Contacts of the helix formed by residues 252 - 273 (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 252 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227J ILE* 5.4 4.7 - - + -
245J SER* 5.6 0.4 - - - +
246J ILE* 3.8 31.4 - - + +
249J ASP* 3.5 31.6 - - + +
250J PRO 3.0 6.9 + - - +
251J GLY* 1.3 73.0 - - - +
253J TYR* 1.3 53.1 + - - +
254J GLN 3.2 1.8 - - - -
255J MET* 2.7 59.8 + - + -
256J LEU 3.0 10.1 + - - +
259J PHE* 4.9 7.2 - - + -
289J LEU* 5.3 0.4 - - + -
292J ASN* 3.6 24.5 - - - +
294J THR 5.2 0.6 + - - +
295J LEU* 3.5 19.9 - - + +
179L ALA* 5.9 2.7 - - + -
183L ARG* 4.5 2.0 - - + +
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Residues in contact with TYR 253 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251J GLY 2.9 11.7 + - - +
252J LEU* 1.3 71.7 - - - +
254J GLN* 1.3 59.7 - - + +
256J LEU* 3.6 19.2 - - + +
257J PRO* 4.3 5.2 - - - +
294J THR* 4.4 7.8 + - + +
295J LEU* 3.4 15.2 - - + +
296J TYR* 3.7 62.5 + + + +
300J TYR* 5.7 4.5 - + - -
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Residues in contact with GLN 254 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220J GLN* 3.0 37.0 + - - +
251J GLY 4.1 2.1 + - - +
252J LEU 3.0 1.0 + - - -
253J TYR* 1.3 80.5 - - + +
255J MET* 1.3 58.2 + - + +
256J LEU 2.9 13.3 - - - +
257J PRO* 4.6 3.1 - - - +
258J ARG* 3.0 32.3 + - - +
186L VAL* 4.8 13.8 - - + +
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Residues in contact with MET 255 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220J GLN* 3.0 56.8 - - + +
223J TYR* 4.3 7.4 - - + -
224J TYR* 4.1 12.1 - - + +
227J ILE* 5.6 0.7 - - + -
251J GLY 5.6 1.1 - - - +
252J LEU* 2.7 47.5 + - + +
254J GLN* 1.3 74.3 - - + +
256J LEU* 1.3 58.4 + - - +
258J ARG* 4.1 10.0 - - - +
259J PHE* 2.9 55.7 + - + -
182L GLN* 3.8 19.1 - - + +
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Residues in contact with LEU 256 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252J LEU* 3.0 6.9 + - - +
253J TYR* 3.6 19.5 - - + +
254J GLN 2.9 13.3 - - - +
255J MET* 1.3 80.6 - - - +
257J PRO* 1.3 71.5 - - + +
258J ARG 2.5 19.4 + - - -
259J PHE* 4.3 5.0 - - - -
260J SER* 4.8 11.4 - - - -
289J LEU* 4.1 24.3 - - + +
295J LEU* 4.2 15.8 - - + +
296J TYR 4.3 11.7 - - - +
297J LEU* 3.7 42.8 - - + -
300J TYR* 3.7 28.3 - - + -
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Residues in contact with PRO 257 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253J TYR* 4.3 7.0 - - + +
254J GLN 4.6 2.9 - - - +
256J LEU* 1.3 91.3 - - + +
258J ARG* 1.3 49.0 + - - +
259J PHE 2.7 18.7 - - - +
260J SER* 4.6 5.4 - - - -
261J THR* 2.7 33.7 + - + +
300J TYR* 3.5 42.0 - - + +
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Residues in contact with ARG 258 (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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224J TYR* 4.0 30.2 + - + +
254J GLN* 3.0 35.4 + - - +
255J MET* 4.1 8.4 - - - +
256J LEU 2.5 16.4 + - - +
257J PRO* 1.3 64.9 - - - +
259J PHE* 1.3 60.6 + - - +
261J THR* 3.1 7.5 + - - +
262J PHE* 3.0 32.6 + - - +
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Residues in contact with PHE 259 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223J TYR 4.4 0.4 - - - -
224J TYR* 3.3 53.4 - + - -
227J ILE* 3.7 25.1 - - + -
228J THR* 4.2 6.7 - - + -
246J ILE* 3.2 25.8 - - + -
252J LEU* 4.9 4.0 - - + -
255J MET* 2.9 49.3 + - + +
256J LEU* 4.3 4.0 - - - -
257J PRO* 2.7 29.7 - - - +
258J ARG* 1.3 70.0 - - - +
260J SER* 1.3 61.5 + - - +
262J PHE* 4.7 2.0 - - + +
263J ILE* 4.4 6.3 - - + +
285J MET* 3.2 26.7 - - + -
289J LEU* 4.5 12.3 - - + -
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Residues in contact with SER 260 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256J LEU* 4.8 12.3 - - - -
257J PRO* 4.5 8.3 - - - -
259J PHE* 1.3 74.2 - - - +
261J THR* 1.3 57.8 + - - -
262J PHE 3.5 0.7 - - - -
263J ILE* 3.4 23.5 - - - +
264J SER* 2.8 34.4 + - - -
289J LEU* 4.3 3.4 - - - +
300J TYR* 4.7 9.1 - - - +
303J GLU* 4.1 14.2 - - - +
304J LEU* 3.4 32.3 - - - +
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Residues in contact with THR 261 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257J PRO* 2.7 30.5 + - + +
258J ARG* 3.1 16.1 + - - +
259J PHE 2.7 11.7 + - - -
260J SER* 1.3 70.6 - - - +
262J PHE* 1.3 55.1 + - - +
264J SER* 3.9 4.5 - - - -
265J GLU* 3.0 30.2 + - - +
303J GLU* 6.2 3.8 - - + -
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Residues in contact with PHE 262 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224J TYR* 3.3 24.5 - - + +
228J THR* 3.6 33.7 - - + -
231J CYS* 6.5 0.7 - - + -
232J VAL* 6.0 5.6 - - + -
258J ARG 3.0 18.1 + - - +
259J PHE* 5.0 2.0 - - + -
261J THR* 1.3 73.8 + - - +
263J ILE* 1.3 65.4 + - + +
265J GLU* 4.2 10.5 - - + -
