Contacts of the helix formed by residues 181 - 196 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E SER* 4.2 8.3 - - - +
156E GLY 3.3 13.9 - - - +
157E ASP 3.5 17.0 - - - +
158E GLY 3.9 0.6 - - - -
159E VAL 3.6 24.0 - - - +
160E THR* 4.1 1.8 - - - +
180E LEU* 1.3 78.3 - - - +
182E GLY* 1.4 55.0 + - - +
183E ARG 3.3 2.0 - - - -
184E ASP* 2.9 36.7 + - - +
185E LEU* 3.5 5.7 + - - +
261E LEU* 5.1 0.4 - - - -
303E THR* 3.9 6.5 - - - -
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Residues in contact with GLY 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E GLY 2.9 5.9 + - - -
157E ASP* 4.3 7.4 - - - -
181E ALA* 1.4 72.1 - - - +
183E ARG* 1.3 54.9 + - - +
185E LEU* 3.3 6.7 + - - +
186E THR* 3.0 30.2 + - - -
213E LYS* 3.2 14.4 + - - -
303E THR* 2.8 29.0 + - - -
306E TYR* 5.6 0.4 - - - -
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Residues in contact with ARG 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E GLU* 1.1 182.9 + - + +
73E HIS* 2.7 45.0 + - - +
75E ILE 3.5 0.2 + - - -
77E THR* 2.1 38.3 - - - +
157E ASP* 3.2 13.5 + - - +
181E ALA 3.0 2.4 + - - -
182E GLY* 1.3 70.3 - - - +
184E ASP* 1.3 67.9 + - - +
186E THR* 3.3 5.8 + - - +
187E ASP* 3.0 34.2 + - - +
206E ARG* 5.0 9.0 - - - +
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Residues in contact with ASP 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E HIS* 3.4 29.6 + - - -
157E ASP 4.3 1.4 - - - +
179E ASP 4.0 5.9 - - - +
180E LEU* 3.6 30.7 - - + -
181E ALA 2.9 23.8 + - - +
183E ARG* 1.3 76.3 - - - +
185E LEU* 1.3 56.3 + - - +
187E ASP* 3.6 6.3 - - - +
188E TYR* 3.1 28.6 + - - +
267E LEU* 4.1 10.6 - - + +
269E MET* 4.0 11.8 - - - +
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Residues in contact with LEU 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E LEU* 3.9 26.0 - - + -
181E ALA 3.5 2.2 + - - +
182E GLY* 3.3 9.1 + - - +
183E ARG 3.1 0.6 - - - -
184E ASP* 1.3 79.8 - - - +
186E THR* 1.3 62.3 + - - +
188E TYR* 4.1 2.9 - - + +
189E LEU* 3.2 8.7 + - - +
213E LYS* 3.6 4.4 - - + +
257E CYS* 3.2 37.6 - - - +
258E PRO* 4.2 3.8 - - + -
260E ALA* 4.0 21.3 - - + -
261E LEU* 3.9 20.0 - - + -
267E LEU* 4.9 0.9 - - + -
303E THR* 3.9 13.0 - - + -
306E TYR* 3.1 41.1 - - + +
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Residues in contact with THR 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E GLY 3.0 9.9 + - - -
183E ARG* 3.3 7.3 + - - -
185E LEU* 1.3 73.7 - - - +
187E ASP* 1.3 62.7 + - - +
189E LEU* 3.4 6.0 + - - +
190E MET* 3.2 22.2 + - - +
206E ARG* 3.7 22.9 - - - +
209E VAL* 3.4 26.6 - - + +
210E ARG* 3.9 22.5 - - + +
213E LYS* 2.6 36.8 + - - +
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Residues in contact with ASP 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E GLU* 4.8 8.5 - - - +
183E ARG* 3.0 23.2 + - - +
184E ASP* 3.6 7.0 - - - +
186E THR* 1.3 76.4 - - - +
188E TYR* 1.3 62.6 + - - +
190E MET* 3.7 15.0 + - - +
191E LYS* 3.4 21.0 + - - +
206E ARG* 3.1 31.0 + - - -
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Residues in contact with TYR 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E ASP 3.1 15.9 + - - +
185E LEU* 4.2 3.8 - - - +
186E THR 3.4 0.2 - - - -
187E ASP* 1.3 77.1 - - - +
189E LEU* 1.3 66.5 + - - +
191E LYS* 3.8 21.4 - - - +
192E ILE* 3.1 52.2 + - + +
256E ARG* 3.3 31.5 + - - +
257E CYS* 4.2 18.4 - - - -
260E ALA* 4.4 5.2 - - + -
266E PHE* 3.3 43.0 + + + +
267E LEU* 3.4 24.0 - - + -
