Contacts of the helix formed by residues 181 - 198 (chain W) in PDB entry 6NE3
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 181 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179W LYS* 4.0 5.1 - - - +
180W LEU* 1.3 77.1 - - - +
182W ASP* 1.3 66.3 + - - +
183W TYR* 3.3 30.6 + - + -
184W GLN* 2.5 30.9 + - - +
185W VAL* 3.1 10.8 + - - +
401W GLU* 4.9 17.8 + - - +
801W ADP 3.8 50.6 + - - -
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Residues in contact with ASP 182 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169W GLU 5.7 1.6 - - - +
180W LEU 3.9 1.4 + - - -
181W ARG* 1.3 73.8 - - - +
183W TYR* 1.3 60.1 + - + +
185W VAL* 3.0 14.8 + - - +
186W ARG* 2.9 45.4 + - - +
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Residues in contact with TYR 183 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181W ARG* 3.6 29.3 + - + +
182W ASP* 1.3 77.1 + - + +
184W GLN* 1.3 82.7 + - + +
186W ARG* 3.3 32.6 + - - +
187W GLY* 2.9 23.7 + - - -
208W GLY 4.7 1.9 + - - -
209W LEU* 4.0 33.0 - - + +
395W ARG* 4.1 25.4 + - - -
400W VAL* 3.6 52.7 - - + +
401W GLU* 4.0 16.0 + - - -
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Residues in contact with GLN 184 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180W LEU* 3.3 17.7 - - + +
181W ARG* 2.5 40.9 + - + +
183W TYR* 1.3 102.1 + - + +
185W VAL* 1.3 56.7 + - - +
188W LEU 2.8 12.8 + - - -
209W LEU 3.6 11.0 + - - +
210W GLY* 3.5 22.8 - - - +
213W LEU* 5.5 2.6 - - - +
214W GLN* 2.6 40.9 + - + +
395W ARG* 5.4 0.9 - - - +
801W ADP 3.1 30.4 + - - -
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Residues in contact with VAL 185 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168W PHE* 3.3 26.7 - - + +
169W GLU* 4.5 2.7 - - - -
170W ASP* 3.5 33.0 - - - +
171W SER 4.3 0.7 - - - +
172W PRO* 4.8 0.2 - - + -
180W LEU* 3.7 26.5 - - + +
181W ARG 3.1 15.7 + - - +
182W ASP* 3.0 15.8 + - - +
184W GLN* 1.3 73.2 - - - +
186W ARG* 1.3 56.5 + - - +
188W LEU* 3.1 13.5 + - + +
189W ASN* 2.4 41.3 + - - +
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Residues in contact with ARG 186 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182W ASP* 2.9 26.4 + - - +
183W TYR* 3.4 35.1 + - - +
185W VAL* 1.3 77.2 - - - +
187W GLY* 1.3 57.4 + - - +
189W ASN* 3.2 14.4 + - - +
190W TRP* 2.9 25.9 + - + +
393W LEU* 6.3 0.7 - - + -
395W ARG* 4.7 12.1 - - - +
400W VAL* 4.5 9.1 - - - +
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Residues in contact with GLY 187 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183W TYR 2.9 14.6 + - - -
184W GLN 3.3 4.5 + - - -
186W ARG* 1.3 77.3 - - - +
188W LEU* 1.3 56.1 + - - +
190W TRP* 3.1 10.8 + - - +
191W LEU* 2.9 32.6 + - - +
203W LEU* 5.5 1.3 - - - +
214W GLN* 3.9 11.2 - - - -
393W LEU* 4.1 18.2 - - - -
395W ARG* 4.5 2.0 - - - +
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Residues in contact with LEU 188 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167W ARG* 6.2 0.4 - - + -
168W PHE* 5.5 4.9 - - + -
172W PRO* 4.7 5.2 - - + -
174W TYR* 3.5 25.1 - - - +
180W LEU* 4.6 8.5 - - + -
184W GLN 2.8 8.9 + - - +
185W VAL* 3.1 16.4 + - + +
187W GLY* 1.3 73.9 - - - +
189W ASN* 1.3 59.9 + - - +
191W LEU* 3.2 5.4 + - + +
192W ILE* 2.9 54.6 + - + +
214W GLN* 3.2 18.8 + - - +
217W SER* 3.9 15.7 - - - +
218W LEU* 3.7 36.1 - - + +
221W TYR* 5.2 0.7 - - + -
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Residues in contact with ASN 189 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166W THR* 3.1 28.8 + - + +
167W ARG* 3.4 18.5 + - - +
168W PHE 3.6 10.2 + - - +
169W GLU* 5.6 2.5 - - - +
185W VAL* 2.4 44.4 + - - +
186W ARG* 3.2 11.3 + - + +
188W LEU* 1.3 75.7 - - - +
190W TRP* 1.3 58.8 + - - +
192W ILE* 3.5 6.2 + - - +
193W SER* 2.9 30.7 + - - -
