Contacts of the helix formed by residues 229 - 239 (chain C) in PDB entry 2WOE
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 THR 229 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227C THR* 4.3 0.7 + - - -
228C ASP* 1.3 94.9 + - - +
230C PHE* 1.3 64.6 + - - +
231C LYS* 3.6 7.1 + - - +
232C SER* 2.6 32.1 + - - -
233C CYS* 3.1 22.2 + - - +
259C TYR* 3.6 10.6 + - - -
263C ASP* 3.9 11.0 - - - +
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Residues in contact with PHE 230 (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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16C GLY* 3.8 21.8 - - - -
19C VAL* 4.2 4.3 - - + -
229C THR* 1.3 73.2 - - - +
231C LYS* 1.3 65.3 + - - +
233C CYS* 3.4 1.0 + - - +
234C LEU* 3.1 38.3 + - + +
252C GLY* 3.4 25.8 - - - -
255C ALA* 3.3 24.0 - - + -
256C GLY* 3.5 14.8 - - - -
259C TYR* 3.5 12.7 - - + -
260C GLY 5.5 0.7 - - - -
263C ASP* 3.1 29.6 + - + +
264C ILE* 3.8 27.4 - - + -
265C PRO* 3.9 14.8 - - + -
268C TRP* 3.9 20.6 - + - -
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Residues in contact with LYS 231 (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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43C ARG* 5.8 4.3 - - - +
229C THR* 3.3 6.9 + - - +
230C PHE* 1.3 80.7 - - - +
232C SER* 1.3 57.6 + - - +
235C ILE* 3.0 56.0 + - + +
263C ASP 4.6 2.7 + - - +
265C PRO* 4.1 20.2 - - + -
268C TRP* 3.8 22.4 - - + -
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Residues in contact with SER 232 (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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227C THR* 3.6 15.0 - - - -
228C ASP* 3.8 5.4 + - - -
229C THR* 2.6 36.2 + - - -
231C LYS* 1.3 73.8 - - - +
233C CYS* 1.3 67.3 + - - +
235C ILE* 4.6 5.8 - - - -
236C GLN* 3.0 40.0 + - - +
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Residues in contact with CYS 233 (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 TYR* 4.3 1.1 - - - +
224C TYR* 3.8 33.9 - - - -
227C THR* 3.2 19.7 + - - +
229C THR 3.1 16.4 + - - +
230C PHE 3.4 4.2 + - - +
232C SER* 1.3 77.6 + - - +
234C LEU* 1.3 55.7 + - + +
236C GLN* 4.0 1.2 - - - +
237C THR* 2.6 37.6 + - - -
251C ALA* 3.8 32.5 - - - -
255C ALA* 4.1 10.3 - - + -
259C TYR* 5.2 2.2 - - + -
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Residues in contact with LEU 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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19C VAL* 5.3 0.4 - - + -
20C GLY* 3.5 19.3 - - - +
23C LEU* 4.3 5.8 - - + -
230C PHE* 3.1 41.1 + - + +
233C CYS* 1.3 80.2 - - + +
235C ILE* 1.3 65.1 + - - +
237C THR* 3.4 1.7 + - - -
238C VAL* 3.0 35.0 + - + +
248C GLY* 3.2 35.2 - - - +
251C ALA* 3.9 9.0 - - + +
252C GLY* 3.6 23.8 - - - +
255C ALA* 4.0 3.4 - - + -
268C TRP* 4.0 18.2 - - + -
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Residues in contact with ILE 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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23C LEU* 4.9 0.7 - - + -
41C ILE* 3.6 18.8 - - + -
42C HIS 4.5 2.7 - - - +
43C ARG* 3.4 29.4 - - + -
231C LYS* 3.0 49.1 + - + +
232C SER* 4.1 4.9 - - - +
234C LEU* 1.3 74.0 - - - +
236C GLN* 1.3 69.7 + - + +
238C VAL* 4.1 3.8 - - - -
239C ASN* 2.6 45.6 + - + +
268C TRP* 3.9 15.9 - - + -
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Residues in contact with GLN 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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223C TYR* 3.5 38.4 + - + -
226C VAL* 4.1 6.2 - - - +
227C THR* 3.2 27.1 - - + +
232C SER* 3.0 27.3 + - - +
233C CYS 4.0 1.3 - - - +
235C ILE* 1.3 83.4 - - + +
237C THR* 1.3 63.4 + - - +
239C ASN* 3.5 4.5 + - - +
240C GLN 3.4 12.1 + - - -
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Residues in contact with THR 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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219C THR* 4.3 10.5 - - + +
220C VAL* 4.9 3.6 - - + -
223C TYR* 3.3 24.4 - - + +
233C CYS* 2.6 24.8 + - - -
234C LEU* 3.7 3.6 - - - -
235C ILE 3.3 0.2 - - - -
236C GLN* 1.3 75.0 - - - +
238C VAL* 1.3 65.2 + - - +
240C GLN* 3.1 20.4 + - - +
241C GLY 4.1 1.6 + - - +
247C THR* 3.4 50.1 + - - +
248C GLY* 3.9 1.3 - - - +
251C ALA* 3.5 17.4 - - + +
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Residues in contact with VAL 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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20C GLY 4.5 1.1 - - - +
23C LEU* 4.0 23.3 - - + -
24C GLY* 3.8 24.2 - - - +
27C VAL* 3.6 9.6 - - + +
35C ILE* 3.6 9.7 - - - +
42C HIS* 4.2 11.7 - - + +
234C LEU* 3.0 22.4 + - + +
235C ILE* 3.4 6.7 - - - +
237C THR* 1.3 75.8 - - - +
239C ASN* 1.3 70.6 + - - +
240C GLN 3.1 0.4 - - - -
241C GLY* 3.0 16.6 + - - -
244C ALA* 3.8 25.5 - - + +
248C GLY* 4.0 14.4 - - - -
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Residues in contact with ASN 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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32C LYS* 3.6 25.6 - - - +
35C ILE* 3.4 23.3 - - + +
40C GLY 4.4 1.6 - - - +
41C ILE* 3.6 12.5 - - + +
42C HIS* 2.8 49.1 + - - +
235C ILE* 2.6 38.9 + - + +
236C GLN* 4.0 4.7 - - - +
237C THR 3.3 0.2 - - - -
238C VAL* 1.3 76.7 - - - +
240C GLN* 1.3 62.4 + - - +
241C GLY 3.2 0.7 - - - -
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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