Contacts of the helix formed by residues 201 - 214 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197D TYR* 3.1 39.6 + - + +
200D ASN* 1.3 88.6 - - + +
202D ILE* 1.3 70.0 + - + +
203D LEU 3.7 0.7 - - - -
204D PRO* 3.8 2.5 - - - +
205D MET* 2.9 47.8 + - + +
238D PHE* 4.4 7.8 - - + +
241D LEU* 4.8 13.5 - - + -
242D VAL* 3.7 34.1 - - + -
245D ASN* 4.5 8.3 - - - +
255D THR* 5.4 7.4 - - + -
243E GLU* 4.7 10.1 - - - +
248E LYS* 5.5 2.9 - - - -
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Residues in contact with ILE 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D PRO* 5.3 3.1 - - + -
121D PHE* 4.4 16.8 - - + -
197D TYR* 3.0 29.4 + - + +
198D ILE* 3.8 23.8 - - + +
201D ILE* 1.3 81.3 - - + +
203D LEU* 1.3 74.0 + - + +
205D MET* 3.2 6.8 + - - +
206D LEU* 2.9 46.2 + - + +
255D THR* 6.6 0.4 - - + -
258D ILE* 6.4 2.0 - - + -
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Residues in contact with LEU 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D ILE* 2.9 42.4 + - + +
199D PRO* 5.8 0.2 - - + -
202D ILE* 1.3 83.7 - - + +
204D PRO* 1.3 63.7 - - + +
206D LEU* 3.3 13.0 + - + +
207D PHE* 2.9 45.1 + - + -
260E PHE* 3.6 35.0 - - + -
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Residues in contact with PRO 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D ILE 3.9 0.7 - - - +
199D PRO 3.6 24.0 - - - +
200D ASN 3.9 9.4 - - - +
201D ILE 3.8 7.9 - - - +
202D ILE 3.6 2.2 - - - -
203D LEU* 1.3 89.8 - - + +
205D MET* 1.3 63.9 + - - +
206D LEU 2.9 5.6 + - - -
207D PHE* 3.0 20.6 + - + +
208D ILE* 3.0 18.6 + - - +
238D PHE* 3.8 14.6 - - + -
239E ASN* 4.8 2.5 - - - +
260E PHE* 4.9 4.5 - - + -
263E TYR* 3.6 35.9 - - + -
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Residues in contact with MET 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D ILE* 2.9 33.5 + - + +
202D ILE* 3.2 5.6 + - - +
204D PRO* 1.3 78.8 - - - +
206D LEU* 1.3 58.6 + - + +
208D ILE* 3.2 22.9 - - - +
209D LEU* 3.5 11.4 + - - +
235D HIS* 3.8 28.0 + - + +
238D PHE* 3.3 51.3 - - + +
258D ILE* 5.4 3.4 - - - -
259D ILE* 3.8 31.6 - - + -
262D ILE* 4.1 14.5 - - + +
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Residues in contact with LEU 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D ILE* 2.9 39.1 + - + +
203D LEU* 3.5 15.9 - - + +
204D PRO 2.9 0.4 + - - -
205D MET* 1.3 76.7 - - + +
207D PHE* 1.3 66.8 + - + +
208D ILE 3.2 0.9 - - - -
209D LEU* 2.9 9.6 + - + +
210D PHE* 2.8 50.4 + - + -
262D ILE* 5.3 5.4 - - + -
303D PHE* 3.6 36.3 - - + -
307D ASN* 6.1 0.9 - - - +
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Residues in contact with PHE 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D LEU* 2.9 40.6 + - + -
204D PRO* 3.7 5.6 - - + +
206D LEU* 1.3 72.9 - - + +
208D ILE* 1.3 58.1 + - + +
210D PHE* 3.0 22.6 + + - +
211D ILE* 2.8 38.3 + - + +
260E PHE* 4.0 26.2 - + - -
263E TYR* 3.8 32.3 - - + +
264E LEU* 3.3 31.2 - - + -
267E PHE* 4.0 26.1 - + + -
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Residues in contact with ILE 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D PRO 3.0 18.4 + - - +
