Contacts of the helix formed by residues 201 - 214 (chain B) in PDB entry 5J0Z
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 ILE 201 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197B TYR* 3.1 38.8 + - + +
200B ASN* 1.3 88.4 - - + +
202B ILE* 1.3 70.7 + - + +
203B LEU 3.6 1.1 - - - -
204B PRO* 3.8 1.9 - - - +
205B MET* 2.9 47.6 + - + +
238B PHE* 4.3 7.6 - - + +
241B LEU* 4.8 18.8 - - + -
242B VAL* 3.7 34.5 - - + -
245B ASN* 4.4 9.0 - - - +
255B THR* 5.4 6.7 - - + -
243C GLU* 4.9 8.5 - - - +
248C LYS* 5.3 2.5 - - - -
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Residues in contact with ILE 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B PRO* 5.3 3.4 - - + -
121B PHE* 4.4 17.3 - - + -
197B TYR* 3.0 29.9 + - + +
198B ILE* 3.8 22.7 - - + +
201B ILE* 1.3 82.4 - - + +
203B LEU* 1.3 74.0 + - + +
205B MET* 3.2 6.4 + - - +
206B LEU* 2.9 45.6 + - + +
255B THR* 6.6 0.2 - - + -
258B ILE* 6.5 1.3 - - + -
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Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B ILE* 2.8 43.3 + - + +
199B PRO* 5.8 0.2 - - + -
202B ILE* 1.3 84.1 - - + +
204B PRO* 1.3 63.9 - - + +
206B LEU* 3.3 13.5 + - + +
207B PHE* 2.9 44.8 + - + -
260C PHE* 3.5 35.9 - - + -
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Residues in contact with PRO 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B ILE 3.9 1.3 - - - +
199B PRO 3.6 23.8 - - - +
200B ASN 3.9 9.9 - - - +
201B ILE 3.8 7.9 - - - -
202B ILE 3.6 2.2 - - - -
203B LEU* 1.3 89.6 - - + +
205B MET* 1.3 66.8 + - - +
206B LEU 2.9 3.4 + - - -
207B PHE* 2.9 21.0 + - + +
208B ILE* 3.0 18.9 + - - +
238B PHE* 3.7 15.3 - - + -
239C ASN* 4.7 2.9 - - - +
260C PHE* 4.8 4.5 - - + -
263C TYR* 3.6 35.9 - - + -
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Residues in contact with MET 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B ILE* 2.9 31.1 + - + +
202B ILE* 3.2 5.4 + - - +
204B PRO* 1.3 78.8 - - - +
206B LEU* 1.3 60.0 + - + +
208B ILE* 3.2 24.4 - - + +
209B LEU* 3.5 11.1 + - - +
235B HIS* 3.8 28.7 + - + +
238B PHE* 3.3 49.9 - - + +
258B ILE* 5.4 2.5 - - - -
259B ILE* 3.8 31.4 - - + -
262B ILE* 4.1 15.0 - - + +
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Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B ILE* 2.9 39.7 + - + +
203B LEU* 3.5 16.2 - - + +
204B PRO 2.9 0.4 + - - -
205B MET* 1.3 77.7 - - + +
207B PHE* 1.3 67.4 + - + +
209B LEU* 2.9 9.4 + - + +
210B PHE* 2.8 49.9 + - + -
262B ILE* 5.3 5.6 - - + -
303B PHE* 3.6 36.6 - - + -
307B ASN* 6.1 0.7 - - - +
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Residues in contact with PHE 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B LEU* 2.9 36.4 + - + -
204B PRO* 2.9 5.8 + - + +
206B LEU* 1.3 75.5 - - + +
208B ILE* 1.3 57.4 + - + +
210B PHE* 3.1 22.3 + + - +
211B ILE* 2.8 37.8 + - + +
260C PHE* 3.9 28.5 - + - -
263C TYR* 3.8 36.6 - - + +
264C LEU* 3.3 30.7 - - + -
267C PHE* 4.0 23.5 - + + -
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Residues in contact with ILE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B PRO 3.0 17.8 + - - +
