Contacts of the helix formed by residues 204 - 221 (chain Q) in PDB entry 5GJQ
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 PRO 204 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339K ARG* 6.3 3.1 - - - -
203Q PRO* 1.4 95.8 - - + +
205Q LYS* 1.3 64.3 + - + +
206Q LEU 3.2 2.0 - - - +
207Q GLN* 2.5 36.2 + - + +
208Q ALA* 3.1 3.3 + - - -
238Q GLY* 6.1 4.7 - - - -
242Q ILE* 5.8 6.5 - - + -
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Residues in contact with LYS 205 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204Q PRO* 1.3 81.9 - - + +
206Q LEU* 1.3 56.6 + - - +
208Q ALA* 2.3 43.9 + - - +
209Q THR* 3.0 5.7 + - + -
238Q GLY* 6.0 2.4 - - - -
239Q TYR* 3.9 24.3 + - + +
242Q ILE* 3.5 29.1 - - + +
243Q ASP* 3.3 34.1 - - - +
245Q PRO* 4.9 5.2 - - + +
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Residues in contact with LEU 206 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164Q ALA* 3.8 29.8 - - + +
167Q VAL* 3.7 33.0 - - + -
168Q GLU* 5.0 8.1 - - + -
171Q LEU* 4.3 0.2 - - - +
197Q ALA* 5.3 0.4 - - + -
200Q ILE* 6.2 0.9 - - + -
202Q CYS 2.6 35.7 - - - +
203Q PRO* 3.8 17.0 - - + -
204Q PRO* 5.1 0.6 - - + +
205Q LYS* 1.3 77.5 - - - +
207Q GLN* 1.3 68.9 + - - +
209Q THR* 2.4 31.6 + - - +
210Q LEU* 3.0 13.3 + - + +
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Residues in contact with GLN 207 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202Q CYS* 3.6 17.7 - - + -
203Q PRO 2.7 25.8 - - - +
204Q PRO* 2.5 11.4 + - + +
206Q LEU* 1.3 82.6 - - + +
208Q ALA* 1.3 54.9 + - - +
210Q LEU* 3.3 17.5 + - + +
211Q ASP* 2.6 59.1 + - - +
234Q GLU* 4.4 11.1 + - - +
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Residues in contact with ALA 208 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204Q PRO 3.1 4.5 + - - +
205Q LYS* 2.3 31.7 + - - +
207Q GLN* 1.3 66.4 - - - +
209Q THR* 1.3 58.6 + - - +
211Q ASP* 2.9 6.2 + - - +
212Q MET* 2.8 33.1 + - - +
235Q ALA* 4.0 22.0 - - - +
238Q GLY* 5.1 6.7 - - - -
239Q TYR* 3.6 29.8 - - + -
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Residues in contact with THR 209 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171Q LEU* 3.5 22.9 - - - +
175Q LYS* 4.6 12.3 - - - +
205Q LYS* 3.0 6.8 + - + +
206Q LEU* 2.4 32.8 + - - +
208Q ALA* 1.3 75.7 - - - +
210Q LEU* 1.3 57.2 + - - +
212Q MET* 4.7 4.3 - - - -
213Q GLN* 2.9 37.6 + - - +
239Q TYR* 3.0 20.0 - - - +
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Residues in contact with LEU 210 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167Q VAL* 4.8 1.1 - - + -
171Q LEU* 3.3 26.2 - - + -
190Q LEU* 4.0 7.9 - - + +
193Q ALA* 3.6 26.0 - - + +
194Q ARG* 3.9 22.1 - - + +
197Q ALA* 3.2 31.2 - - + -
206Q LEU* 3.5 10.3 - - + +
207Q GLN* 3.4 25.6 - - + +
208Q ALA 3.2 0.2 - - - -
209Q THR* 1.3 81.0 + - - +
211Q ASP* 1.3 61.6 + - - +
213Q GLN* 4.4 0.7 - - - -
214Q SER* 3.2 21.4 + - - -
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Residues in contact with ASP 211 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207Q GLN* 2.6 45.9 + - - +
208Q ALA* 2.9 10.6 + - - +
210Q LEU* 1.3 81.1 - - - +
212Q MET* 1.3 57.5 - - - +
213Q GLN 3.0 0.9 - - - -
214Q SER* 2.5 29.6 + - - -
215Q GLY 2.9 9.2 + - - -
231Q TYR* 3.4 31.1 - - + +
234Q GLU* 3.6 16.2 - - - +
235Q ALA* 3.8 17.3 + - + -
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Residues in contact with MET 212 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208Q ALA 2.8 12.6 + - - +
209Q THR* 4.2 3.4 - - - +
211Q ASP* 1.3 71.2 - - - +
213Q GLN* 1.3 52.7 + - - +
215Q GLY* 3.0 4.4 + - - +
216Q ILE* 2.7 43.8 + - + +
231Q TYR* 4.4 4.5 - - - +
232Q PHE* 4.0 11.2 - - + -
235Q ALA* 2.6 32.9 - - + +
239Q TYR* 3.2 35.7 - - + -
246Q LYS* 5.5 0.2 - - + -
249Q THR* 3.3 27.4 - - + -
250Q SER* 3.0 35.0 - - - +
253Q TYR* 4.4 6.3 - - + -
