Contacts of the helix formed by residues 171 - 196 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169R SER* 3.6 10.0 + - - +
170R ASP* 1.3 75.5 - - - +
172R ASP* 1.3 61.3 + - - +
173R ILE* 3.1 10.5 - - + +
174R ASN* 3.1 7.8 + - + +
175R ALA* 3.0 28.6 + - - +
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Residues in contact with ASP 172 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171R ASN* 1.3 74.0 - - - +
173R ILE* 1.3 56.8 + - - +
175R ALA* 3.9 7.2 - - - +
176R ALA* 2.9 29.5 + - - +
236R ASN 5.2 6.1 - - - +
237R ASN* 5.7 0.4 - - - -
238R PHE* 4.2 31.8 - - + +
241R ILE* 5.5 0.7 - - - +
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Residues in contact with ILE 173 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161R PHE* 5.8 8.3 - - + -
171R ASN* 3.1 7.4 - - + +
172R ASP* 1.3 77.5 - - - +
174R ASN* 1.3 60.1 + - - +
176R ALA* 3.3 6.0 + - - +
177R LEU* 2.9 28.6 + - - +
230R VAL* 5.4 7.5 - - + +
234R ARG* 5.6 13.7 - - + +
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Residues in contact with ASN 174 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166R THR 5.0 5.2 - - - +
167R ARG* 4.3 14.1 - - - +
169R SER 3.6 23.6 - - - +
170R ASP* 5.2 0.4 - - - -
171R ASN* 3.1 11.3 + - + +
173R ILE* 1.3 78.7 - - - +
175R ALA* 1.3 57.6 + - - +
177R LEU* 3.2 8.1 + - - +
178R ASP* 2.9 28.5 + - - +
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Residues in contact with ALA 175 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171R ASN 3.0 16.1 + - - +
172R ASP* 4.0 7.2 - - - +
174R ASN* 1.3 77.1 - - - +
176R ALA* 1.3 58.0 + - - +
178R ASP* 3.4 7.2 + - - +
179R TYR* 2.9 28.1 + - - +
238R PHE* 5.8 5.2 - - + -
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Residues in contact with ALA 176 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172R ASP 2.9 20.7 + - - +
173R ILE* 3.6 7.4 - - - +
174R ASN 3.2 0.2 - - - -
175R ALA* 1.3 74.5 - - - +
177R LEU* 1.3 59.2 + - - +
179R TYR* 3.2 7.1 + - - +
180R GLY* 2.9 25.6 + - - -
226R ILE* 6.1 0.2 - - - +
230R VAL* 5.0 13.7 - - + -
238R PHE* 6.0 1.8 - - + +
241R ILE* 4.2 24.9 - - + +
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Residues in contact with LEU 177 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173R ILE 2.9 14.0 + - - +
174R ASN* 3.5 10.8 - - - +
176R ALA* 1.3 77.5 - - - +
178R ASP* 1.3 56.8 + - - +
180R GLY* 3.9 0.8 - - - -
181R TYR* 2.9 30.8 + - - +
226R ILE* 5.8 4.5 - - - +
230R VAL* 5.5 6.7 - - + +
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Residues in contact with ASP 178 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174R ASN 2.9 16.2 + - - +
175R ALA* 3.8 7.6 - - - +
176R ALA 3.3 0.2 - - - -
177R LEU* 1.3 75.5 - - - +
179R TYR* 1.3 59.0 + - - +
181R TYR* 3.8 6.8 - - - +
182R THR* 2.9 27.5 + - - -
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Residues in contact with TYR 179 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175R ALA 2.9 18.1 + - - +
176R ALA* 3.2 8.7 + - - +
178R ASP* 1.3 75.2 - - - +
180R GLY* 1.3 60.2 + - - +
182R THR* 3.0 8.8 + - - -
183R LEU* 2.9 28.1 + - - +
242R LYS* 6.1 6.7 - - + -
245R LEU* 6.1 4.3 - - + -
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Residues in contact with GLY 180 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176R ALA 2.9 15.9 + - - -
