Contacts of the helix formed by residues 181 - 196 (chain J) in PDB entry 3LUE
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 ALA 181 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155J SER* 4.2 8.7 - - - +
156J GLY 3.3 14.4 - - - +
157J ASP 3.5 17.3 - - - +
158J GLY 3.9 0.9 - - - -
159J VAL 3.6 24.0 - - - +
160J THR* 4.1 1.6 - - - +
180J LEU* 1.3 78.4 - - - +
182J GLY* 1.4 55.4 + - - +
183J ARG 3.3 1.8 - - - -
184J ASP* 2.9 35.8 + - - +
185J LEU* 3.5 5.7 + - - +
261J LEU* 5.1 0.9 - - - -
303J THR* 3.9 6.1 - - - -
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Residues in contact with GLY 182 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156J GLY 2.9 6.4 + - - -
157J ASP* 4.3 8.1 - - - -
181J ALA* 1.4 71.7 - - - +
183J ARG* 1.3 54.4 + - - +
185J LEU* 3.3 6.8 + - - +
186J THR* 3.0 31.6 + - - -
213J LYS* 3.2 14.9 + - - -
303J THR* 2.8 29.0 + - - -
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Residues in contact with ARG 183 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72J GLU* 1.1 183.0 + - + +
73J HIS* 2.7 45.8 + - + +
75J ILE 3.5 0.2 + - - -
77J THR* 2.1 38.1 - - - +
157J ASP* 3.2 14.5 + - - +
181J ALA 3.0 2.8 + - - -
182J GLY* 1.3 70.1 - - - +
184J ASP* 1.3 68.5 + - - +
186J THR* 3.3 6.5 + - - +
187J ASP* 3.0 33.9 + - - +
206J ARG* 5.0 8.1 - - - +
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Residues in contact with ASP 184 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73J HIS* 3.4 29.4 + - - -
157J ASP 4.3 1.0 - - - +
179J ASP 4.0 6.1 - - - +
180J LEU* 3.6 31.6 - - + -
181J ALA 2.9 23.4 + - - +
183J ARG* 1.3 76.2 - - - +
185J LEU* 1.3 57.2 + - - +
187J ASP* 3.6 6.4 - - - +
188J TYR* 3.1 28.8 + - - +
267J LEU* 4.1 10.3 - - + +
269J MET* 4.0 11.3 - - - +
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Residues in contact with LEU 185 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180J LEU* 3.9 25.4 - - + -
181J ALA 3.5 2.4 + - - +
182J GLY* 3.3 9.8 + - - +
183J ARG 3.1 0.4 - - - -
184J ASP* 1.3 79.2 - - - +
186J THR* 1.3 62.7 + - - +
188J TYR* 4.1 2.9 - - + +
189J LEU* 3.2 8.5 + - - +
213J LYS* 3.6 4.7 - - + -
257J CYS* 3.2 37.4 - - - +
258J PRO* 4.2 3.1 - - + -
260J ALA* 4.0 21.8 - - + -
261J LEU* 3.9 19.7 - - + -
267J LEU* 4.9 0.9 - - + -
303J THR* 3.9 13.0 - - + -
306J TYR* 3.1 41.5 - - + +
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Residues in contact with THR 186 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182J GLY 3.0 9.8 + - - -
183J ARG* 3.3 7.5 + - - -
185J LEU* 1.3 74.3 - - - +
187J ASP* 1.3 61.5 + - - +
189J LEU* 3.4 5.8 + - - +
190J MET* 3.2 22.7 + - - +
206J ARG* 3.7 23.3 - - - +
209J VAL* 3.4 26.7 - - + +
210J ARG* 3.9 21.4 - - + +
213J LYS* 2.6 37.0 + - - +
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Residues in contact with ASP 187 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72J GLU* 4.8 8.3 - - - +
183J ARG* 3.0 23.8 + - - +
184J ASP* 3.6 7.1 - - - +
186J THR* 1.3 75.4 - - - +
188J TYR* 1.3 62.6 - - - +
190J MET* 3.7 15.0 + - - +
191J LYS* 3.4 20.6 + - - +
206J ARG* 3.1 31.2 + - - -
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Residues in contact with TYR 188 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184J ASP 3.1 15.9 + - - +
185J LEU* 4.2 4.0 - - - +
187J ASP* 1.3 77.3 - - - +
189J LEU* 1.3 65.8 + - - +
191J LYS* 3.6 21.7 + - - +
192J ILE* 3.1 51.6 + - + +
