Contacts of the helix formed by residues 233 - 253 (chain C) in PDB entry 5ZRV
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 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 PRO 2.8 6.9 + - - -
232C PRO* 1.3 76.3 - - - +
234C GLU* 1.3 63.2 + - - +
235C ARG 3.2 1.8 - - - -
236C THR* 3.2 14.2 + - - +
237C ILE* 3.4 8.1 + - - -
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Residues in contact with GLU 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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231C PRO 3.1 8.5 + - - -
233C GLU* 1.3 76.5 - - - +
235C ARG* 1.3 60.7 + - - +
237C ILE* 3.7 2.4 + - - +
238C GLU* 3.3 15.4 + - - -
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Residues in contact with ARG 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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230C LYS* 5.5 3.4 - - - +
231C PRO 3.7 8.9 + - - -
232C PRO 4.9 0.4 - - - -
233C GLU 3.2 1.2 - - - +
234C GLU* 1.3 75.4 - - - +
236C THR* 1.3 54.0 + - - +
238C GLU* 2.9 4.8 + - - +
239C TYR* 2.5 36.0 + - - -
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Residues in contact with THR 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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224C PRO* 5.9 2.9 - - - -
225C LEU* 5.3 11.7 - - - +
232C PRO 5.3 1.4 + - - -
233C GLU* 3.2 11.5 + - - +
235C ARG* 1.3 76.2 - - - +
237C ILE* 1.3 60.5 + - - +
239C TYR* 3.6 7.7 + - - +
240C LEU* 3.8 8.8 + - - -
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Residues in contact with ILE 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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92C SER 6.0 1.3 - - - -
93C SER* 6.0 2.0 - - - -
233C GLU 3.4 10.8 + - - -
234C GLU* 3.7 4.0 + - - +
235C ARG 3.2 0.4 - - - -
236C THR* 1.3 76.4 - - - +
238C GLU* 1.3 58.3 + - - +
239C TYR 3.4 0.4 + - - -
240C LEU* 4.2 5.6 + - - -
241C GLU 4.5 3.6 + - - -
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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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234C GLU 3.3 10.8 + - - -
235C ARG* 2.9 10.1 + - - +
237C ILE* 1.3 75.7 - - - +
239C TYR* 1.3 61.2 + - - +
240C LEU 3.5 0.9 - - - -
241C GLU* 4.2 7.2 + - - +
242C GLU 4.6 3.5 + - - -
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Residues in contact with TYR 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 ARG 2.5 18.0 + - - -
236C THR* 3.6 5.3 + - - +
237C ILE 3.4 0.4 - - - -
238C GLU* 1.3 73.7 - - - +
240C LEU* 1.3 62.0 + - - +
241C GLU 3.2 2.9 - - - -
242C GLU* 3.3 11.6 + - - -
243C VAL* 3.4 9.4 + - - -
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Residues in contact with LEU 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 THR 3.8 9.5 + - - -
237C ILE 4.2 4.2 + - - -
238C GLU 3.5 0.4 - - - -
239C TYR* 1.3 75.1 - - - +
241C GLU* 1.3 59.5 + - - +
242C GLU 3.2 0.2 - - - -
243C VAL* 4.5 2.2 - - - +
244C ALA* 2.9 26.0 + - - -
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Residues in contact with GLU 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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237C ILE 4.5 4.4 + - - -
238C GLU* 4.2 8.8 + - - +
239C TYR 3.2 1.2 - - - -
240C LEU* 1.3 76.6 - - - +
242C GLU* 1.3 55.5 + - - +
244C ALA* 3.4 1.8 + - - +
245C ILE* 2.9 23.6 + - - -
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Residues in contact with GLU 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 4.6 3.4 + - - -
239C TYR 3.3 7.8 + - - -
240C LEU 3.2 0.4 - - - -
241C GLU* 1.3 73.9 - - - +
243C VAL* 1.3 58.3 + - - +
244C ALA 3.2 1.3 - - - -
245C ILE* 3.2 2.3 + - - +
246C THR* 2.9 25.6 + - - -
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Residues in contact with VAL 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C TYR 3.4 12.7 + - - -
240C LEU* 3.5 3.6 + - - +