205D MET* 3.2 20.9 - - + +
207D PHE* 1.3 77.1 - - + +
209D LEU* 1.3 58.4 + - - +
211D ILE* 3.9 7.4 - - - +
212D SER 3.5 3.3 + - - -
231D THR* 3.4 25.7 - - - +
234D ALA* 4.0 7.9 - - + +
235D HIS* 3.2 48.5 - - + +
238D PHE* 5.5 5.4 - - + -
266D TYR* 3.2 22.8 + - - +
232E LEU* 4.1 18.2 - - + -
236E ILE* 4.1 24.2 - - + -
263E TYR* 5.1 6.5 - - + -
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Residues in contact with LEU 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D MET 3.6 10.3 - - - +
206D LEU* 2.9 15.1 + - + +
208D ILE* 1.3 81.9 - - - +
210D PHE* 1.3 67.7 + - + +
212D SER* 3.0 31.9 + - - +
213D TRP* 3.4 35.9 + - + +
262D ILE* 4.5 11.9 - - + -
265D PHE* 4.3 15.3 - - + +
266D TYR* 3.3 25.4 - - + +
303D PHE* 3.6 40.2 - - + -
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Residues in contact with PHE 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D LEU* 2.8 56.8 + - + -
207D PHE* 3.6 16.8 - + - +
209D LEU* 1.3 71.2 - - + +
211D ILE* 1.3 69.1 + - - +
213D TRP* 2.9 58.3 + + + +
214D THR* 3.5 5.9 + - - +
303D PHE* 4.8 4.7 - + - -
267E PHE* 3.5 30.5 - + + -
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Residues in contact with ILE 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D PHE* 2.8 26.5 + - + +
208D ILE* 3.9 5.4 - - - +
210D PHE* 1.3 74.7 - - - +
212D SER* 1.3 63.1 + - - +
214D THR* 2.7 31.9 + - - -
227D LEU* 3.4 16.4 - - + +
231D THR* 3.6 18.8 - - + -
229E VAL* 4.4 7.0 - - + -
232E LEU* 3.8 27.6 - - + -
263E TYR 5.9 0.4 - - - +
266E TYR* 4.9 1.1 - - + +
267E PHE* 3.6 30.3 - - + +
270E VAL* 4.0 32.3 - - + -
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Residues in contact with SER 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D ILE 3.5 3.8 + - - -
209D LEU* 3.0 22.5 + - - +
211D ILE* 1.3 76.7 - - - +
213D TRP* 1.3 73.5 + - - +
215D ALA* 3.3 21.1 + - - +
216D PHE* 5.4 1.4 - - - -
227D LEU* 4.6 5.1 - - - +
228D VAL* 3.8 16.1 - - - +
231D THR* 3.6 23.5 - - - +
265D PHE 4.2 7.3 + - - -
266D TYR* 3.8 17.9 - - - -
269D ALA* 4.5 5.7 - - - +
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Residues in contact with TRP 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D LEU* 3.8 28.1 - - + +
210D PHE* 2.9 48.4 + + + +
212D SER* 1.3 84.8 + - - +
214D THR* 1.3 58.6 + - - +
215D ALA 3.0 6.6 + - - -
216D PHE* 3.2 47.9 + + + +
217D TRP* 3.7 10.9 - - + -
265D PHE* 4.0 28.0 + + - -
269D ALA* 5.2 1.1 - - + -
299D PHE* 3.5 26.9 - + + -
300D PRO* 3.9 39.3 - - + -
303D PHE* 4.0 17.7 - + + -
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Residues in contact with THR 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D PHE 3.5 7.5 + - - +
211D ILE* 2.7 29.1 + - + +
213D TRP* 1.3 71.5 - - - +
215D ALA* 1.3 57.2 + - - +
216D PHE 3.2 2.7 + - - -
217D TRP* 3.4 19.5 + - - +
218D SER 3.9 3.1 + - - -
227D LEU* 3.1 23.7 - - - +
221E TYR* 3.6 10.2 + - - -
267E PHE* 5.8 0.7 - - + -
270E VAL* 3.5 23.0 - - + +
271E ILE* 4.9 12.6 - - + -
274E THR* 3.2 28.0 + - + +
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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