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Residues in contact with LEU 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E LEU 3.2 18.0 + - - +
186E THR 3.5 2.7 - - - +
188E TYR* 1.3 78.0 - - - +
190E MET* 1.3 50.9 + - - +
192E ILE* 3.2 15.2 + - + +
193E LEU* 2.8 49.2 + - + +
209E VAL* 3.2 38.6 - - + +
212E ILE* 4.1 13.5 - - + -
213E LYS* 3.6 21.3 - - + +
217E CYS* 4.5 9.9 - - - -
250E ILE* 5.3 2.7 - - + -
253E GLU* 4.6 13.5 - - + +
257E CYS* 3.6 21.3 - - + -
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Residues in contact with MET 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E THR 3.2 6.4 + - - +
187E ASP* 3.7 28.5 - - - +
188E TYR 3.4 0.2 - - - -
189E LEU* 1.3 78.9 - - - +
191E LYS* 1.3 51.5 + - - +
193E LEU* 3.4 4.3 + - - +
194E THR* 2.8 43.5 + - - +
200E PHE* 4.3 20.3 - - + +
206E ARG* 3.7 44.4 - - + +
209E VAL* 3.8 35.2 - - + -
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Residues in contact with LYS 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E ASP 3.4 14.5 + - - +
188E TYR* 3.8 31.0 - - - +
189E LEU 3.3 0.2 - - - -
190E MET* 1.3 75.6 - - - +
192E ILE* 1.3 71.3 + - - +
194E THR* 3.8 7.5 - - + -
195E GLU* 2.9 51.5 + - + +
173F HIS 5.9 1.3 - - - -
175F ILE 6.1 0.7 - - - -
176F LEU* 5.2 14.8 - - + -
284F LYS* 5.1 17.2 - - - +
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Residues in contact with ILE 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188E TYR* 3.1 58.3 + - + +
189E LEU* 3.3 18.8 - - + +
191E LYS* 1.3 78.9 - - - +
193E LEU* 1.3 61.8 + - + +
195E GLU* 3.2 25.8 + - - +
196E ARG* 3.3 11.6 + - - +
253E GLU* 3.9 45.2 - - + +
256E ARG* 3.8 32.7 + - + +
257E CYS* 4.3 7.0 - - + +
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Residues in contact with LEU 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E LEU* 2.8 30.8 + - + +
190E MET 3.6 4.7 - - - +
191E LYS 3.2 0.2 - - - -
192E ILE* 1.3 75.6 - - - +
194E THR* 1.3 54.2 + - - +
196E ARG* 3.1 13.2 + - - +
198E TYR* 2.7 46.7 + - + +
200E PHE* 3.8 27.4 - - + -
209E VAL* 4.6 2.7 - - + -
212E ILE* 3.9 21.1 - - + -
248E ILE* 4.5 5.6 - - + -
250E ILE* 3.9 26.2 - - + -
253E GLU* 3.9 25.4 - - + +
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Residues in contact with THR 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E MET* 2.8 27.1 + - - +
191E LYS* 4.0 8.7 - - + +
193E LEU* 1.3 67.0 - - - +
195E GLU* 1.3 65.9 + - + +
196E ARG 3.1 1.3 - - - -
197E GLY* 3.0 14.9 + - - -
198E TYR 3.5 24.0 + - - +
200E PHE* 3.8 18.5 + - - +
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Residues in contact with GLU 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E LYS* 2.9 49.1 + - + +
192E ILE* 3.2 24.7 + - - +
194E THR* 1.3 73.4 - - + +
196E ARG* 1.3 57.6 + - - +
197E GLY* 2.8 11.5 + - - -
256E ARG* 5.4 3.0 + - - +
110F LEU* 6.4 3.4 - - + -
113F LYS* 3.5 11.5 + - - +
175F ILE 5.5 2.6 - - - +
177F ARG* 5.9 0.9 + - - -
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Residues in contact with ARG 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E ILE 3.3 9.6 + - - +
193E LEU 3.1 13.3 + - - +
195E GLU* 1.3 73.9 - - - +
197E GLY* 1.3 62.6 + - - +
198E TYR* 3.4 23.6 + - + -
237E GLU* 2.9 32.5 + - - -
249E THR* 3.0 33.5 + - - +
251E GLY* 4.1 1.0 - - - +
252E ASN 5.2 1.0 - - - +
253E GLU* 3.2 34.2 + - - +
113F LYS* 3.1 31.2 + - - +
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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