Contacts of the helix formed by residues 276 - 291 (chain J) in PDB entry 5FUR
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 LEU 276 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274J ASN 2.9 9.7 + - - +
275J ASN* 1.3 70.9 - - - +
277J ALA* 1.3 78.5 + - + +
279J LEU* 3.7 1.3 - - - +
280J ILE* 2.8 35.8 + - + +
321J PRO* 4.9 4.3 - - + -
325J ASN* 3.8 38.4 - - + +
326J HIS* 3.2 49.8 - - + +
329J LEU* 4.0 15.6 - - + +
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Residues in contact with ALA 277 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236J GLU* 5.3 0.9 - - - +
275J ASN* 3.2 9.2 + - - +
276J LEU* 1.3 87.6 - - + +
278J LEU* 1.3 61.9 + - + +
280J ILE* 3.3 8.1 + - - +
281J TYR* 2.9 61.3 + - + +
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Residues in contact with LEU 278 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231J CYS* 3.3 29.6 - - - +
232J VAL* 3.6 35.7 - - + +
270J ASN* 3.3 33.7 - - - +
275J ASN* 3.2 35.0 + - - +
277J ALA* 1.3 75.3 - - + +
279J LEU* 1.3 55.6 + - - +
281J TYR* 3.2 12.4 + - + +
282J LEU* 2.9 39.6 + - + +
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Residues in contact with LEU 279 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267J VAL* 3.5 42.4 - - + +
270J ASN* 3.4 28.0 - - + +
271J VAL* 3.8 21.1 - - + +
274J ASN* 4.7 3.4 - - - -
275J ASN 3.0 20.0 + - - +
276J LEU 3.7 0.9 - - - +
278J LEU* 1.3 73.6 - - - +
280J ILE* 1.3 57.1 + - - +
282J LEU* 3.2 4.4 + - + +
283J MET* 2.9 33.6 + - - +
311J CYS* 4.4 6.3 - - - -
317J LEU* 4.9 7.0 - - + -
329J LEU* 3.3 34.5 - - + -
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Residues in contact with ILE 280 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276J LEU* 2.8 23.9 + - + +
277J ALA* 3.4 14.8 - - - +
279J LEU* 1.3 71.1 - - - +
281J TYR* 1.3 61.4 + - + +
283J MET* 3.4 1.6 + - - +
284J ARG* 2.9 69.3 + - + +
325J ASN 5.4 2.5 - - - +
328J ALA* 4.0 30.3 - - + +
329J LEU* 3.7 12.2 - - + +
332J PHE* 4.3 27.8 - - + -
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Residues in contact with TYR 281 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231J CYS* 3.2 27.4 - - - -
232J VAL 5.5 0.4 - - - -
233J GLY 4.6 8.6 + - - -
234J SER* 5.3 4.0 + - - -
236J GLU* 2.9 51.4 + - + +
239J ARG* 3.3 43.2 + - + +
243J LEU* 3.4 5.0 - - - +
277J ALA* 2.9 48.9 + - + +
278J LEU* 3.5 15.3 - - + +
280J ILE* 1.3 76.9 - - + +
282J LEU* 1.3 57.2 + - - +
284J ARG* 3.9 25.1 - - - +
285J MET* 3.0 20.3 + - - +
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Residues in contact with LEU 282 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231J CYS* 3.9 23.1 - - - -
239J ARG* 4.7 2.0 - - - +
262J PHE* 4.9 2.2 - - + +
263J ILE* 3.7 36.4 - - + +
266J GLY* 3.8 30.7 - - - +
267J VAL* 3.6 19.5 - - + -
270J ASN* 4.4 7.4 - - - +
278J LEU* 2.9 30.8 + - + +
279J LEU* 3.6 7.0 - - + +
281J TYR* 1.3 73.9 - - - +
283J MET* 1.3 61.7 + - - +
285J MET* 3.2 6.5 + - - +
286J VAL* 3.0 32.2 + - - +
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Residues in contact with MET 283 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267J VAL* 3.9 24.2 - - + -
279J LEU 2.9 27.7 + - - +
280J ILE* 3.7 5.8 - - - +
282J LEU* 1.3 76.4 - - - +
284J ARG* 1.3 62.9 + - - +
286J VAL* 3.1 11.4 + - + +
287J LYS* 2.9 20.4 + - - +
307J ALA* 4.7 2.7 - - + +
308J VAL* 4.2 22.4 - - + +
311J CYS* 3.6 33.4 - - + -
329J LEU* 4.0 8.3 - - + -
332J PHE* 3.8 18.4 - - + -
333J ALA* 3.9 28.0 - - + +
336J LEU* 3.6 12.1 - - + +
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Residues in contact with ARG 284 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236J GLU* 2.7 34.1 + - - +
