Contacts of the helix formed by residues 201 - 213 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A TYR* 3.1 39.4 + - + +
200A ASN* 1.3 87.1 - - + +
202A ILE* 1.3 71.1 + - + +
203A LEU 3.6 0.7 - - - -
204A PRO* 3.8 2.4 - - - +
205A MET* 2.9 47.0 + - + +
238A PHE* 4.4 7.2 - - + +
241A LEU* 4.8 19.3 - - + -
242A VAL* 3.7 33.4 - - + -
245A ASN* 4.4 8.5 - - - +
255A THR* 5.4 7.9 - - + -
259A ILE* 5.7 0.2 - - + -
243B GLU* 4.9 8.3 - - - +
248B LYS* 5.6 2.0 - - - -
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Residues in contact with ILE 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PRO* 5.3 3.8 - - + -
121A PHE* 4.4 17.3 - - + -
197A TYR* 3.0 30.4 + - + +
198A ILE* 3.8 22.4 - - + +
201A ILE* 1.3 83.0 - - + +
203A LEU* 1.3 73.9 + - + +
205A MET* 3.2 6.2 + - - +
206A LEU* 2.9 47.1 + - + +
255A THR* 6.5 0.4 - - + -
258A ILE* 6.4 1.1 - - + -
409A PLC 3.7 33.2 - - + -
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Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ILE* 2.9 37.6 + - + +
202A ILE* 1.3 77.0 - - + +
204A PRO* 1.3 63.5 - - + +
206A LEU* 3.3 10.1 + - + +
207A PHE* 2.9 46.7 + - + -
409A PLC 3.6 32.1 - - + -
260B PHE* 3.6 35.4 - - + -
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Residues in contact with PRO 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ILE 3.9 1.1 - - - +
199A PRO 3.6 23.3 - - - +
200A ASN 3.9 9.2 - - - +
201A ILE 3.8 8.3 - - - -
202A ILE 3.6 2.7 - - - -
203A LEU* 1.3 89.8 - - + +
205A MET* 1.3 63.8 + - - +
206A LEU 2.9 5.5 + - - -
207A PHE* 2.9 21.5 + - + +
208A ILE* 3.0 19.2 + - - +
238A PHE* 3.8 15.0 - - + -
239B ASN* 4.8 2.0 - - - +
260B PHE* 4.9 3.8 - - + -
263B TYR* 3.5 38.1 - - + -
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Residues in contact with MET 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ILE* 2.9 32.4 + - + +
202A ILE* 3.6 5.2 - - - +
204A PRO* 1.3 79.5 - - - +
206A LEU* 1.3 58.7 + - + +
208A ILE* 3.2 22.9 - - + +
209A LEU* 3.5 11.4 + - - +
235A HIS* 3.8 28.2 + - + +
238A PHE* 3.3 51.0 - - + +
258A ILE* 5.4 3.4 - - - -
259A ILE* 3.8 31.2 - - + -
262A ILE* 4.1 13.9 - - + +
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Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ILE* 2.9 41.1 + - + +
203A LEU* 3.5 13.2 - - + +
205A MET* 1.3 76.8 - - + +
207A PHE* 1.3 68.8 + - + +
209A LEU* 2.9 10.6 + - + +
210A PHE* 2.8 50.7 + - + -
258A ILE* 6.6 0.2 - - + -
262A ILE* 5.3 5.4 - - + -
303A PHE* 3.6 36.1 - - + -
409A PLC 3.8 20.0 - - + -
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Residues in contact with PHE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A LEU* 2.9 49.7 + - + -
204A PRO* 2.9 7.0 + - + +
206A LEU* 1.3 72.1 - - + +
208A ILE* 1.3 57.3 + - + +
210A PHE* 3.1 21.8 + + - +
211A ILE* 2.8 38.8 + - + +
260B PHE* 4.1 14.8 - + - -
263B TYR* 3.7 33.0 - - + +
264B LEU* 3.2 32.8 - - + -
267B PHE* 3.9 27.9 - + + -
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Residues in contact with ILE 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A PRO 3.0 18.7 + - - +
205A MET* 3.2 20.9 - - + +
207A PHE* 1.3 76.3 - - + +
209A LEU* 1.3 59.3 + - - +
211A ILE* 3.9 7.4 - - - +
212A SER* 3.5 3.3 + - - -
231A THR* 3.4 26.5 - - - +
234A ALA* 4.0 7.6 - - + +
235A HIS* 3.2 48.0 - - + +
238A PHE* 5.5 4.5 - - + -
266A TYR* 3.2 23.3 + - - +
232B LEU* 4.0 24.9 - - + -
236B ILE* 4.1 19.5 - - + -
263B TYR* 5.2 5.4 - - + -
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Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A MET 3.6 10.1 - - - +
206A LEU* 2.9 15.6 + - + +
208A ILE* 1.3 81.5 - - - +
210A PHE* 1.3 67.4 + - + +
212A SER* 3.0 31.1 + - - +
213A TRP* 3.4 36.7 + - + +
262A ILE* 4.5 11.7 - - + -
265A PHE* 4.3 15.5 - - + +
266A TYR* 3.3 26.2 - - + +
303A PHE* 3.6 39.5 - - + -
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Residues in contact with PHE 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LEU* 2.8 56.6 + - + -
207A PHE* 3.1 15.0 + + - +
209A LEU* 1.3 73.1 - - + +
211A ILE* 1.3 68.9 + - - +
213A TRP* 2.9 59.0 + + + +
214A THR* 3.5 6.3 + - - +
303A PHE* 4.8 5.4 - + - -
267B PHE* 3.4 31.4 - + + -
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Residues in contact with ILE 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A PHE* 2.8 25.5 + - + +
208A ILE* 3.9 7.0 - - + +
210A PHE* 1.3 74.7 - - - +
212A SER* 1.3 62.4 + - - +
214A THR* 2.7 32.3 + - - -
227A LEU* 3.4 16.7 - - + +
231A THR* 3.6 18.4 - - + -
229B VAL* 4.4 7.2 - - + -
232B LEU* 3.8 27.4 - - + -
263B TYR 6.0 0.2 - - - +
266B TYR 4.9 0.4 - - - +
267B PHE* 3.7 30.5 - - + +
270B VAL* 3.9 33.9 - - + -
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Residues in contact with SER 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A ILE 3.5 3.2 + - - -
209A LEU* 3.0 21.0 + - - +
211A ILE* 1.3 76.3 - - - +
213A TRP* 1.3 74.9 + - - +
214A THR 3.3 0.9 + - - -
215A ALA* 3.3 20.3 + - - +
216A PHE* 5.4 1.4 - - - -
227A LEU* 4.6 4.9 - - - +
228A VAL* 3.8 15.7 - - - +
231A THR* 3.6 22.6 - - - +
265A PHE 4.2 7.1 + - - -
266A TYR* 3.8 17.8 - - - -
269A ALA* 4.5 5.7 - - - +
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Residues in contact with TRP 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A LEU* 3.8 27.6 - - + +
210A PHE* 2.9 43.3 + + + +
212A SER* 1.3 85.4 + - - +
214A THR* 1.3 58.3 + - - +
215A ALA 3.0 7.0 + - - -
216A PHE* 3.2 47.2 + + + +
217A TRP* 3.7 10.6 - - + -
265A PHE* 3.9 27.5 + + - -
269A ALA* 5.2 1.1 - - + -
299A PHE* 3.5 27.3 - + + -
300A PRO* 3.9 37.9 - - + -
303A PHE* 4.0 21.5 - + + -
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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