256J ARG* 3.3 31.3 + - - +
257J CYS* 4.2 18.4 - - - -
260J ALA* 4.4 4.0 - - + -
266J PHE* 3.3 43.5 + + + +
267J LEU* 3.4 26.9 - - + -
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Residues in contact with LEU 189 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185J LEU 3.2 17.6 + - - +
186J THR 3.5 2.9 - - - +
187J ASP 3.3 0.2 - - - -
188J TYR* 1.3 78.4 - - - +
190J MET* 1.3 50.8 + - - +
192J ILE* 3.2 16.2 + - + +
193J LEU* 2.8 49.0 + - + +
209J VAL* 3.2 38.8 - - + +
212J ILE* 4.1 13.7 - - + -
213J LYS* 3.6 21.5 - - + +
217J CYS* 4.5 10.1 - - - -
250J ILE* 5.3 2.2 - - + -
253J GLU* 4.6 13.0 - - + +
257J CYS* 3.6 21.8 - - + -
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Residues in contact with MET 190 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186J THR 3.2 6.6 + - - +
187J ASP* 3.7 29.6 - - - +
189J LEU* 1.3 79.1 - - - +
191J LYS* 1.3 51.8 + - - +
193J LEU* 3.4 4.1 + - - +
194J THR* 2.8 43.2 + - - +
200J PHE* 4.3 20.1 - - + +
206J ARG* 3.7 44.0 - - - +
209J VAL* 3.8 35.4 - - + -
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Residues in contact with LYS 191 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187J ASP 3.4 13.5 + - - +
188J TYR* 3.8 30.8 - - - +
189J LEU 3.3 0.6 - - - -
190J MET* 1.3 76.4 - - - +
192J ILE* 1.3 71.5 + - - +
194J THR* 3.8 8.0 - - + -
195J GLU* 2.9 51.3 + - + +
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Residues in contact with ILE 192 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188J TYR* 3.1 58.3 + - + +
189J LEU* 3.3 19.5 - - + +
191J LYS* 1.3 78.5 - - - +
193J LEU* 1.3 61.2 + - - +
195J GLU* 3.2 26.1 + - - +
196J ARG* 3.3 12.1 + - - +
253J GLU* 3.9 45.2 - - + +
256J ARG* 3.8 33.3 + - + +
257J CYS* 4.3 7.0 - - + +
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Residues in contact with LEU 193 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189J LEU* 2.8 30.8 + - + +
190J MET 3.6 4.7 - - - +
192J ILE* 1.3 74.5 - - - +
194J THR* 1.3 54.5 + - - +
196J ARG* 3.1 13.0 + - - +
198J TYR* 2.7 47.1 + - + +
200J PHE* 3.8 27.1 - - + -
209J VAL* 4.6 2.9 - - + -
212J ILE* 3.9 21.1 - - + -
248J ILE* 4.5 5.4 - - + -
250J ILE* 3.9 26.0 - - + -
253J GLU* 3.9 26.0 - - + +
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Residues in contact with THR 194 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190J MET* 2.8 26.1 + - - +
191J LYS* 4.0 7.4 - - + +
193J LEU* 1.3 67.2 - - - +
195J GLU* 1.3 65.9 + - + +
196J ARG 3.1 1.6 - - - -
197J GLY* 3.0 14.8 + - - -
198J TYR* 3.5 23.7 + - - +
200J PHE* 3.8 17.8 + - - +
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Residues in contact with GLU 195 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191J LYS* 2.9 48.1 + - + +
192J ILE* 3.2 24.9 + - - +
194J THR* 1.3 73.6 - - + +
196J ARG* 1.3 57.3 + - - +
197J GLY 2.8 11.1 + - - -
256J ARG* 5.4 3.2 + - - +
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Residues in contact with ARG 196 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192J ILE 3.3 9.6 + - - +
193J LEU 3.1 13.2 + - - +
195J GLU* 1.3 73.7 - - - +
197J GLY* 1.3 61.2 + - - +
198J TYR* 3.4 24.6 + - + -
237J GLU* 2.9 32.1 + - - -
249J THR* 3.0 34.2 + - - +
251J GLY* 4.1 0.8 - - - +
252J ASN 5.2 0.8 - - - +
253J GLU* 3.2 33.6 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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