Contacts of the helix formed by residues 201 - 218 (chain S) 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 ARG 201 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24J TYR* 3.8 28.9 + - - -
27J LYS* 6.3 0.4 - - - +
28J ILE* 5.0 2.6 - - - +
31J LEU* 3.3 21.4 - - - +
200S ARG* 1.3 69.4 - - - +
202S ALA* 1.3 68.1 + - - +
203S LEU 3.2 1.8 - - - -
204S ASP* 3.4 21.8 + - - +
205S LEU* 5.1 0.5 - - - +
241S ARG* 3.3 40.1 + - - +
242S HIS 5.7 0.2 - - - -
243S ASP* 4.0 17.9 - - + +
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Residues in contact with ALA 202 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72S LEU* 5.7 9.0 - - - +
75S ILE* 5.7 6.9 - - + +
162S GLU* 5.6 10.8 - - + -
200S ARG* 3.6 3.6 - - + -
201S ARG* 1.3 79.3 - - - +
203S LEU* 1.3 62.6 + - + +
205S LEU* 3.2 23.1 + - - +
206S VAL* 3.6 4.9 + - - +
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Residues in contact with LEU 203 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161S PRO 4.4 1.8 - - - +
162S GLU* 4.2 22.7 - - - +
165S ALA* 2.6 41.3 - - + -
195S ILE* 3.4 16.4 - - + +
198S GLN* 2.7 38.8 - - + +
200S ARG* 3.9 26.6 + - + +
201S ARG 3.2 0.6 - - - -
202S ALA* 1.3 76.7 - - + +
204S ASP* 1.3 53.6 + - - +
206S VAL* 3.0 9.3 + - + +
207S ALA* 2.8 37.2 + - + +
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Residues in contact with ASP 204 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198S GLN 5.9 0.4 - - - -
200S ARG 4.0 11.9 - - - -
201S ARG* 3.4 15.4 + - - +
202S ALA 3.2 0.4 - - - -
203S LEU* 1.3 76.9 - - - +
205S LEU* 1.3 60.0 + - - +
207S ALA* 3.4 8.9 + - - +
208S ALA* 3.3 19.4 + - - +
238S ALA* 4.9 18.6 - - + -
241S ARG* 5.5 5.6 - - - -
243S ASP* 2.9 26.7 - - + +
246S GLY* 4.4 8.4 - - - -
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Residues in contact with LEU 205 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72S LEU 5.6 2.9 - - - +
73S GLU* 6.0 2.0 - - - -
75S ILE* 4.8 11.2 - - + -
76S LYS* 4.7 25.8 - - + +
201S ARG 5.1 0.9 - - - +
202S ALA* 3.2 12.7 + - - +
203S LEU 3.1 0.8 - - - -
204S ASP* 1.3 78.6 - - - +
206S VAL* 1.3 62.8 + - - +
208S ALA* 3.4 18.8 - - - +
209S LYS* 4.3 5.4 + - - +
243S ASP* 3.2 15.7 + - - +
245S ASP* 3.5 38.4 - - + -
246S GLY 5.0 1.3 - - - +
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Residues in contact with VAL 206 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75S ILE* 6.3 4.2 - - + +
162S GLU 5.7 2.0 - - - +
165S ALA* 4.4 5.8 - - + -
166S TYR* 4.2 18.6 - - + +
169S LEU* 2.9 51.5 - - + +
202S ALA 3.6 3.2 + - - +
203S LEU* 3.0 21.4 + - + +
205S LEU* 1.3 81.2 - - - +
207S ALA* 1.3 60.6 + - - +
208S ALA 3.2 0.9 + - - -
209S LYS* 3.3 13.7 + - - +
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Residues in contact with ALA 207 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169S LEU* 4.8 0.4 - - - -
195S ILE* 5.2 17.7 - - + +
196S SER* 5.8 2.7 - - - +
203S LEU* 2.8 20.1 + - + +
204S ASP* 3.4 8.9 + - - +
206S VAL* 1.3 71.7 - - - +
208S ALA* 1.3 53.0 + - - +
210S CYS* 2.6 21.3 + - + +
211S TYR* 2.5 44.4 + - + -
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Residues in contact with ALA 208 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204S ASP 3.3 10.7 + - - +
205S LEU* 3.4 14.6 - - - +
206S VAL 3.2 0.6 - - - -
207S ALA* 1.3 76.5 - - - +
209S LYS* 1.3 56.7 + - + +
211S TYR* 3.3 7.3 + - - +
212S TYR* 2.8 35.2 + - - +
245S ASP* 5.1 8.1 - - - -
246S GLY* 4.1 21.8 - - - +
249S THR* 4.0 18.9 + - - -
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Residues in contact with LYS 209 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79S VAL* 4.4 26.2 - - + -
83S GLU* 5.7 4.6 - - - +
169S LEU* 4.5 15.5 - - + -
205S LEU 4.9 4.7 - - - +
206S VAL* 3.3 13.0 + - - +
208S ALA* 1.3 78.5 - - + +
210S CYS* 1.3 62.4 + - - +
212S TYR* 3.2 15.6 - - + +
