Contacts of the helix formed by residues 202 - 217 (chain E) in PDB entry 4QOZ
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 THR 202 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174E VAL* 3.9 1.8 - - - -
175E ARG* 3.4 46.8 - - - +
177E GLU* 3.7 30.0 + - + +
201E ASP* 1.3 79.6 - - - +
203E PHE* 1.3 65.7 + - - +
204E PRO* 3.4 14.3 - - - +
205E GLN* 3.5 17.3 + - - +
206E VAL* 3.2 17.7 + - - +
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Residues in contact with PHE 203 (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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151E ILE* 3.8 22.2 - - + -
154E PHE* 4.1 24.5 - + - -
174E VAL* 3.7 26.5 - - + +
175E ARG 4.6 1.2 + - - -
202E THR* 1.3 77.5 - - - +
204E PRO* 1.3 69.0 - - + +
206E VAL* 3.3 1.5 + - - -
207E LEU* 2.9 49.3 + - + +
239E LEU* 3.5 28.9 - - + -
242E GLN* 3.5 31.4 - - + +
243E CYS* 4.2 6.1 - - - -
246E SER* 3.7 17.5 - - - +
248E LEU* 4.1 12.1 - - + -
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Residues in contact with PRO 204 (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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177E GLU* 6.3 1.1 - - - -
202E THR* 3.6 14.1 - - - +
203E PHE* 1.3 93.5 - - + +
205E GLN* 1.3 57.6 + - + +
207E LEU* 3.7 0.6 - - + +
208E LYS* 3.0 25.8 + - - +
246E SER* 4.1 22.7 - - - +
248E LEU* 4.3 10.5 - - + -
344E MET* 3.3 25.7 - - + +
347E PHE* 4.5 21.5 - - + -
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Residues in contact with GLN 205 (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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175E ARG* 5.5 1.4 + - - -
201E ASP* 3.7 40.9 + - + +
202E THR* 3.5 17.0 + - - +
203E PHE 3.3 0.6 - - - -
204E PRO* 1.3 77.7 - - + +
206E VAL* 1.3 58.3 + - - +
208E LYS* 3.0 11.5 - - - +
209E LYS* 2.9 36.9 + - - +
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Residues in contact with VAL 206 (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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154E PHE* 4.0 18.2 - - + -
172E GLN* 3.7 33.9 - - + +
173E TYR 3.7 19.1 - - - +
174E VAL* 4.0 20.4 - - + -
201E ASP* 3.8 19.7 - - + +
202E THR 3.2 16.4 + - - +
203E PHE* 3.3 3.3 + - + +
205E GLN* 1.3 72.9 - - - +
207E LEU* 1.3 66.8 - - - +
209E LYS* 3.0 9.8 + - + +
210E VAL* 2.9 23.1 + - + +
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Residues in contact with LEU 207 (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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154E PHE* 4.0 24.6 - - + -
203E PHE* 2.9 43.4 + - + +
204E PRO 3.7 3.8 - - - +
206E VAL* 1.3 75.5 - - - +
208E LYS* 1.3 58.0 + - - +
210E VAL* 3.1 10.5 + - + +
211E ILE* 2.9 44.9 + - + +
239E LEU* 5.6 3.1 - - + -
243E CYS* 5.3 0.7 - - - -
248E LEU* 4.2 5.2 - - + -
251E PRO* 4.4 11.7 - - + -
253E PHE* 4.7 11.7 - - + -
344E MET* 4.1 8.3 - - + -
345E PRO* 4.0 30.5 - - + -
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Residues in contact with LYS 208 (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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204E PRO 3.0 14.5 + - - +
205E GLN* 3.0 17.7 - - - +
207E LEU* 1.3 76.6 - - - +
209E LYS* 1.3 63.0 + - + +
211E ILE* 3.2 5.5 + - + +
212E ASP* 3.0 50.4 + - - +
215E LYS* 5.9 2.4 - - - +
344E MET* 3.7 29.8 - - + +
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Residues in contact with LYS 209 (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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170E PHE* 3.8 15.7 - - + -
172E GLN* 3.9 25.6 - - - +
201E ASP* 2.7 31.1 + - - +
205E GLN* 2.9 24.0 + - - +
206E VAL* 3.0 10.3 + - - +
208E LYS* 1.3 79.0 - - + +
210E VAL* 1.3 62.0 + - - +
212E ASP* 3.4 9.7 + - - +
213E TRP* 3.0 24.1 + - - +