177R LEU 3.9 0.9 - - - -
179R TYR* 1.3 74.8 - - - +
181R TYR* 1.3 57.2 + - - +
183R LEU* 3.3 6.8 + - - +
184R LEU* 2.9 30.5 + - - +
226R ILE* 4.7 20.3 - - - +
245R LEU* 5.4 12.6 - - - +
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Residues in contact with TYR 181 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177R LEU 2.9 18.1 + - - +
178R ASP* 3.9 7.9 - - - +
180R GLY* 1.3 75.9 - - - +
182R THR* 1.3 56.7 + - - +
184R LEU* 4.3 5.7 - - - +
185R LEU* 2.9 30.1 + - - +
226R ILE* 5.4 0.8 - - - +
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Residues in contact with THR 182 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178R ASP 2.9 19.6 + - - -
179R TYR* 3.0 9.4 + - - -
181R TYR* 1.3 75.7 - - - +
183R LEU* 1.3 61.2 + - - +
185R LEU* 3.4 5.7 + - - +
186R SER* 2.9 27.7 + - - -
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Residues in contact with LEU 183 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179R TYR 2.9 12.0 + - - +
180R GLY* 3.7 9.2 - - - +
182R THR* 1.3 74.5 - - - +
184R LEU* 1.3 60.6 + - - +
186R SER* 3.0 9.0 + - - -
187R MET* 2.9 27.7 + - - +
245R LEU 6.1 1.1 - - - +
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Residues in contact with LEU 184 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180R GLY 2.9 16.4 + - - +
181R TYR* 4.3 5.6 - - - +
183R LEU* 1.3 76.9 - - - +
185R LEU* 1.3 56.9 + - - +
187R MET* 3.4 6.0 + - - +
188R PHE* 2.9 32.6 + - - +
219R MET* 4.3 16.5 - - + +
222R PHE* 6.0 7.9 - - + +
223R ARG* 6.4 1.8 - - - -
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Residues in contact with LEU 185 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181R TYR 2.9 22.3 + - - +
182R THR* 3.7 7.2 - - - +
183R LEU 3.2 0.2 - - - -
184R LEU* 1.3 77.4 - - - +
186R SER* 1.3 57.9 + - - +
188R PHE* 4.8 2.7 - - - -
189R ALA* 2.8 33.7 + - - +
212R PHE* 5.7 10.0 - - + +
215R ALA* 4.5 4.5 - - + +
216R SER* 5.7 8.7 - - - +
219R MET* 5.0 5.3 - - + +
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Residues in contact with SER 186 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71R LYS 4.1 20.2 - - - -
72R ARG* 4.5 17.9 - - - +
73R LEU* 4.8 8.3 - - - +
182R THR 2.9 15.4 + - - -
183R LEU* 3.0 10.7 + - - -
185R LEU* 1.3 74.6 - - - +
187R MET* 1.3 60.1 + - - +
189R ALA* 3.8 3.2 - - - +
190R ARG* 2.9 29.6 + - - +
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Residues in contact with MET 187 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183R LEU 2.9 14.3 + - - +
184R LEU* 3.9 7.2 - - - +
186R SER* 1.3 76.6 - - - +
188R PHE* 1.3 58.4 + - - +
190R ARG* 3.1 7.9 + - - +
191R GLU* 2.9 27.8 + - - +
263R SER* 6.4 1.6 - - - -
266R VAL* 5.5 11.0 - - + -
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Residues in contact with PHE 188 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184R LEU 2.9 17.6 + - - +
185R LEU* 4.5 0.9 - - - +
187R MET* 1.3 76.8 - - - +
189R ALA* 1.3 58.1 + - - +
191R GLU* 3.3 8.0 + - - +
192R VAL* 2.9 28.2 + - - +
215R ALA* 3.9 25.8 - - + +
218R ILE* 5.1 5.6 - - + -
219R MET* 4.0 13.5 - - + +
266R VAL* 5.5 7.4 - - + +
270R THR* 5.6 0.7 - - - -
