Contacts of the helix formed by residues 201 - 214 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A GLU* 5.0 7.4 - - - +
248A LYS* 5.6 2.0 - - - -
197E TYR* 3.1 40.2 + - + +
200E ASN* 1.3 86.5 - - + +
202E ILE* 1.3 69.3 + - + +
203E LEU 3.7 0.9 - - - -
204E PRO* 3.8 2.5 - - - +
205E MET* 2.9 48.6 + - + +
238E PHE* 4.3 8.2 - - + +
241E LEU* 4.8 17.9 - - + -
242E VAL* 3.7 34.1 - - + -
245E ASN* 4.4 8.3 - - - +
255E THR* 5.4 7.0 - - + -
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Residues in contact with ILE 202 (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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120E PRO* 5.3 3.4 - - + -
121E PHE* 4.4 17.0 - - + -
197E TYR* 3.0 30.3 + - + +
198E ILE* 3.2 23.3 + - + +
201E ILE* 1.3 81.3 - - + +
203E LEU* 1.3 72.2 + - + +
205E MET* 3.2 6.1 + - - +
206E LEU* 2.9 46.8 + - + +
255E THR* 6.6 0.4 - - + -
258E ILE* 6.4 1.8 - - + -
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Residues in contact with LEU 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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260A PHE* 3.7 34.8 - - + -
198E ILE* 2.9 42.6 + - + +
202E ILE* 1.3 82.6 - - + +
204E PRO* 1.3 62.8 - - + +
206E LEU* 3.3 14.8 + - + +
207E PHE* 2.9 46.4 + - + -
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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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239A ASN* 4.9 1.6 - - - +
260A PHE* 5.0 3.1 - - + -
263A TYR* 3.6 37.2 - - + -
198E ILE 3.9 1.6 - - - +
199E PRO 3.6 23.3 - - - +
200E ASN 3.9 9.4 - - - +
201E ILE 3.8 8.1 - - - -
202E ILE 3.6 2.5 - - - -
203E LEU* 1.3 89.7 - - + +
205E MET* 1.3 67.4 + - - +
206E LEU 2.9 3.3 + - - -
207E PHE* 2.9 22.2 + - + +
208E ILE* 3.0 18.3 + - - +
238E PHE* 3.8 14.1 - - + -
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Residues in contact with MET 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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201E ILE* 2.9 32.6 + - + +
202E ILE* 3.2 5.4 + - - +
204E PRO* 1.3 79.4 - - - +
206E LEU* 1.3 58.5 + - + +
208E ILE* 3.2 22.6 - - + +
209E LEU* 3.5 11.3 + - - +
235E HIS* 3.8 28.5 + - + +
238E PHE* 3.3 51.1 - - + +
239E ASN 4.5 0.2 - - - +
258E ILE* 5.4 3.4 - - - -
259E ILE* 3.8 31.6 - - + -
262E ILE* 4.1 14.9 - - + +
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Residues in contact with LEU 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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202E ILE* 2.9 42.0 + - + +
203E LEU* 3.5 13.2 - - + +
204E PRO 2.9 0.8 + - - -
205E MET* 1.3 78.3 - - + +
207E PHE* 1.3 61.4 + - + +
209E LEU* 2.9 8.8 + - + +
210E PHE* 2.8 56.7 + - + -
258E ILE* 6.6 0.2 - - + -
262E ILE* 5.3 5.8 - - + -
303E PHE* 3.6 35.7 - - + -
307E ASN* 6.1 1.1 - - - +
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Residues in contact with PHE 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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260A PHE* 4.2 10.3 - + - -
263A TYR* 3.7 29.2 - - + +
264A LEU* 3.3 30.7 - - + -
267A PHE* 3.9 28.1 - + + -
203E LEU* 2.9 52.8 + - + -
204E PRO* 2.9 9.2 + - + +
206E LEU* 1.3 75.5 - - + +
208E ILE* 1.3 58.4 + - + +
210E PHE* 3.1 21.5 + + - +
211E ILE* 2.9 38.6 + - + +
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Residues in contact with ILE 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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232A LEU* 4.1 24.7 - - + -
