Contacts of the helix formed by residues 276 - 291 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274K ASN 2.9 8.5 + - - +
275K ASN* 1.3 69.7 - - - +
277K ALA* 1.3 71.0 + - + +
279K LEU* 3.8 1.6 - - - +
280K ILE* 3.0 30.8 + - + +
325K ASN* 3.2 54.7 - - + +
326K HIS* 3.7 32.3 - - + +
328K ALA* 6.2 0.7 - - + -
329K LEU* 4.0 21.8 - - + +
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Residues in contact with ALA 277 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275K ASN* 3.2 9.5 + - - +
276K LEU* 1.3 86.0 - - + +
278K LEU* 1.3 69.6 + - + +
280K ILE* 3.2 26.6 + - - +
281K TYR* 3.3 21.1 + - + +
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Residues in contact with LEU 278 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231K CYS* 4.7 4.0 - - - +
232K VAL* 4.5 33.0 - - + +
270K ASN* 4.1 18.6 - - - +
275K ASN* 3.2 33.2 + - - +
277K ALA* 1.3 76.6 - - + +
279K LEU* 1.3 58.3 + - - +
281K TYR* 3.1 27.7 + - + +
282K LEU* 2.9 44.4 + - + +
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Residues in contact with LEU 279 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267K VAL* 3.6 48.7 - - + +
270K ASN* 3.6 26.2 - - + +
271K VAL* 4.0 13.5 - - + +
274K ASN* 4.6 2.5 - - - -
275K ASN 3.0 26.6 + - - +
276K LEU 3.8 1.3 - - - +
277K ALA 3.3 0.2 - - - -
278K LEU* 1.3 76.3 - - - +
280K ILE* 1.3 56.1 + - - +
282K LEU* 3.4 3.8 + - + -
283K MET* 3.0 36.2 + - - +
311K CYS* 5.2 3.8 - - - -
317K LEU* 5.5 3.4 - - + -
326K HIS* 6.2 0.2 - - + -
329K LEU* 3.5 34.1 - - + -
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Residues in contact with ILE 280 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276K LEU* 3.0 18.7 + - + +
277K ALA* 3.2 21.6 + - - +
279K LEU* 1.3 76.2 - - - +
281K TYR* 1.3 73.0 + - + +
283K MET* 3.5 3.0 + - - +
284K ARG* 3.1 46.8 + - - +
328K ALA* 4.2 17.0 - - + +
329K LEU* 4.2 8.2 - - + +
332K PHE* 4.0 42.4 - - + -
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Residues in contact with TYR 281 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231K CYS* 3.2 28.7 - - - -
232K VAL* 5.3 4.7 - - - -
233K GLY 5.3 5.3 + - - -
236K GLU* 3.2 39.0 + - + +
239K ARG* 3.5 35.0 + - + +
277K ALA* 3.3 24.1 + - + +
278K LEU* 3.1 25.0 + - + +
280K ILE* 1.3 78.3 - - + +
282K LEU* 1.3 58.5 + - - +
284K ARG* 3.7 31.8 + - - +
285K MET 3.1 19.4 + - - -
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Residues in contact with LEU 282 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231K CYS* 4.5 19.1 - - - -
239K ARG* 5.1 1.8 - - - +
262K PHE* 4.6 8.1 - - + +
263K ILE* 3.8 35.4 - - + +
266K GLY* 4.0 19.1 - - - +
267K VAL* 3.9 26.7 - - + -
270K ASN* 4.6 2.2 - - - +
278K LEU* 2.9 35.6 + - + +
279K LEU* 3.8 8.1 - - + +
280K ILE 3.3 0.2 - - - -
281K TYR* 1.3 74.8 - - - +
283K MET* 1.3 62.1 + - - +
285K MET* 3.2 6.3 + - - +
286K VAL* 3.0 32.1 + - - +
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Residues in contact with MET 283 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267K VAL* 3.8 29.8 - - + -
279K LEU* 3.0 35.6 + - - +
280K ILE* 3.7 5.8 - - - +
282K LEU* 1.3 76.5 - - - +
284K ARG* 1.3 62.3 + - - +
286K VAL* 3.2 11.2 + - + +
287K LYS* 3.1 17.3 + - - +
307K ALA* 5.0 3.8 - - + +
308K VAL* 4.4 19.7 - - + -
311K CYS* 4.4 16.6 - - - -
329K LEU* 4.1 13.9 - - + -
332K PHE* 3.8 18.8 - - + -
333K ALA* 4.4 20.4 - - + -
336K LEU* 3.4 24.3 - - + +
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Residues in contact with ARG 284 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236K GLU* 2.5 38.4 + - - +
