 + - - +
179u TYR* 2.9 27.5 + - - +
238u PHE* 5.8 5.4 - - + -
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Residues in contact with ALA 176 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172u ASP 2.9 20.3 + - - +
173u ILE* 3.6 6.7 - - - +
174u ASN 3.2 0.2 - - - -
175u ALA* 1.3 75.0 - - - +
177u LEU* 1.3 59.8 + - - +
179u TYR* 3.2 8.3 + - - +
180u GLY* 2.9 26.0 + - - -
226u ILE* 6.1 0.2 - - - +
230u VAL* 5.0 14.6 - - + -
238u PHE* 6.0 1.7 - - + +
241u ILE* 4.2 25.4 - - + +
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Residues in contact with LEU 177 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173u ILE 2.9 14.3 + - - +
174u ASN* 3.2 10.7 + - - +
176u ALA* 1.3 77.3 - - - +
178u ASP* 1.3 56.3 + - - +
180u GLY* 3.5 0.7 + - - -
181u TYR* 2.9 30.9 + - - +
226u ILE* 5.9 5.1 - - - +
230u VAL* 5.5 6.6 - - + +
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Residues in contact with ASP 178 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174u ASN 2.9 16.2 + - - +
175u ALA* 3.8 7.9 - - - +
177u LEU* 1.3 76.0 - - - +
179u TYR* 1.3 57.9 + - - +
181u TYR* 3.8 6.2 - - - +
182u THR* 2.9 28.2 + - - -
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Residues in contact with TYR 179 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175u ALA 2.9 17.9 + - - +
176u ALA* 3.2 9.2 + - - +
178u ASP* 1.3 74.8 - - - +
180u GLY* 1.3 60.9 + - - +
182u THR* 3.0 8.1 + - - -
183u LEU* 2.9 26.9 + - - +
242u LYS* 6.1 6.5 - - + -
245u LEU* 6.1 4.3 - - + -
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Residues in contact with GLY 180 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176u ALA 2.9 14.6 + - - -
177u LEU* 3.9 1.1 - - - -
179u TYR* 1.3 75.6 - - - +
181u TYR* 1.3 56.4 + - - +
183u LEU* 3.3 7.2 + - - +
184u LEU* 2.9 31.5 + - - +
226u ILE* 4.7 20.1 - - - +
245u LEU* 5.4 12.0 - - - +
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Residues in contact with TYR 181 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177u LEU 2.9 19.0 + - - +
178u ASP* 3.9 7.4 - - - +
180u GLY* 1.3 75.5 - - - +
182u THR* 1.3 57.2 + - - +
184u LEU* 4.3 5.3 - - - +
185u LEU* 2.9 30.0 + - - +
226u ILE* 5.4 0.6 - - - +
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Residues in contact with THR 182 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178u ASP 2.9 19.3 + - - -
179u TYR* 3.0 8.7 + - - -
181u TYR* 1.3 76.1 - - - +
183u LEU* 1.3 60.6 + - - +
185u LEU* 3.5 5.7 + - - +
186u SER* 2.9 27.5 + - - -
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Residues in contact with LEU 183 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179u TYR 2.9 11.8 + - - +
180u GLY* 3.7 9.2 - - - +
182u THR* 1.3 74.4 - - - +
184u LEU* 1.3 61.1 + - - +
186u SER* 3.0 9.5 + - - -
187u MET* 2.9 27.4 + - - +
245u LEU 6.1 1.1 - - - +
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Residues in contact with LEU 184 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180u GLY 2.9 18.4 + - - +
181u TYR* 4.3 5.6 - - - +
183u LEU* 1.3 75.9 - - - +
185u LEU* 1.3 57.9 + - - +
187u MET* 3.9 5.6 - - - +
188u PHE* 2.9 33.1 + - - +
219u MET* 4.3 17.2 - - + +
222u PHE* 6.0 7.6 - - + +
223u ARG* 6.4 1.6 - - - -
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Residues in contact with LEU 185 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181u TYR 2.9 22.5 + - - +
182u THR* 3.7 7.2 - - - +
184u LEU* 1.3 77.3 - - - +
186u SER* 1.3 57.4 + - - +
188u PHE* 4.8 3.1 - - - -
189u ALA* 2.8 33.4 + - - +
212u PHE* 5.7 9.1 - - + +
215u ALA* 4.5 4.4 - - + +
216u SER* 5.7 9.4 - - - +
219u MET* 5.0 5.3 - - + +
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Residues in contact with SER 186 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71u LYS 4.1 19.7 - - - -
72u ARG* 4.5 18.0 - - - +
73u LEU* 4.8 8.8 - - - +
182u THR 2.9 15.2 + - - -
183u LEU* 3.0 11.8 + - - -
185u LEU* 1.3 75.4 - - - +
187u MET* 1.3 59.8 + - - +
189u ALA* 3.8 4.2 - - - +
190u ARG* 2.9 30.3 + - - +