239J ARG* 5.7 0.2 - - - +
240J ALA* 5.2 7.1 - - - +
243J LEU* 3.2 38.4 - - + +
280J ILE* 2.9 62.2 + - + +
281J TYR* 3.8 12.4 - - - +
283J MET* 1.3 71.3 - - - +
285J MET* 1.3 57.2 + - - +
287J LYS* 3.4 3.6 + - - +
288J ALA* 3.0 28.1 + - - +
332J PHE* 3.7 30.9 - - + -
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Residues in contact with MET 285 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227J ILE* 3.8 12.6 - - + -
228J THR* 5.7 2.9 - - + -
231J CYS* 5.5 0.7 - - - -
239J ARG* 3.1 38.1 - - - +
243J LEU* 3.4 8.5 - - + +
246J ILE* 3.8 20.6 - - + -
259J PHE* 3.2 47.8 - - + -
263J ILE* 3.4 29.4 - - + -
281J TYR 3.0 9.1 + - - +
282J LEU* 3.2 7.4 + - - +
284J ARG* 1.3 73.1 - - - +
286J VAL* 1.3 65.5 + - - +
288J ALA* 3.4 4.5 + - - +
289J LEU* 3.1 24.5 + - + +
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Residues in contact with VAL 286 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263J ILE* 3.8 22.2 - - + -
282J LEU 3.0 17.9 + - - +
283J MET* 3.1 14.6 + - + +
285J MET* 1.3 73.3 - - - +
287J LYS* 1.3 58.3 + - - +
289J LEU* 3.3 9.6 + - - +
290J MET* 3.0 29.8 + - + +
304J LEU* 3.5 49.1 - - + -
307J ALA* 6.3 0.9 - - + -
308J VAL* 4.4 4.7 - - + -
336J LEU* 3.6 25.1 - - + -
340J ILE* 5.2 0.4 - - + -
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Residues in contact with LYS 287 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283J MET 2.9 13.2 + - - +
284J ARG* 3.6 12.3 - - - +
285J MET 3.3 0.2 - - - -
286J VAL* 1.3 72.8 - - - +
288J ALA* 1.3 61.2 + - - +
290J MET* 3.2 3.3 + - - +
291J ASP* 2.7 62.1 + - - +
332J PHE* 4.6 17.7 - - + -
336J LEU* 3.8 20.4 - - + +
339J GLN* 2.7 35.8 + - - +
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Residues in contact with ALA 288 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243J LEU* 3.5 28.0 - - + +
246J ILE* 3.6 12.8 - - + -
247J ALA* 3.7 16.6 - - + +
284J ARG 3.0 17.9 + - - +
285J MET* 3.5 8.1 - - - +
287J LYS* 1.3 75.4 - - - +
289J LEU* 1.3 63.2 + - - +
291J ASP* 3.1 5.4 + - - -
292J ASN* 2.9 23.4 + - - +
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Residues in contact with LEU 289 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246J ILE* 3.6 25.5 - - + +
252J LEU* 5.3 0.4 - - + -
256J LEU* 4.1 21.3 - - + +
259J PHE* 4.5 11.0 - - + -
260J SER* 4.3 10.5 - - - +
263J ILE* 3.7 29.6 - - + -
285J MET* 3.1 16.4 + - + +
286J VAL* 3.4 11.2 - - + +
288J ALA* 1.3 72.6 - - - +
290J MET* 1.3 62.1 + - - +
292J ASN* 3.1 19.2 + - - +
295J LEU* 3.4 27.9 - - + +
297J LEU* 3.2 28.9 - - + +
304J LEU* 5.3 2.7 - - + -
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Residues in contact with MET 290 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286J VAL* 3.0 17.7 + - + +
287J LYS* 3.5 9.2 - - - +
289J LEU* 1.3 74.2 - - - +
291J ASP* 1.3 57.9 + - - +
292J ASN 3.5 0.9 - - - +
295J LEU 5.8 0.4 - - - +
297J LEU* 3.7 26.8 - - + +
301J VAL* 4.5 9.0 - - + -
304J LEU* 3.6 32.8 - - + -
336J LEU* 4.6 1.8 - - + -
339J GLN* 3.7 27.3 + - + +
340J ILE* 4.1 28.7 - - + -
343J HIS* 4.5 12.1 - - + -
344J PHE* 3.5 31.4 - - + -
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Residues in contact with ASP 291 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247J ALA* 4.9 6.7 - - + +
287J LYS* 2.7 49.2 + - - +
288J ALA* 3.7 6.1 - - - +
290J MET* 1.3 75.1 - - - +
292J ASN* 1.3 63.3 + - - +
293J PRO* 3.2 10.6 - - - +
339J GLN* 2.6 33.4 + - - +
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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