239K ARG* 5.3 4.2 - - - +
240K ALA* 5.5 4.9 - - - +
243K LEU* 3.5 36.5 - - + +
280K ILE* 3.1 38.3 + - - +
281K TYR* 3.7 31.0 - - - +
283K MET* 1.3 76.9 - - - +
285K MET* 1.3 62.7 + - - +
287K LYS* 3.2 16.8 + - - +
288K ALA* 3.3 10.0 + - - +
332K PHE* 3.5 28.7 - - + -
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Residues in contact with MET 285 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227K ILE* 4.2 7.9 - - + -
228K THR* 5.6 4.7 - - + -
231K CYS* 5.4 1.1 - - - -
239K ARG* 3.0 38.4 - - - +
243K LEU* 3.3 10.3 - - + +
246K ILE* 4.0 26.0 - - + -
259K PHE* 3.5 38.4 - - + -
263K ILE* 3.3 33.4 - - + -
281K TYR 3.1 9.9 + - - +
282K LEU* 3.2 8.9 + - - +
284K ARG* 1.3 71.5 - - - +
286K VAL* 1.3 64.2 + - - +
288K ALA* 3.3 4.6 + - - +
289K LEU* 3.1 22.0 + - - +
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Residues in contact with VAL 286 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263K ILE* 3.6 19.7 - - + -
282K LEU 3.0 20.0 + - - +
283K MET* 3.2 16.8 + - + +
285K MET* 1.3 75.1 - - - +
287K LYS* 1.3 56.3 + - - +
289K LEU* 3.5 8.9 + - + +
290K MET* 2.9 34.8 + - + +
304K LEU* 3.5 50.3 - - + -
308K VAL* 4.7 4.7 - - + -
336K LEU* 4.1 17.7 - - + -
340K ILE* 5.2 0.7 - - + -
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Residues in contact with LYS 287 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283K MET 3.1 11.2 + - - +
284K ARG* 3.2 15.2 + - - +
286K VAL* 1.3 73.4 - - - +
288K ALA* 1.3 65.7 + - - +
290K MET* 3.3 4.0 + - - +
291K ASP* 2.9 57.0 + - - +
332K PHE* 5.8 4.7 - - + -
336K LEU* 4.0 17.5 - - + +
339K GLN* 2.5 42.7 + - - +
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Residues in contact with ALA 288 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243K LEU* 3.0 37.0 - - + +
246K ILE* 3.6 16.6 - - + -
247K ALA* 3.6 13.4 - - - +
284K ARG 3.3 8.9 + - - +
285K MET 3.3 9.6 + - - +
287K LYS* 1.3 78.2 - - - +
289K LEU* 1.3 64.0 + - - +
291K ASP* 2.9 15.4 + - - +
292K ASN 3.1 9.7 + - - -
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Residues in contact with LEU 289 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246K ILE* 3.5 26.6 - - + +
256K LEU* 4.2 13.5 - - + -
259K PHE* 4.5 15.7 - - + -
260K SER* 4.0 19.1 - - - +
263K ILE* 3.3 33.7 - - + -
285K MET* 3.1 5.6 + - + +
286K VAL* 3.7 10.3 - - + +
288K ALA* 1.3 75.9 - - - +
290K MET* 1.3 58.0 + - - +
292K ASN* 3.0 21.9 + - - +
295K LEU* 3.7 22.0 - - + -
297K LEU* 3.3 33.0 - - + +
304K LEU* 5.4 4.3 - - + -
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Residues in contact with MET 290 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286K VAL* 2.9 26.8 + - + +
287K LYS* 3.3 9.8 + - - +
289K LEU* 1.3 73.8 - - - +
291K ASP* 1.3 60.8 + - - +
292K ASN 5.4 0.4 - - - -
297K LEU* 4.1 17.5 - - + +
301K VAL* 4.3 11.7 - - + -
304K LEU* 3.4 41.7 - - + -
336K LEU* 5.4 0.7 - - + -
339K GLN* 4.1 13.2 - - + +
340K ILE* 4.3 22.7 - - + -
343K HIS* 3.6 20.0 - - + -
344K PHE* 3.3 39.7 - - + -
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Residues in contact with ASP 291 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247K ALA* 4.3 12.3 - - + +
287K LYS* 2.9 44.6 + - - +
288K ALA* 2.9 7.4 + - - +
290K MET* 1.3 76.3 - - - +
292K ASN* 1.3 58.7 + - - +
293K PRO* 3.1 15.8 - - - +
339K GLN* 2.4 33.5 + - - -
343K HIS* 5.5 1.8 - - - -
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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