Contacts of the helix formed by residues 201 - 214 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197C TYR* 3.1 39.0 + - + +
200C ASN* 1.3 87.8 - - + +
202C ILE* 1.3 71.6 + - + +
203C LEU 3.7 1.3 - - - -
204C PRO* 3.8 2.1 - - - +
205C MET* 2.9 47.0 + - + +
238C PHE* 4.3 7.4 - - + +
241C LEU* 4.8 18.4 - - + -
242C VAL* 3.7 33.9 - - + -
245C ASN* 4.4 8.1 - - - +
255C THR* 5.4 7.0 - - + -
259C ILE* 5.7 0.2 - - + -
243D GLU* 4.9 7.9 - - - +
248D LYS* 5.3 2.5 - - - -
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Residues in contact with ILE 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C PRO* 5.3 3.4 - - + -
121C PHE* 4.4 17.0 - - + -
197C TYR* 3.0 30.0 + - + +
198C ILE* 3.2 23.8 + - + +
201C ILE* 1.3 81.7 - - + +
203C LEU* 1.3 67.3 + - + +
205C MET* 3.2 6.5 + - - +
206C LEU* 2.9 52.4 + - + +
255C THR* 6.6 0.4 - - + -
258C ILE* 6.4 1.6 - - + -
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Residues in contact with LEU 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C ILE* 2.9 42.8 + - + +
199C PRO* 5.8 0.2 - - + -
202C ILE* 1.3 83.3 - - + +
204C PRO* 1.3 63.1 - - + +
206C LEU* 3.3 12.9 + - + +
207C PHE* 2.9 46.4 + - + -
260D PHE* 3.6 35.2 - - + -
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Residues in contact with PRO 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C ILE 3.9 1.1 - - - +
199C PRO 3.6 23.8 - - - +
200C ASN 3.9 9.6 - - - +
201C ILE 3.8 8.1 - - - -
202C ILE 3.6 1.8 - - - -
203C LEU* 1.3 89.4 - - + +
205C MET* 1.3 66.3 + - - +
206C LEU 2.9 3.5 + - - -
207C PHE* 2.9 21.3 + - + +
208C ILE* 3.0 18.8 + - - +
238C PHE* 3.7 15.0 - - + -
239D ASN* 4.8 2.9 - - - +
260D PHE* 4.9 4.7 - - + -
263D TYR* 3.6 35.4 - - + -
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Residues in contact with MET 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C ILE* 2.9 32.1 + - + +
202C ILE* 3.2 5.1 + - - +
204C PRO* 1.3 78.1 - - - +
206C LEU* 1.3 60.0 + - + +
208C ILE* 3.2 22.6 - - + +
209C LEU* 3.5 11.3 + - - +
235C HIS* 3.8 28.2 + - + +
238C PHE* 3.3 51.9 - - + +
239C ASN 4.5 0.2 - - - +
258C ILE* 5.4 3.4 - - - -
259C ILE* 3.8 31.9 - - + -
262C ILE* 4.1 13.7 - - + +
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Residues in contact with LEU 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C ILE* 2.9 41.1 + - + +
203C LEU* 3.5 14.4 - - + +
204C PRO 2.9 0.4 + - - -
205C MET* 1.3 77.9 - - + +
207C PHE* 1.3 61.7 + - + +
209C LEU* 2.9 9.2 + - + +
210C PHE* 2.8 56.4 + - + -
258C ILE* 6.6 0.2 - - + -
262C ILE* 5.3 5.8 - - + -
303C PHE* 3.6 35.7 - - + -
307C ASN* 6.1 0.4 - - - +
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Residues in contact with PHE 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C LEU* 2.9 40.7 + - + -
204C PRO* 2.9 5.8 + - + +
206C LEU* 1.3 71.8 - - + +
208C ILE* 1.3 58.3 + - + +
210C PHE* 3.0 22.1 + + - +
211C ILE* 2.8 38.3 + - + +
260D PHE* 3.9 25.8 - + - -
263D TYR* 3.8 32.8 - - + +
264D LEU* 3.4 29.4 - - + -
267D PHE* 4.4 23.8 - + + -
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Residues in contact with ILE 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C PRO 3.0 18.1 + - - +