266J GLY* 3.2 19.8 + - - -
282J LEU* 4.9 2.2 - - + +
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Residues in contact with ILE 263 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259J PHE* 4.4 2.2 - - + -
260J SER* 3.1 30.0 + - - +
262J PHE* 1.3 79.1 - - + +
264J SER* 1.3 58.7 + - - +
266J GLY* 3.0 4.9 + - - -
267J VAL* 2.9 31.6 + - + +
282J LEU* 3.7 32.8 - - + +
283J MET* 5.7 0.2 - - + -
285J MET* 3.4 45.1 - - + -
286J VAL* 3.8 25.4 - - + -
289J LEU* 3.7 17.5 - - + -
304J LEU* 5.5 0.4 - - + -
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Residues in contact with SER 264 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260J SER* 2.8 24.1 + - - -
261J THR* 3.9 4.5 - - - -
263J ILE* 1.3 71.6 - - - +
265J GLU* 1.3 62.4 + - - +
267J VAL* 3.3 9.8 + - - +
268J ARG* 3.0 23.2 + - - +
303J GLU* 3.0 34.4 + - - +
304J LEU* 4.6 5.0 - - - +
307J ALA* 4.0 15.3 - - - +
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Residues in contact with GLU 265 (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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261J THR 3.0 18.3 + - - +
262J PHE* 4.2 13.5 - - + +
264J SER* 1.3 76.2 - - - +
266J GLY* 1.3 57.4 + - - +
268J ARG* 2.8 45.9 + - - +
269J VAL* 3.0 39.5 + - + +
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Residues in contact with GLY 266 (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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262J PHE* 3.2 13.4 + - - -
263J ILE 3.0 8.2 + - - -
265J GLU* 1.3 78.4 - - - +
267J VAL* 1.3 56.1 + - - +
269J VAL* 4.4 4.7 - - - -
270J ASN* 2.7 44.2 + - - +
282J LEU* 3.8 10.5 - - - -
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Residues in contact with VAL 267 (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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263J ILE* 2.9 19.6 + - + +
264J SER* 3.3 10.7 + - - +
266J GLY* 1.3 71.9 - - - +
268J ARG* 1.3 62.0 + - - +
271J VAL* 2.9 33.0 + - + +
279J LEU* 3.5 9.8 - - + +
282J LEU* 3.6 28.0 - - + -
283J MET* 3.9 16.2 - - + -
307J ALA* 4.3 22.2 - - + +
310J THR* 5.6 4.3 - - + -
311J CYS* 3.8 24.0 - - - -
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Residues in contact with ARG 268 (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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264J SER 3.0 12.8 + - - +
265J GLU* 2.8 47.2 + - - +
267J VAL* 1.3 80.4 - - - +
269J VAL* 1.3 66.9 + - - +
271J VAL* 3.0 13.4 + - - +
272J VAL* 3.1 22.4 + - + +
310J THR* 6.5 1.3 - - - -
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Residues in contact with VAL 269 (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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265J GLU* 3.0 34.0 + - + +
266J GLY* 3.9 5.6 - - - +
268J ARG* 1.3 81.0 - - + +
270J ASN* 1.3 67.6 + - - +
272J VAL* 3.1 12.7 + - - +
273J GLN* 3.0 37.6 + - + +
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Residues in contact with ASN 270 (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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232J VAL* 6.2 1.4 - - - +
266J GLY* 2.7 37.4 + - - +
269J VAL* 1.3 77.4 - - - +
271J VAL* 1.3 63.4 + - - +
273J GLN* 4.0 12.6 - - - +
274J ASN 3.0 17.8 + - - -
275J ASN* 3.3 17.9 + - + +
278J LEU* 3.3 38.8 - - + +
279J LEU* 3.4 23.3 - - + +
282J LEU* 4.4 3.6 - - + +
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Residues in contact with VAL 271 (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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267J VAL* 2.9 24.7 + - + +
268J ARG* 3.0 6.0 + - - +
270J ASN* 1.3 73.4 - - - +
272J VAL* 1.3 67.0 + - + +
273J GLN 3.2 3.8 + - - -
274J ASN* 3.2 21.8 + - - -
279J LEU* 3.8 20.6 - - + +
310J THR* 4.9 14.6 - - + -
311J CYS* 4.4 15.3 - - - -
314J SER* 3.9 25.4 - - - +
316J GLN* 4.2 17.8 - - + +
317J LEU* 5.5 6.2 - - + +
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Residues in contact with VAL 272 (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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268J ARG* 3.1 18.6 + - + +
269J VAL* 3.1 12.7 + - - +
271J VAL* 1.3 83.8 - - + +
273J GLN* 1.3 71.1 + - - -
316J GLN* 6.3 1.1 - - + -
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Residues in contact with GLN 273 (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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269J VAL* 3.0 27.9 + - + +
270J ASN* 3.2 18.6 + - - +
271J VAL 3.2 0.6 - - - -
272J VAL* 1.3 91.1 + - - +
274J ASN* 1.3 62.2 + - - +
275J ASN* 3.1 14.4 + - + +
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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
------------------------------------------------------------
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