242C GLU* 1.3 75.5 - - - +
244C ALA* 1.3 57.3 + - - +
246C THR* 3.4 2.1 + - - +
247C PHE* 3.0 23.6 + - - -
300D TYR* 6.6 0.2 - - - +
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Residues in contact with ALA 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 LEU 2.9 18.7 + - - -
241C GLU* 3.7 2.2 - - - +
243C VAL* 1.3 78.3 - - - +
245C ILE* 1.3 56.0 + - - +
247C PHE* 3.2 2.7 + - - +
248C ALA* 2.8 24.9 + - - -
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Residues in contact with ILE 245 (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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241C GLU 2.9 16.4 + - - -
242C GLU* 3.2 4.2 + - - +
244C ALA* 1.3 75.5 - - - +
246C THR* 1.3 58.2 + - - +
248C ALA* 3.2 12.3 + - - +
249C LYS* 3.4 11.6 + - - -
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Residues in contact with THR 246 (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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242C GLU 2.9 15.7 + - - -
243C VAL* 3.8 2.5 - - - +
245C ILE* 1.3 75.0 - - - +
247C PHE* 1.3 62.6 + - - +
248C ALA 3.3 0.2 - - - -
249C LYS 4.7 0.7 - - - -
250C GLY* 4.4 7.4 + - - -
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Residues in contact with PHE 247 (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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243C VAL 3.0 15.0 + - - -
244C ALA* 3.6 3.6 - - - +
246C THR* 1.3 79.4 - - - +
248C ALA* 1.3 62.2 + - - +
249C LYS 3.5 0.2 - - - -
250C GLY* 3.3 3.9 + - - -
251C LEU* 3.2 17.5 + - - -
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Residues in contact with ALA 248 (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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86C ARG 5.6 0.5 - - - +
87C SER* 5.3 11.7 - - - +
244C ALA 2.8 15.9 + - - -
245C ILE* 3.2 6.0 + - - +
247C PHE* 1.3 75.6 - - - +
249C LYS* 1.3 63.8 - - - +
251C LEU* 3.1 11.4 + - - +
252C ALA* 3.4 8.3 + - - -
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Residues in contact with LYS 249 (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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245C ILE 3.4 12.7 + - - -
246C THR 4.7 0.2 - - - -
248C ALA* 1.3 74.9 - - - +
250C GLY* 1.3 60.8 + - - +
252C ALA* 3.3 11.1 + - - +
253C ASP* 3.5 8.8 + - - -
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Residues in contact with GLY 250 (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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246C THR 4.4 6.2 + - - -
247C PHE* 3.3 9.1 + - - -
248C ALA 3.2 1.0 - - - -
249C LYS* 1.3 78.8 - - - +
251C LEU* 1.3 56.0 + - - +
253C ASP 5.4 0.4 - - - -
254C LYS* 2.8 24.3 + - - -
255C LYS* 3.0 15.0 + - - -
256C ILE* 4.1 6.0 + - - -
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Residues in contact with LEU 251 (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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247C PHE 3.2 8.8 + - - -
248C ALA* 3.1 9.4 + - - +
250C GLY* 1.3 76.0 - - - +
252C ALA* 1.3 64.5 + - - +
254C LYS* 3.6 9.7 + - - +
256C ILE 5.0 5.4 - - - -
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Residues in contact with ALA 252 (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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86C ARG 4.9 11.9 - - - -
248C ALA 3.4 8.1 + - - -
249C LYS* 3.3 6.7 + - - +
250C GLY 3.3 1.0 - - - -
251C LEU* 1.3 79.6 - - - +
253C ASP* 1.3 57.0 + - - +
254C LYS 3.9 0.3 + - - -
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Residues in contact with ASP 253 (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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249C LYS 3.5 11.4 + - - -
250C GLY* 3.7 1.1 - - - -
252C ALA* 1.3 75.2 - - - +
254C LYS* 1.3 62.6 + - - +
255C LYS* 3.3 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