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Residues in contact with MET 187 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183u LEU 2.9 14.0 + - - +
184u LEU* 3.9 7.0 - - - +
186u SER* 1.3 76.6 - - - +
188u PHE* 1.3 57.2 + - - +
190u ARG* 3.1 7.8 + - - +
191u GLU* 2.9 26.7 + - - +
263u SER* 6.4 1.6 - - - -
266u VAL* 5.4 11.3 - - + +
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Residues in contact with PHE 188 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184u LEU 2.9 18.1 + - - +
185u LEU* 4.5 0.7 - - - +
187u MET* 1.3 75.8 - - - +
189u ALA* 1.3 57.7 + - - +
191u GLU* 3.3 9.1 + - - +
192u VAL* 2.9 28.9 + - - +
215u ALA* 3.9 16.7 - - + +
218u ILE* 5.1 5.6 - - + -
219u MET* 4.0 22.9 - - + +
266u VAL* 5.5 8.2 - - + +
270u THR* 5.6 0.5 - - - -
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Residues in contact with ALA 189 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73u LEU* 5.8 8.5 - - + -
74u PRO* 5.3 3.7 - - - +
185u LEU 2.8 23.3 + - - +
186u SER* 3.9 4.5 - - - +
188u PHE* 1.3 77.9 - - - +
190u ARG* 1.3 57.0 + - - +
192u VAL* 3.4 3.4 + - - +
193u VAL* 2.9 28.8 + - - +
199u THR* 5.9 6.0 - - - -
212u PHE* 5.6 5.8 - - + -
215u ALA* 3.6 16.7 - - + +
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Residues in contact with ARG 190 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72u ARG 4.9 9.9 - - - +
74u PRO* 5.3 7.1 - - + -
186u SER 2.9 18.7 + - - +
187u MET* 3.1 7.6 + - - +
189u ALA* 1.3 74.4 - - - +
191u GLU* 1.3 59.3 + - - +
193u VAL* 3.3 7.3 + - - +
194u VAL* 2.9 27.0 + - - +
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Residues in contact with GLU 191 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187u MET 2.9 13.3 + - - +
188u PHE* 3.3 11.4 + - - +
190u ARG* 1.3 75.2 - - - +
192u VAL* 1.3 59.4 + - - +
194u VAL* 3.1 9.1 + - - +
195u CYS* 2.9 26.7 + - - +
266u VAL* 4.4 10.8 - - + +
267u SER* 4.8 8.3 - - - -
270u THR* 3.9 26.0 - - - -
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Residues in contact with VAL 192 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188u PHE 2.9 16.5 + - - +
189u ALA* 3.8 7.0 - - - +
190u ARG 3.4 0.2 - - - -
191u GLU* 1.3 75.5 - - - +
193u VAL* 1.3 61.9 + - - +
195u CYS* 3.2 10.0 + - - +
196u GLY 3.1 16.6 + - - -
197u CYS* 3.6 20.5 + - + +
199u THR* 5.2 9.9 - - - -
214u LEU* 5.6 5.2 - - + -
215u ALA* 4.8 12.3 - - + +
270u THR* 5.0 3.7 - - - -
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Residues in contact with VAL 193 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74u PRO* 4.0 25.1 - - + -
189u ALA 2.9 17.4 + - - +
190u ARG* 3.7 5.8 - - - +
192u VAL* 1.3 75.8 - - - +
194u VAL* 1.3 63.0 + - - +
196u GLY* 3.2 13.8 + - - +
197u CYS 5.0 2.9 - - - -
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Residues in contact with VAL 194 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87u SER* 5.8 1.4 - - - -
190u ARG 2.9 14.5 + - - +
191u GLU* 3.1 12.5 + - - +
193u VAL* 1.3 78.9 - - - +
195u CYS* 1.3 60.6 + - - +
196u GLY* 3.4 1.0 + - - -
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Residues in contact with CYS 195 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87u SER* 4.5 8.7 - - - -
90u GLN* 5.1 7.1 - - - +
191u GLU 2.9 12.7 + - - +
192u VAL* 3.2 13.0 + - - +
194u VAL* 1.3 75.5 - - - +
196u GLY* 1.3 56.3 + - - +
197u CYS* 3.3 11.7 + - + +
270u THR* 5.5 5.8 - - - +
271u LYS* 6.1 1.6 - - - -
274u ILE* 4.5 22.2 - - + -
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Residues in contact with GLY 196 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87u SER* 4.2 23.7 - - - +
90u GLN* 6.3 1.1 - - - -
91u ILE* 4.5 11.5 - - - +
192u VAL 3.1 5.0 + - - -
193u VAL* 3.2 10.2 + - - -
194u VAL 3.2 4.6 - - - -
195u CYS* 1.3 76.1 - - - +
197u CYS* 1.3 64.0 + - - +
198u MET* 3.7 1.9 + - - -
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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
------------------------------------------------------------
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