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Residues in contact with ALA 189 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73R LEU* 5.8 8.3 - - + -
74R PRO* 5.3 4.3 - - + +
185R LEU 2.8 23.5 + - - +
186R SER* 3.9 4.9 - - - +
188R PHE* 1.3 78.3 - - - +
190R ARG* 1.3 56.3 + - - +
192R VAL* 3.4 3.1 + - - +
193R VAL* 2.9 29.5 + - - +
199R THR* 5.9 5.8 - - - -
212R PHE* 5.6 5.6 - - + -
215R ALA* 3.6 17.2 - - + +
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Residues in contact with ARG 190 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72R ARG 4.9 9.4 - - - +
74R PRO* 5.3 6.7 - - + -
186R SER 2.9 19.6 + - - +
187R MET* 3.1 7.2 + - - +
189R ALA* 1.3 74.6 - - - +
191R GLU* 1.3 59.8 + - - +
193R VAL* 3.3 6.9 + - - +
194R VAL* 2.9 27.5 + - - +
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Residues in contact with GLU 191 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187R MET 2.9 12.3 + - - +
188R PHE* 3.3 11.0 + - - +
190R ARG* 1.3 74.5 - - - +
192R VAL* 1.3 60.0 + - - +
194R VAL* 3.1 10.1 + - - +
195R CYS* 2.9 26.9 + - - +
266R VAL* 4.4 10.8 - - + +
267R SER* 4.8 8.3 - - - -
270R THR* 3.9 26.2 - - - -
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Residues in contact with VAL 192 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188R PHE 2.9 16.3 + - - +
189R ALA* 3.8 8.1 - - - +
191R GLU* 1.3 76.3 - - - +
193R VAL* 1.3 61.4 + - - +
195R CYS* 3.2 9.7 + - - +
196R GLY 3.1 16.8 + - - -
197R CYS* 3.6 20.7 + - + +
199R THR* 5.2 10.1 - - - -
214R LEU* 5.6 4.9 - - + -
215R ALA* 4.8 11.7 - - + +
270R THR* 5.0 3.9 - - - -
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Residues in contact with VAL 193 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74R PRO* 4.0 24.7 - - + -
189R ALA 2.9 18.1 + - - +
190R ARG* 3.7 5.6 - - - +
191R GLU 3.2 0.2 - - - -
192R VAL* 1.3 74.8 - - - +
194R VAL* 1.3 63.2 + - - +
196R GLY* 3.2 13.7 + - - +
197R CYS 5.0 3.4 - - - -
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Residues in contact with VAL 194 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87R SER* 5.8 1.4 - - - -
190R ARG 2.9 14.5 + - - +
191R GLU* 3.1 12.8 + - - +
193R VAL* 1.3 79.3 - - - +
195R CYS* 1.3 59.6 + - - +
196R GLY* 3.4 0.7 + - - -
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Residues in contact with CYS 195 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87R SER* 4.5 8.2 - - - -
90R GLN* 5.1 7.6 - - - +
191R GLU 2.9 12.5 + - - +
192R VAL* 3.2 12.1 + - - +
194R VAL* 1.3 76.9 - - - +
196R GLY* 1.3 55.8 + - - +
197R CYS* 3.3 13.2 + - + +
270R THR* 5.5 5.4 - - - +
271R LYS* 6.1 1.3 - - - -
274R ILE* 4.5 22.0 - - + -
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Residues in contact with GLY 196 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87R SER* 4.2 24.4 - - - +
90R GLN* 6.3 0.7 - - - -
91R ILE* 4.5 11.5 - - - +
192R VAL 3.1 5.6 + - - -
193R VAL* 3.2 10.0 + - - -
194R VAL 3.2 4.8 - - - -
195R CYS* 1.3 76.3 - - - +
197R CYS* 1.3 63.7 + - - +
198R MET* 3.7 1.6 + - - -
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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) + - + + + + + -
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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