Contacts of the helix formed by residues 236 - 248 (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 GLU 236 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233K GLY 4.8 1.8 - - - -
234K SER 2.9 13.9 + - - +
235K CYS* 1.3 69.3 - - - +
237K ALA* 1.3 59.8 + - - +
239K ARG* 3.5 7.7 + - + +
240K ALA* 3.2 21.3 + - + +
281K TYR* 3.2 27.8 + - + +
284K ARG* 2.5 45.9 + - - +
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Residues in contact with ALA 237 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235K CYS* 3.1 3.6 + - + -
236K GLU* 1.3 76.6 - - - +
238K LYS* 1.3 55.8 + - - +
240K ALA* 3.4 7.5 + - - +
241K GLU* 3.0 26.6 + - - +
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Residues in contact with LYS 238 (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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226K GLU* 4.7 9.9 + - - +
227K ILE* 6.3 1.0 - - - +
230K ALA* 3.7 26.0 - - + -
235K CYS* 2.7 30.4 + - + +
237K ALA* 1.3 70.3 - - - +
239K ARG* 1.3 58.9 + - - +
241K GLU* 2.3 53.3 + - - +
242K ALA* 2.8 28.0 + - - +
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Residues in contact with ARG 239 (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* 3.3 28.3 + - - +
228K THR* 5.1 0.2 - - - +
230K ALA 3.0 21.1 + - - +
231K CYS* 3.3 41.5 - - - +
233K GLY 5.1 3.1 - - - +
235K CYS 3.1 9.8 + - - +
236K GLU* 3.5 14.8 + - + +
237K ALA 3.5 0.2 - - - -
238K LYS* 1.3 75.6 - - - +
240K ALA* 1.3 60.9 + - - +
242K ALA* 3.1 12.0 + - - +
243K LEU* 3.0 34.1 + - + +
281K TYR* 3.5 31.0 + - + +
282K LEU* 4.8 1.2 - - - +
284K ARG* 5.3 2.0 - - - +
285K MET* 3.0 51.5 - - - +
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Residues in contact with ALA 240 (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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236K GLU* 3.2 14.5 + - + +
237K ALA* 3.6 10.5 - - - +
238K LYS 3.4 0.2 - - - -
239K ARG* 1.3 74.8 - - - +
241K GLU* 1.3 61.0 + - - +
243K LEU* 3.2 27.4 + - + +
244K GLN* 3.3 11.8 + - - +
284K ARG* 5.5 5.9 - - - +
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Residues in contact with GLU 241 (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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237K ALA 3.0 16.7 + - - +
238K LYS* 2.3 51.7 + - - +
239K ARG 3.4 0.2 - - - -
240K ALA* 1.3 74.0 - - - +
242K ALA* 1.3 72.8 + - - +
244K GLN* 3.0 21.2 + - + +
245K SER* 3.0 18.0 + - - -
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Residues in contact with ALA 242 (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 11.2 - - + +
230K ALA* 3.4 32.5 - - + -
238K LYS* 2.8 13.1 + - - +
239K ARG* 3.1 23.1 + - - +
241K GLU* 1.3 76.7 + - - +
243K LEU* 1.3 61.8 + - - +
245K SER* 3.6 7.9 - - - -
246K ILE* 3.1 29.9 + - - +
285K MET* 6.4 0.2 - - - -
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Residues in contact with LEU 243 (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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239K ARG* 3.0 32.4 + - + +
240K ALA* 3.3 19.1 - - + +
242K ALA* 1.3 72.5 - - - +
244K GLN* 1.3 64.4 + - - +
246K ILE* 3.4 1.7 + - - -
247K ALA* 3.2 8.5 + - - +
284K ARG* 3.5 38.4 - - + +
285K MET* 3.3 43.5 - - + +
288K ALA* 3.0 29.2 - - + +
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Residues in contact with GLN 244 (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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240K ALA 3.3 7.8 + - - +
241K GLU* 3.0 15.1 + - + +
243K LEU* 1.3 77.4 - - - +
245K SER* 1.3 60.9 + - - +
247K ALA* 3.0 17.3 + - - +
248K THR* 2.8 45.5 + - + +
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Residues in contact with SER 245 (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* 3.4 24.0 - - - +
241K GLU* 3.0 16.9 + - - -
242K ALA* 3.6 14.4 - - - -
244K GLN* 1.3 72.7 - - - +
246K ILE* 1.3 58.3 + - - -
248K THR* 2.9 21.4 + - - -
249K ASP* 3.0 35.4 + - - +
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Residues in contact with ILE 246 (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* 3.6 24.5 - - + -
239K ARG* 5.7 0.2 - - - +
242K ALA 3.1 17.8 + - - +
243K LEU* 3.8 4.7 - - - +
244K GLN 3.4 0.4 - - - -
245K SER* 1.3 73.7 - - - +
247K ALA* 1.3 52.6 + - - +
252K LEU* 4.1 10.5 - - + +
259K PHE* 3.2 45.8 - - + -
285K MET* 4.0 16.2 - - + +
288K ALA* 3.6 8.2 - - + +
289K LEU* 3.5 39.2 + - + +
292K ASN* 2.8 27.9 + - - +
295K LEU* 4.3 1.0 - - - +
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Residues in contact with ALA 247 (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 3.2 10.1 + - - +
244K GLN* 3.0 15.0 + - - +
246K ILE* 1.3 76.2 - - - +
248K THR* 1.3 59.1 + - - +
288K ALA* 3.6 25.4 - - + +
291K ASP* 4.3 12.1 - - + +
292K ASN* 3.4 24.6 - - - -
293K PRO* 3.8 9.4 - - - +
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Residues in contact with THR 248 (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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244K GLN* 2.8 44.6 + - + +
245K SER* 2.9 4.1 + - - -
247K ALA* 1.3 79.3 - - - +
249K ASP* 1.3 68.2 + - - +
250K PRO* 3.4 7.3 - - - +
292K ASN* 4.6 0.9 - - - -
293K PRO* 5.9 0.7 - - - -
294K THR* 4.9 3.3 + - - -
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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