205C MET* 3.2 20.2 - - + +
207C PHE* 1.3 76.3 - - + +
209C LEU* 1.3 59.4 + - - +
211C ILE* 3.9 7.8 + - + -
212C SER 3.5 3.3 + - - -
231C THR* 3.4 26.6 - - + +
234C ALA* 3.9 7.9 - - + +
235C HIS* 3.2 48.5 - - + +
238C PHE* 5.5 4.9 - - + -
266C TYR* 3.2 22.8 + - - +
232D LEU* 4.2 17.0 - - + -
236D ILE* 4.0 25.8 - - + -
263D TYR* 5.0 6.7 - - + -
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Residues in contact with LEU 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C MET 3.6 10.3 - - - +
206C LEU* 2.9 15.1 + - + +
208C ILE* 1.3 80.9 - - - +
210C PHE* 1.3 68.0 + - + +
212C SER* 3.0 31.1 + - - +
213C TRP* 3.4 35.7 + - + +
262C ILE* 4.5 11.4 - - + -
265C PHE* 4.3 15.3 - - + +
266C TYR* 3.3 25.8 - - + +
303C PHE* 3.6 39.9 - - + -
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Residues in contact with PHE 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C LEU* 2.8 57.5 + - + -
207C PHE* 3.6 18.6 - + - +
209C LEU* 1.3 72.3 - - + +
211C ILE* 1.3 68.6 + - - +
213C TRP* 2.9 58.0 + + + +
214C THR* 3.4 6.3 + - - +
303C PHE* 4.9 5.4 - + - -
267D PHE* 3.6 27.8 - + + -
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Residues in contact with ILE 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C PHE* 2.8 27.8 + - + +
208C ILE* 3.9 6.5 - - + +
210C PHE* 1.3 75.6 - - - +
212C SER* 1.4 52.1 + - - +
214C THR* 2.7 42.3 + - - -
227C LEU* 3.4 17.5 - - + +
231C THR* 3.7 18.6 - - + -
229D VAL* 4.5 6.5 - - + -
232D LEU* 3.8 27.4 - - + -
263D TYR 5.9 0.2 - - - +
266D TYR* 5.0 0.9 - - + +
267D PHE* 3.6 31.2 - - + +
270D VAL* 4.1 32.1 - - + -
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Residues in contact with SER 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C ILE 3.5 3.6 + - - -
209C LEU* 3.0 23.2 + - - +
211C ILE* 1.4 76.3 - - - +
213C TRP* 1.3 73.1 + - - +
215C ALA* 3.3 21.1 + - - +
216C PHE* 5.4 1.6 - - - -
227C LEU* 4.6 4.8 - - - +
228C VAL* 3.7 16.4 - - - +
231C THR* 3.6 23.7 - - - +
265C PHE 4.2 7.1 + - - -
266C TYR* 3.7 17.9 - - - -
269C ALA* 4.5 5.2 - - - +
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Residues in contact with TRP 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C LEU* 3.4 27.7 + - + +
210C PHE* 2.9 48.0 + + + +
212C SER* 1.3 85.9 + - - +
214C THR* 1.3 60.2 + - - +
215C ALA 3.0 6.2 + - - -
216C PHE* 3.2 47.9 + + + +
217C TRP* 3.7 10.6 - - + -
265C PHE* 3.9 28.6 + + - -
269C ALA* 5.2 0.9 - - + -
299C PHE* 3.5 26.2 - + + -
300C PRO* 4.0 38.1 - - + -
303C PHE* 4.0 17.5 - + + -
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Residues in contact with THR 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C PHE 3.4 8.2 + - - +
211C ILE* 2.7 28.2 + - - +
213C TRP* 1.3 69.8 - - - +
215C ALA* 1.3 55.6 + - - +
216C PHE 3.2 2.4 + - - -
217C TRP* 3.4 20.8 + - - +
218C SER 3.9 3.5 + - - -
227C LEU* 3.1 24.2 - - - +
221D TYR* 3.8 9.9 + - - -
267D PHE* 5.8 0.9 - - + -
270D VAL* 3.6 22.4 - - + +
271D ILE* 4.9 12.8 - - + -
274D THR* 3.3 27.3 + - + +
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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