236A ILE* 4.2 18.2 - - + -
263A TYR* 5.2 5.2 - - + -
204E PRO 3.0 17.8 + - - +
205E MET* 3.2 21.8 - - + +
207E PHE* 1.3 75.8 - - + +
209E LEU* 1.3 59.9 + - - +
211E ILE* 3.9 7.4 - - + +
212E SER* 3.5 3.6 + - - -
231E THR* 3.4 25.8 - - - +
234E ALA* 4.0 8.1 - - + +
235E HIS* 3.2 47.8 - - + +
238E PHE* 5.5 4.9 - - + -
266E TYR* 3.2 22.4 + - - +
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Residues in contact with LEU 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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205E MET 3.6 10.5 - - - +
206E LEU* 2.9 15.9 + - + +
208E ILE* 1.3 81.1 - - - +
210E PHE* 1.3 67.7 + - + +
212E SER* 3.0 29.6 + - - +
213E TRP* 3.4 36.3 + - + +
262E ILE* 4.5 11.2 - - + -
265E PHE* 4.3 10.8 - - + +
266E TYR* 3.3 31.2 - - + +
303E PHE* 3.6 40.8 - - + -
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Residues in contact with PHE 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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267A PHE* 3.5 29.8 - + + -
206E LEU* 2.8 56.7 + - + -
207E PHE* 3.1 16.6 + + - +
209E LEU* 1.3 71.7 - - + +
211E ILE* 1.3 67.8 + - - +
213E TRP* 2.9 59.4 + + + +
214E THR* 3.5 6.2 + - - +
303E PHE* 4.8 4.9 - + - -
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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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229A VAL* 4.5 6.3 - - + -
232A LEU* 4.0 25.4 - - + -
266A TYR* 5.0 0.7 - - + -
267A PHE* 3.6 31.0 - - + +
270A VAL* 3.9 33.4 - - + -
207E PHE* 2.9 27.3 + - + +
208E ILE* 3.9 6.1 - - - +
209E LEU 3.3 0.2 - - - -
210E PHE* 1.3 73.9 - - - +
212E SER* 1.3 64.0 + - - +
214E THR* 2.8 32.5 + - - -
227E LEU* 3.4 16.8 - - + +
231E THR* 3.6 18.6 - - + -
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Residues in contact with SER 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 ILE 3.5 3.8 + - - -
209E LEU* 3.0 22.7 + - - +
211E ILE* 1.3 76.5 - - - +
213E TRP* 1.3 74.0 + - - +
215E ALA* 3.3 20.8 + - - +
216E PHE* 5.4 1.4 - - - -
227E LEU* 4.6 4.6 - - - +
228E VAL* 3.8 16.9 - - - +
231E THR* 3.6 23.5 - - - +
265E PHE 4.2 7.4 + - - -
266E TYR* 4.0 16.6 - - - -
269E ALA* 4.5 5.9 - - - +
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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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209E LEU* 3.8 27.8 - - + +
210E PHE* 2.9 44.7 + + + +
212E SER* 1.3 84.5 + - - +
214E THR* 1.3 58.9 + - - +
215E ALA 3.1 6.4 + - - -
216E PHE* 3.2 48.4 + + + +
217E TRP* 3.7 10.9 - - + -
265E PHE* 4.0 27.1 + + - -
269E ALA* 5.2 0.7 - - + -
299E PHE* 3.5 25.9 - + + -
300E PRO* 3.9 38.1 - - + -
303E PHE* 4.0 21.1 - + + -
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Residues in contact with THR 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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221A TYR* 3.7 9.4 + - - -
267A PHE* 5.9 0.2 - - + -
270A VAL* 3.6 16.8 - - + +
271A ILE* 4.9 12.8 - - + -
274A THR* 3.2 33.5 + - + +
210E PHE 3.5 8.0 + - - +
211E ILE* 2.8 28.8 + - - +
213E TRP* 1.3 69.9 - - - +
215E ALA* 1.3 57.1 + - - +
216E PHE 3.2 2.9 + - - -
217E TRP* 3.4 20.3 + - - +
218E SER 3.9 4.2 + - - -
227E LEU* 3.1 23.8 - - - +
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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