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Residues in contact with TRP 190 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186W ARG* 2.9 13.6 + - + +
187W GLY* 3.1 12.1 + - - +
189W ASN* 1.3 76.6 - - - +
191W LEU* 1.3 78.4 + - + +
193W SER* 2.5 25.1 + - - -
194W LEU* 2.9 45.9 + - + +
202W ILE 3.2 31.0 - - - -
203W LEU* 3.7 11.4 - - + -
388W LEU 5.3 1.2 + - - -
389W ARG 5.0 5.5 + - - -
390W PRO 4.8 4.2 + - - -
391W PHE* 4.1 7.9 - - - -
392W LEU 3.2 37.1 + - - -
393W LEU* 3.6 32.5 - - + -
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Residues in contact with LEU 191 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187W GLY 2.9 16.7 + - - +
188W LEU* 3.2 6.5 + - + +
190W TRP* 1.3 104.8 - - + +
192W ILE* 1.3 58.3 + - - +
194W LEU* 3.2 14.2 + - + +
195W TYR* 2.9 26.7 + - - +
201W GLY 6.5 0.7 - - - -
203W LEU* 4.1 19.7 - - + +
214W GLN* 3.8 31.0 - - + +
215W THR* 5.3 2.5 - - - -
218W LEU* 3.8 37.3 - - + +
333W LEU* 4.4 16.7 - - + +
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Residues in contact with ILE 192 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167W ARG* 3.7 44.4 - - + +
168W PHE* 6.5 0.2 - - + -
188W LEU* 2.9 36.3 + - + +
189W ASN 4.1 1.1 - - - +
191W LEU* 1.3 75.9 - - - +
193W SER* 1.3 56.6 + - - +
195W TYR* 3.2 6.8 + - + +
196W GLU* 2.9 29.1 + - - +
218W LEU* 3.9 19.1 - - + -
221W TYR* 3.7 24.7 - - + -
222W MET* 4.4 3.4 - - + -
226W ARG* 3.4 27.8 - - - +
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Residues in contact with SER 193 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166W THR* 6.4 2.5 - - - -
167W ARG* 6.1 0.2 - - - +
189W ASN 2.9 15.4 + - - -
190W TRP* 2.5 32.1 + - - -
192W ILE* 1.3 75.0 - - - +
194W LEU* 1.3 58.5 + - - +
196W GLU* 3.3 7.4 + - - +
197W ASN* 2.9 41.5 + - - +
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Residues in contact with LEU 194 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190W TRP* 2.9 64.2 + - + +
191W LEU* 3.3 17.0 - - + +
193W SER* 1.3 77.3 + - - +
195W TYR* 1.3 57.5 + - - +
197W ASN* 3.5 1.0 + - - -
198W GLY 3.0 21.5 + - - -
199W ILE* 3.0 50.5 + - + +
201W GLY* 4.2 19.5 - - - +
333W LEU* 6.1 3.1 - - + -
390W PRO 3.9 20.2 - - - +
391W PHE* 4.5 0.4 - - + -
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Residues in contact with TYR 195 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191W LEU 2.9 13.2 + - - +
192W ILE* 3.2 11.6 + - + +
194W LEU* 1.3 74.8 - - - +
196W GLU* 1.3 82.5 + - - +
198W GLY* 3.3 11.2 + - - -
199W ILE 5.3 0.7 - - - -
218W LEU* 6.1 0.4 - - + -
222W MET* 4.4 6.5 - - + -
226W ARG* 3.7 25.6 - - + -
228W ILE* 3.4 25.1 - - + +
303W ARG* 6.0 1.7 - - - -
304W TYR* 3.2 42.8 - + - +
331W ASN* 3.8 24.5 + - - +
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Residues in contact with GLU 196 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167W ARG* 3.9 19.5 - - - +
192W ILE 2.9 18.8 + - - +
193W SER* 3.3 8.3 + - - +
195W TYR* 1.3 93.2 - - - +
197W ASN* 1.3 65.8 + - - +
198W GLY* 3.4 1.0 + - - -
226W ARG* 2.4 38.0 + - - -
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Residues in contact with ASN 197 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193W SER* 2.9 22.7 + - - +
194W LEU* 5.4 0.4 - - - +
195W TYR 3.3 0.2 - - - -
196W GLU* 1.3 82.5 - - - +
198W GLY* 1.3 62.9 + - - +
199W ILE* 3.6 18.9 + - + +
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Residues in contact with GLY 198 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194W LEU 3.0 5.5 + - - -
195W TYR* 3.3 9.3 + - - -
196W GLU 3.2 5.4 + - - -
197W ASN* 1.3 78.6 - - - +
199W ILE* 1.3 58.7 + - - +
200W ASN* 4.4 3.5 + - - -
331W ASN* 5.6 5.4 - - - -
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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
------------------------------------------------------------
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