Contacts of the helix formed by residues 236 - 248 (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 GLU 236 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233J GLY 5.0 0.2 - - - -
234J SER 2.9 12.6 + - - +
235J CYS* 1.3 68.9 - - - +
237J ALA* 1.3 56.5 + - - +
239J ARG* 4.5 4.3 - - + +
240J ALA* 3.0 30.1 + - + +
277J ALA* 5.3 1.0 - - - +
281J TYR* 2.9 38.5 + - + +
284J ARG* 2.7 40.2 + - - +
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Residues in contact with ALA 237 (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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235J CYS* 4.8 2.5 - - + -
236J GLU* 1.3 76.8 - - - +
238J LYS* 1.3 55.6 + - - +
240J ALA* 3.5 5.4 + - - +
241J GLU* 3.0 25.1 + - - +
172L TYR* 3.1 23.6 + - + +
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Residues in contact with LYS 238 (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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226J GLU* 4.7 8.0 + - - +
230J ALA* 3.7 27.7 - - + +
235J CYS* 2.8 29.2 + - + +
237J ALA* 1.3 70.7 - - - +
239J ARG* 1.3 58.7 + - - +
241J GLU* 2.6 19.0 + - - +
242J ALA* 3.0 25.1 + - - +
172L TYR* 3.5 12.3 + - + +
175L LEU* 2.5 47.1 - - - +
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Residues in contact with ARG 239 (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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227J ILE* 3.1 35.6 + - - +
228J THR* 5.1 0.2 - - - +
230J ALA 3.1 21.6 + - - +
231J CYS* 3.3 29.7 - - - +
233J GLY 4.8 1.8 - - - +
235J CYS 3.0 11.4 + - - +
236J GLU* 4.2 6.7 - - + +
238J LYS* 1.3 74.9 - - - +
240J ALA* 1.3 63.5 + - - +
242J ALA* 2.9 24.1 + - - +
243J LEU* 3.0 24.8 + - + +
281J TYR* 3.3 53.2 + - + +
282J LEU* 4.5 1.8 - - - +
285J MET* 3.1 39.4 - - - +
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Residues in contact with ALA 240 (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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236J GLU* 3.0 21.8 + - + +
237J ALA* 3.7 6.1 - - - +
239J ARG* 1.3 73.3 - - - +
241J GLU* 1.3 61.3 + - - +
243J LEU* 3.2 20.1 + - + +
244J GLN* 3.1 21.4 + - - +
284J ARG* 5.2 6.2 - - - +
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Residues in contact with GLU 241 (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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237J ALA 3.0 9.0 + - - +
238J LYS* 2.6 31.6 + - - +
240J ALA* 1.3 74.3 - - - +
242J ALA* 1.3 69.4 + - - +
244J GLN* 3.2 9.2 + - + +
245J SER* 3.0 27.9 + - - -
172L TYR* 2.8 59.6 - - + +
175L LEU* 2.6 32.1 - - - +
176L ARG* 5.5 10.3 - - + +
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Residues in contact with ALA 242 (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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227J ILE* 4.2 13.4 - - + +
230J ALA* 3.8 16.6 - - + -
238J LYS 3.0 13.7 + - - +
239J ARG* 2.9 36.3 + - - +
241J GLU* 1.3 78.1 + - - +
243J LEU* 1.3 57.1 + - - +
245J SER* 3.6 6.4 - - - -
246J ILE* 3.1 36.3 + - - +
175L LEU* 5.9 0.2 - - + -
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Residues in contact with LEU 243 (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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239J ARG* 3.0 32.0 + - + +
240J ALA* 3.2 14.6 + - - +
242J ALA* 1.3 72.3 - - - +
244J GLN* 1.3 66.0 + - - +
246J ILE* 3.2 5.9 + - - +
247J ALA* 3.1 18.9 + - - +
281J TYR* 3.4 12.8 - - - +
284J ARG* 3.2 47.8 - - + +
285J MET* 3.4 37.7 - - + +
288J ALA* 3.5 12.6 - - + +
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Residues in contact with GLN 244 (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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240J ALA 3.1 11.9 + - - +
241J GLU* 3.4 12.3 - - + +
243J LEU* 1.3 72.6 - - - +
245J SER* 1.3 60.8 + - - +
247J ALA* 3.1 10.5 + - - +
248J THR* 2.8 53.5 + - + +
176L ARG* 4.9 15.9 - - - +
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Residues in contact with SER 245 (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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227J ILE* 3.6 20.9 - - - +
241J GLU* 3.0 20.9 + - - -
242J ALA* 3.6 10.3 - - - -
244J GLN* 1.3 73.2 - - - +
246J ILE* 1.3 57.9 + - - -
248J THR* 3.0 5.9 + - - -
249J ASP* 2.9 54.0 + - - +
252J LEU* 5.6 0.7 - - - +
175L LEU* 5.2 7.5 - - - +
176L ARG* 6.3 2.7 - - - -
179L ALA* 4.9 4.2 - - - +
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Residues in contact with ILE 246 (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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227J ILE* 3.8 21.5 - - + -
242J ALA 3.1 18.4 + - - +
243J LEU* 3.2 5.6 + - - +
245J SER* 1.3 75.0 - - - +
247J ALA* 1.3 55.1 + - - +
252J LEU* 3.8 14.9 - - + +
259J PHE* 3.2 43.1 - - + -
285J MET* 3.7 20.2 - - + +
288J ALA* 3.6 15.9 - - + +
289J LEU* 3.6 29.6 + - + -
292J ASN* 2.9 22.1 + - - +
295J LEU* 4.3 0.5 - - - +
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Residues in contact with ALA 247 (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 3.1 10.1 + - - +
244J GLN* 3.1 14.3 + - - +
246J ILE* 1.3 75.6 - - - +
248J THR* 1.3 60.6 + - - +
288J ALA* 3.7 26.0 - - + +
291J ASP* 4.9 6.1 - - + +
292J ASN* 3.6 23.0 - - - +
293J PRO* 4.1 7.1 - - - +
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Residues in contact with THR 248 (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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244J GLN* 2.8 44.7 + - + +
245J SER* 3.0 2.3 + - - -
247J ALA* 1.3 79.0 - - - +
249J ASP* 1.3 68.4 + - - +
250J PRO* 3.5 1.9 - - - +
292J ASN* 4.5 1.5 - - - +
293J PRO* 6.0 0.4 - - - -
294J THR* 5.3 1.7 + - - -
183L ARG* 3.2 5.0 + - - -
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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