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Residues in contact with VAL 210 (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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154E PHE* 3.6 44.6 - - + -
156E VAL* 4.4 9.4 - - + -
170E PHE* 3.4 33.2 - - + -
206E VAL 2.9 15.8 + - - +
207E LEU* 3.1 11.4 + - + +
209E LYS* 1.3 75.9 - - - +
211E ILE* 1.3 61.2 + - + +
213E TRP* 3.1 6.7 + - + +
214E MET* 2.9 46.2 + - + +
253E PHE* 5.5 2.2 - - + -
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Residues in contact with ILE 211 (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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207E LEU* 2.9 35.4 + - + +
208E LYS* 3.2 5.1 + - + +
210E VAL* 1.3 75.9 - - + +
212E ASP* 1.3 68.1 + - - +
214E MET* 3.3 6.9 + - - +
215E LYS* 2.9 35.3 + - + +
253E PHE* 3.9 28.3 - - + -
342E PRO* 3.7 28.0 - - + +
343E GLN* 3.6 24.7 - - - +
344E MET* 3.6 20.2 - - + +
345E PRO* 4.2 1.6 - - + -
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Residues in contact with ASP 212 (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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208E LYS* 3.0 51.0 + - - +
209E LYS* 3.8 10.5 - - - +
211E ILE* 1.3 78.1 - - - +
213E TRP* 1.3 57.7 + - - +
215E LYS* 3.2 17.5 + - - +
216E LEU* 3.0 36.3 + - + +
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Residues in contact with TRP 213 (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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131E CYS* 5.3 1.8 - - - -
156E VAL* 3.6 33.4 - - + -
158E LEU* 3.9 28.3 - - + -
168E ASP* 3.2 36.2 + - + -
169E THR 3.8 19.5 + - - -
170E PHE* 3.7 34.1 - + + -
209E LYS 3.0 13.8 + - - +
210E VAL 3.1 8.0 + - - +
212E ASP* 1.3 78.0 - - - +
214E MET* 1.3 78.1 + - + +
216E LEU* 3.3 15.0 + - + +
217E LYS* 3.2 43.7 + - + +
219E LEU* 5.4 0.9 - - + -
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Residues in contact with MET 214 (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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131E CYS* 4.4 8.3 - - - -
156E VAL* 5.7 3.1 - - + -
210E VAL* 2.9 35.9 + - + +
211E ILE* 3.7 8.3 - - - +
213E TRP* 1.3 91.0 - - + +
215E LYS* 1.3 61.6 + - - +
217E LYS* 3.2 8.9 + - - +
218E GLU 3.3 8.5 + - - -
219E LEU* 3.3 31.9 + - + +
225E TYR* 3.5 40.6 - - + +
227E LEU* 4.5 3.1 - - + -
253E PHE* 4.0 21.8 - - + -
342E PRO* 3.7 22.9 - - + -
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Residues in contact with LYS 215 (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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208E LYS* 5.9 2.6 - - - +
211E ILE* 2.9 30.8 + - + +
212E ASP* 3.6 16.0 + - - +
214E MET* 1.3 73.8 - - - +
216E LEU* 1.3 61.5 + - - +
218E GLU* 3.0 23.9 + - - +
219E LEU 5.0 1.3 - - - +
342E PRO* 3.3 33.6 + - + +
343E GLN* 4.7 11.7 - - - +
344E MET* 5.1 2.2 - - - +
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Residues in contact with LEU 216 (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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212E ASP* 3.0 17.6 + - + +
213E TRP* 3.5 19.1 - - + +
215E LYS* 1.3 77.4 - - - +
217E LYS* 1.3 64.8 + - + +
218E GLU* 3.2 8.7 + - - +
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Residues in contact with LYS 217 (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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129E TYR* 5.1 1.4 - - + -
158E LEU* 3.9 22.9 - - + +
167E GLU* 5.1 9.7 + - - +
168E ASP* 2.5 44.2 + - - +
213E TRP* 3.2 37.2 + - + +
214E MET* 3.2 9.0 + - - +
215E LYS 3.2 1.0 - - - -
216E LEU* 1.3 79.4 - - - +
218E GLU* 1.3 71.2 + - - +
219E LEU* 3.3 15.3 + - + +
223E TYR* 3.2 18.4 - - - -
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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
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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