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Residues in contact with GLN 213 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171Q LEU* 3.5 26.2 - - + -
174Q SER* 5.0 5.0 + - - -
175Q LYS* 3.3 41.3 - - - +
178Q HIS* 5.2 7.7 - - - +
190Q LEU* 3.6 10.5 - - + +
209Q THR 2.9 19.4 + - - +
212Q MET* 1.3 78.3 - - - +
214Q SER* 1.3 57.0 + - - +
216Q ILE* 3.0 28.0 + - + +
217Q ILE* 2.9 41.8 + - - +
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Residues in contact with SER 214 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190Q LEU* 3.0 18.7 - - - +
194Q ARG* 2.1 39.3 + - - +
210Q LEU 3.2 14.1 + - - -
211Q ASP 2.5 16.7 + - - -
213Q GLN* 1.3 71.1 - - - +
215Q GLY* 1.3 62.3 + - - -
217Q ILE* 3.2 1.9 + - - +
218Q HIS* 2.8 32.9 + - - -
231Q TYR* 3.8 14.8 - - - -
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Residues in contact with GLY 215 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211Q ASP 2.9 10.5 + - - -
212Q MET 3.0 4.7 + - - -
214Q SER* 1.3 76.0 - - - +
216Q ILE* 1.3 56.6 + - - +
219Q ALA* 2.9 25.5 + - - +
228Q ALA* 3.2 22.1 - - - +
231Q TYR* 3.3 18.3 - - - -
232Q PHE* 3.4 16.7 - - - -
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Residues in contact with ILE 216 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178Q HIS* 4.2 17.3 - - + +
212Q MET* 2.7 23.1 + - + +
213Q GLN* 3.0 30.5 + - + +
215Q GLY* 1.3 71.9 - - - +
217Q ILE* 1.3 64.5 + - + +
219Q ALA* 2.7 23.6 + - + +
220Q ALA* 3.0 13.2 + - - +
232Q PHE* 4.4 11.9 - - + -
253Q TYR* 5.3 15.3 - - + -
318Q ILE* 3.2 37.0 - - + +
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Residues in contact with ILE 217 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174Q SER* 5.2 0.2 - - - +
178Q HIS* 5.3 2.0 - - + -
183Q LEU* 3.8 25.1 - - + -
186Q ALA* 4.2 4.5 - - + +
187Q ARG* 3.5 32.3 - - + +
190Q LEU* 2.9 43.5 - - + -
194Q ARG* 6.1 0.4 - - - +
213Q GLN* 2.9 22.3 + - - +
214Q SER 3.2 5.6 + - - +
216Q ILE* 1.3 80.1 - - + +
218Q HIS* 1.3 58.6 + - + +
220Q ALA 4.6 0.2 - - - +
221Q GLU* 2.9 60.0 + - + +
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Residues in contact with HIS 218 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373J GLU* 3.2 26.8 + - + -
375J ARG* 5.1 3.4 - - - -
187Q ARG* 3.8 21.7 + - - -
194Q ARG* 3.9 11.1 + - - -
214Q SER 2.8 25.7 + - - +
215Q GLY 3.5 0.4 - - - -
216Q ILE 3.1 0.4 - - - -
217Q ILE* 1.3 77.9 - - + +
219Q ALA* 1.3 60.0 + - - +
221Q GLU* 3.8 15.9 + - - -
223Q LYS* 4.0 9.8 + - - +
224Q ASP* 3.8 28.2 + - - +
225Q TRP* 4.5 2.3 + - - -
227Q THR* 3.7 12.0 - - + +
228Q ALA* 3.4 25.9 - - + +
231Q TYR* 3.2 27.1 - + - -
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Residues in contact with ALA 219 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215Q GLY 2.9 12.1 + - - +
216Q ILE* 2.7 15.3 + - - +
218Q HIS* 1.3 79.6 - - - +
220Q ALA* 1.3 57.8 + - - +
222Q GLU* 3.9 4.3 + - - +
225Q TRP* 3.3 34.1 - - - +
228Q ALA* 4.9 1.6 - - + -
232Q PHE* 4.6 11.2 - - + -
318Q ILE* 4.7 8.7 - - + -
321Q THR* 5.1 1.0 + - - -
322Q HIS* 3.6 28.9 - - + +
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Residues in contact with ALA 220 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178Q HIS* 4.8 11.2 - - - +
183Q LEU* 3.3 28.8 - - + +
216Q ILE 3.0 11.2 + - - +
217Q ILE 4.6 0.4 - - - +
219Q ALA* 1.3 75.4 - - - +
221Q GLU* 1.3 52.9 + - - +
222Q GLU* 2.3 45.0 + - - +
318Q ILE* 5.2 7.9 - - + -
321Q THR* 5.5 3.6 - - - -
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Residues in contact with GLU 221 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183Q LEU* 4.0 10.7 - - + +
187Q ARG* 2.9 37.7 + - + +
217Q ILE* 2.9 34.3 + - + +
218Q HIS* 3.8 19.3 + - - -
220Q ALA* 1.3 73.7 - - - +
222Q GLU* 1.3 71.1 + - - +
223Q LYS* 3.4 24.4 - - + +
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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