Contacts of the helix formed by residues 233 - 244 (chain C) in PDB entry 3FUX
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 PRO 233 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231C GLY 3.8 3.6 - - - +
232C TYR* 1.3 90.9 - - + +
234C LYS* 1.3 64.6 + - - +
235C ALA* 3.4 2.0 - - + +
236C ARG* 3.1 24.9 + - + +
237C VAL* 3.0 24.0 + - + +
267C LEU* 5.6 2.5 - - + -
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Residues in contact with LYS 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C LEU* 3.5 33.3 - - + +
225C ASN* 3.0 28.4 + - - +
228C ALA* 3.8 26.7 - - + -
232C TYR 3.2 5.8 + - - -
233C PRO* 1.3 70.9 - - - +
235C ALA* 1.3 57.1 + - - +
237C VAL* 3.3 2.3 + - - +
238C GLU* 2.9 33.7 + - + +
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Residues in contact with ALA 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C PRO* 3.4 1.0 - - + -
234C LYS* 1.3 78.1 - - - +
236C ARG* 1.3 57.5 + - + +
238C GLU* 3.5 10.6 + - - +
239C GLU* 3.0 39.4 + - + +
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Residues in contact with ARG 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C PRO* 3.1 26.8 + - + +
235C ALA* 1.3 77.3 - - + +
237C VAL* 1.3 59.8 - - - +
239C GLU* 3.3 22.3 + - - +
240C ALA* 2.9 30.7 + - - +
266C GLY 3.0 20.9 + - - -
267C LEU* 2.5 41.8 + - + +
268C GLU 3.7 10.9 - - - -
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Residues in contact with VAL 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C LEU* 3.8 25.6 - - + -
227C LEU* 3.8 30.7 - - + -
228C ALA 5.4 0.7 - - - +
232C TYR* 3.8 24.2 - - + -
233C PRO 3.0 20.2 + - - +
234C LYS* 3.7 7.0 - - - +
236C ARG* 1.3 71.7 - - - +
238C GLU* 1.3 67.5 + - - +
240C ALA* 3.2 2.5 + - - +
241C LEU* 2.9 36.1 + - + +
263C LEU* 5.2 2.0 - - + -
267C LEU* 3.6 22.9 - - + -
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Residues in contact with GLU 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C LEU* 3.7 28.6 - - + +
234C LYS* 2.9 19.8 + - - +
235C ALA* 3.6 11.1 - - - +
237C VAL* 1.3 77.4 - - - +
239C GLU* 1.3 56.3 + - + +
241C LEU* 3.5 7.5 + - + +
242C ARG* 3.0 32.0 + - - +
248C PRO* 6.1 5.4 - - + -
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Residues in contact with GLU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C ALA* 3.0 25.6 + - + +
236C ARG* 3.5 26.3 - - - +
238C GLU* 1.3 74.0 - - + +
240C ALA* 1.3 56.4 + - - +
242C ARG* 3.2 39.6 + - - +
243C ALA* 2.7 36.9 + - - +
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Residues in contact with ALA 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C ARG* 2.9 17.6 + - - +
237C VAL 3.7 3.1 - - - +
239C GLU* 1.3 72.3 - - - +
241C LEU* 1.3 61.9 + - - +
243C ALA* 3.8 6.0 - - - +
244C LEU* 2.9 38.7 + - + +
263C LEU* 3.8 20.6 - - + -
266C GLY* 4.3 22.4 - - - +
267C LEU* 4.0 10.1 - - + -
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Residues in contact with LEU 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C LEU* 4.0 20.2 - - + -
224C LEU* 4.4 17.0 - - + +
237C VAL* 2.9 34.7 + - + +
238C GLU* 3.7 6.5 - - - +
240C ALA* 1.3 72.0 - - - +
242C ARG* 1.3 63.5 + - - +
244C LEU* 3.4 2.6 + - - -
245C GLY 3.2 2.9 + - - -
246C LEU* 2.9 63.1 + - + +
247C PRO 4.7 1.1 - - - +
248C PRO* 4.2 19.7 - - + +
250C VAL* 4.1 17.7 - - + -
263C LEU* 4.1 15.5 - - + -
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Residues in contact with ARG 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C GLU* 3.0 16.9 + - - +
239C GLU* 3.2 58.6 + - - +
241C LEU* 1.3 73.5 - - - +
243C ALA* 1.3 65.2 + - - +
245C GLY* 2.9 22.2 + - - -
246C LEU 4.5 3.8 + - - -
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Residues in contact with ALA 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C GLU 2.7 20.6 + - - +
240C ALA* 3.4 7.2 + - - +
242C ARG* 1.3 81.7 - - - +
244C LEU* 1.3 61.9 + - + +
245C GLY 3.3 1.0 + - - -
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Residues in contact with LEU 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C ALA* 2.9 26.7 + - + +
241C LEU 4.0 2.9 - - - +
242C ARG 3.2 0.4 - - - -
243C ALA* 1.3 78.8 - - + +
245C GLY* 1.3 62.4 + - - +
246C LEU* 3.2 21.2 + - + +
259C ALA 5.0 0.9 - - - +
262C ARG* 3.7 41.2 + - + +
263C LEU* 3.6 37.7 - - + +
266C GLY* 5.3 3.6 - - - -
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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