213S TYR* 2.8 36.6 - - + -
6Y GLN* 5.5 8.5 + - - +
9Y ASP* 5.0 14.3 - - - +
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Residues in contact with CYS 210 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169S LEU* 3.9 17.3 - - + +
172S VAL* 5.6 9.3 - - + +
191S LEU* 5.1 8.7 - - - -
192S MET* 4.3 23.3 - - - -
195S ILE* 4.9 11.2 - - + -
206S VAL 3.6 1.4 + - - -
207S ALA* 2.6 30.9 - - - +
209S LYS* 1.3 75.0 - - - +
211S TYR* 1.3 66.2 + - - -
213S TYR* 2.9 10.8 + - - +
214S HIS* 2.9 36.2 + - - -
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Residues in contact with TYR 211 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192S MET* 5.9 3.6 - - + -
207S ALA* 2.5 28.5 + - + +
208S ALA* 3.8 7.0 - - - +
210S CYS* 1.3 76.6 - - + +
212S TYR* 1.3 64.6 + - - +
214S HIS* 3.0 21.5 + + + +
215S ALA* 3.3 10.9 + - - +
231S LEU* 5.8 3.1 - - + -
234S ARG* 6.0 5.2 - - + -
249S THR* 5.0 1.8 - - - +
250S LEU* 4.8 18.2 - - + -
253S LEU* 3.5 26.7 - - + +
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Residues in contact with TYR 212 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208S ALA 2.8 15.0 + - - +
209S LYS* 3.2 20.2 - - + +
210S CYS 3.1 0.2 - - - -
211S TYR* 1.3 77.1 - - - +
213S TYR* 1.3 67.6 + + - +
215S ALA* 4.7 2.4 - - - +
216S ARG* 3.6 16.3 + - - +
249S THR* 5.1 3.8 - - - +
253S LEU* 4.1 15.5 - - + +
287S ARG* 5.1 8.5 - - - +
13Y LEU* 4.2 25.1 - - + -
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Residues in contact with TYR 213 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83S GLU* 5.3 4.7 + - - -
172S VAL* 5.0 16.8 - - + -
173S ILE* 4.3 31.9 - - + +
176S MET* 4.2 28.5 - - + -
177S ASN* 5.7 6.3 - - - -
188S SER* 5.7 0.7 - - - -
209S LYS* 2.8 38.3 + - + -
210S CYS* 2.9 8.0 + - - +
212S TYR* 1.3 84.7 - + - +
214S HIS* 1.3 70.6 + - - +
216S ARG* 2.9 24.8 + - + +
217S VAL* 3.4 7.8 + - - +
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Residues in contact with HIS 214 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172S VAL* 6.2 3.1 - - + -
188S SER* 4.8 21.8 + - - -
192S MET* 3.9 31.4 - - + -
210S CYS* 2.9 32.2 + - - -
211S TYR* 3.0 12.0 + + - +
213S TYR* 1.3 79.5 - - + +
215S ALA* 1.3 65.6 + - - +
217S VAL* 3.9 1.9 + - - +
218S TYR* 3.3 20.9 + - - -
227S VAL* 5.4 10.1 - - + -
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Residues in contact with ALA 215 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211S TYR 3.3 10.3 + - - +
212S TYR 4.7 0.9 - - - +
214S HIS* 1.3 78.0 - - - +
216S ARG* 1.3 62.3 + - - +
218S TYR* 2.7 33.8 - - - +
223S LYS 5.9 0.9 - - - -
227S VAL* 5.3 6.5 - - + +
253S LEU* 4.2 27.1 - - + +
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Residues in contact with ARG 216 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176S MET* 4.9 8.5 - - + -
212S TYR 3.6 14.9 + - - +
213S TYR* 2.9 20.8 + - + +
215S ALA* 1.3 81.0 - - - +
217S VAL* 1.3 72.8 + - + +
218S TYR 3.2 6.6 - - - +
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Residues in contact with VAL 217 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176S MET* 3.7 36.8 - - + +
181S TYR* 5.0 13.0 - - + -
184S ALA* 5.7 2.5 - - + -
185S GLN* 4.0 24.9 - - + +
188S SER* 6.0 1.3 - - - +
213S TYR 3.4 7.5 + - - +
214S HIS 4.7 2.0 - - - +
216S ARG* 1.3 76.6 - - + +
218S TYR* 1.3 72.9 + - - +
219S GLU* 4.4 2.1 - - - +
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Residues in contact with TYR 218 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185S GLN* 5.0 6.1 - - + +
214S HIS 3.3 18.5 + - - -
215S ALA* 2.7 20.9 + - - +
216S ARG 3.2 8.0 - - - +
217S VAL* 1.3 91.5 - - - +
219S GLU* 1.3 59.9 + - - +
223S LYS* 3.1 31.4 - - + +
227S VAL* 4.7 10.1 - - + -
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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