205B MET* 3.2 20.6 - - + +
207B PHE* 1.3 76.2 - - + +
209B LEU* 1.3 60.2 + - - +
211B ILE* 4.2 7.6 - - + -
212B SER 3.5 3.5 + - - -
231B THR* 3.4 25.3 - - - +
234B ALA* 4.0 7.2 - - + -
235B HIS* 3.2 49.6 - - + +
238B PHE* 5.5 5.2 - - + -
266B TYR* 3.2 22.4 + - - +
232C LEU* 4.2 17.7 - - + -
236C ILE* 4.0 25.4 - - + -
263C TYR* 5.0 6.7 - - + -
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Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B MET 3.6 10.5 - - - +
206B LEU* 2.9 14.6 + - + +
208B ILE* 1.3 81.6 - - - +
210B PHE* 1.3 68.5 + - + +
212B SER* 3.0 31.4 + - - +
213B TRP* 3.4 35.4 + - + +
262B ILE* 4.5 11.4 - - + -
265B PHE* 4.3 15.3 - - + +
266B TYR* 3.3 25.6 - - + +
303B PHE* 3.6 40.6 - - + -
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Residues in contact with PHE 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B LEU* 2.8 55.0 + - + -
207B PHE* 3.1 17.9 + + - +
209B LEU* 1.3 71.8 - - + +
211B ILE* 1.3 68.6 + - - +
213B TRP* 2.9 59.1 + + + +
214B THR* 3.5 6.6 + - - +
303B PHE* 4.8 5.4 - + - -
267C PHE* 3.4 30.2 - + + -
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Residues in contact with ILE 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B PHE* 2.8 28.1 + - + +
208B ILE* 3.9 5.6 - - + +
210B PHE* 1.3 74.5 - - - +
212B SER* 1.3 62.0 + - - +
214B THR* 2.7 31.6 + - - -
227B LEU* 3.5 16.4 - - + +
231B THR* 3.6 18.6 - - + -
229C VAL* 4.5 6.5 - - + -
232C LEU* 3.7 28.3 - - + -
263C TYR 5.8 0.4 - - - +
266C TYR* 4.9 0.9 - - + +
267C PHE* 3.6 34.1 - - + +
270C VAL* 4.0 28.3 - - + -
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Residues in contact with SER 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ILE 3.5 3.6 + - - -
209B LEU* 3.0 19.3 + - - +
211B ILE* 1.3 76.5 - - - +
213B TRP* 1.3 75.5 + - - +
214B THR 3.3 0.7 + - - -
215B ALA* 3.3 20.4 + - - +
216B PHE* 5.4 1.4 - - - -
227B LEU* 4.6 4.9 - - - +
228B VAL* 3.8 16.2 - - - +
231B THR* 3.6 23.7 - - - +
265B PHE 4.2 8.0 + - - -
266B TYR* 3.8 17.4 - - - -
269B ALA* 4.5 5.0 - - - +
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Residues in contact with TRP 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B LEU* 3.8 27.5 - - + +
210B PHE* 2.9 47.7 + + + +
212B SER* 1.3 85.1 + - - +
214B THR* 1.3 59.8 + - - +
215B ALA 3.0 6.1 + - - -
216B PHE* 3.2 47.9 + + + +
217B TRP* 3.7 10.5 - - + -
265B PHE* 3.9 27.7 + + - -
269B ALA* 5.2 0.9 - - + -
299B PHE* 3.5 26.6 - + + -
300B PRO* 3.9 40.6 - - + -
303B PHE* 4.0 17.7 - + + -
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Residues in contact with THR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B PHE 3.5 7.1 + - - +
211B ILE* 2.7 29.3 + - - +
213B TRP* 1.3 70.4 - - - +
215B ALA* 1.3 54.4 + - - +
216B PHE 3.2 4.3 + - - -
217B TRP* 3.4 14.5 + - - -
218B SER 3.9 3.5 + - - -
227B LEU* 3.1 24.0 - - - +
221C TYR* 3.7 10.0 + - - -
267C PHE* 5.7 0.9 - - + -
270C VAL* 3.4 22.5 - - + +
271C ILE* 4.8 13.9 - - + -
274C THR* 3.2 32.6 + - + +
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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