Contacts of the helix formed by residues 229 - 239 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228B ASP* 1.3 93.5 - - - +
230B PHE* 1.3 64.1 + - - +
231B LYS* 3.6 5.4 + - - +
232B SER* 2.6 34.7 + - - +
233B CYS* 3.1 23.2 + - - +
259B TYR* 3.7 8.8 - - - -
263B ASP* 3.7 14.6 - - - +
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Residues in contact with PHE 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B GLY* 3.7 24.2 - - - -
19B VAL* 4.1 4.5 - - + -
229B THR* 1.3 72.0 - - - +
231B LYS* 1.3 65.2 + - - +
233B CYS* 3.5 0.3 - - - +
234B LEU* 3.0 41.3 + - + +
252B GLY* 3.4 26.7 - - - -
255B ALA* 3.6 8.7 - - + -
256B GLY* 3.5 20.0 - - - -
259B TYR* 3.5 10.4 - - + -
260B GLY 5.4 0.7 - - - -
263B ASP* 3.0 33.2 + - + +
264B ILE* 3.8 34.1 - - + -
265B PRO* 3.8 14.8 - - + -
268B TRP* 3.9 16.6 - + - -
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Residues in contact with LYS 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ARG* 5.1 8.9 - - - +
229B THR* 3.4 5.4 + - - +
230B PHE* 1.3 79.9 - - - +
232B SER* 1.3 59.5 + - - +
235B ILE* 2.9 58.7 + - + +
263B ASP* 4.4 2.3 + - - +
265B PRO* 3.9 23.1 - - + +
268B TRP* 3.9 23.0 - - + -
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Residues in contact with SER 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B THR* 3.6 10.8 - - - -
228B ASP* 4.1 2.4 + - - -
229B THR* 2.6 37.0 + - - +
231B LYS* 1.3 75.4 - - - +
233B CYS* 1.3 67.6 + - - +
235B ILE* 4.6 5.2 - - - +
236B GLN* 2.9 46.0 + - - +
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Residues in contact with CYS 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B TYR* 4.1 2.6 - - - +
224B TYR* 3.9 25.1 - - - -
227B THR* 3.2 26.7 - - - +
229B THR 3.1 14.2 + - - +
230B PHE 3.5 4.3 - - - +
232B SER* 1.3 81.9 + - - +
234B LEU* 1.3 57.9 + - - +
236B GLN* 4.0 1.4 - - - +
237B THR* 2.8 33.5 + - - -
251B ALA* 4.0 23.1 - - - -
255B ALA* 4.0 21.3 - - + -
259B TYR* 5.2 0.9 - - + -
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 5.3 0.4 - - + -
20B GLY* 3.7 17.7 - - - +
23B LEU* 4.4 4.9 - - + -
230B PHE* 3.0 44.9 + - + +
233B CYS* 1.3 76.8 - - - +
235B ILE* 1.3 65.8 + - - +
237B THR* 3.2 1.2 + - - -
238B VAL* 2.9 35.8 + - + +
248B GLY* 3.1 35.7 - - - +
251B ALA* 4.0 8.1 - - + +
252B GLY* 3.5 27.6 - - - +
255B ALA* 4.4 2.5 - - + -
268B TRP* 3.9 18.4 - - + -
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Residues in contact with ILE 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 5.0 0.7 - - + -
41B ILE* 3.6 28.9 - - + -
42B HIS 4.3 9.4 - - - +
43B ARG* 3.9 25.8 - - + -
231B LYS* 2.9 47.1 + - + +
232B SER* 4.1 4.9 - - - +
234B LEU* 1.3 73.9 - - - +
236B GLN* 1.3 69.3 + - + +
238B VAL* 4.2 3.6 - - - -
239B ASN* 2.8 36.0 + - + +
268B TRP* 3.9 14.6 - - + -
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Residues in contact with GLN 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B TYR* 3.5 39.7 + - + -
226B VAL* 4.2 6.6 - - - +
227B THR* 3.2 28.5 - - + +
232B SER* 2.9 28.1 + - - +
233B CYS 4.1 1.6 - - - +
235B ILE* 1.3 82.7 - - + +
237B THR* 1.3 64.1 + - - +
239B ASN* 4.0 3.9 - - - +
240B GLN 3.4 12.1 + - - -
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Residues in contact with THR 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B THR* 4.4 9.8 - - + +
220B VAL* 5.3 2.0 + - + -
223B TYR* 3.2 25.5 - - + +
233B CYS* 2.8 22.2 + - - -
234B LEU* 3.7 4.0 - - - -
235B ILE 3.2 0.2 - - - -
236B GLN* 1.3 76.6 - - - +
238B VAL* 1.3 63.9 + - - +
240B GLN* 3.2 20.1 + - - +
241B GLY 4.1 1.9 + - - +
247B THR* 3.5 50.6 + - - +
248B GLY* 3.8 1.8 - - - +
251B ALA* 3.6 15.6 - - + +
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Residues in contact with VAL 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 3.8 20.4 - - + -
24B GLY* 3.7 33.0 - - - +
27B VAL* 3.5 19.8 - - + +
35B ILE* 3.7 0.9 - - - +
42B HIS* 4.2 13.2 - - + +
234B LEU* 2.9 30.4 + - + +
235B ILE* 3.7 1.1 - - - +
237B THR* 1.3 75.4 - - - +
239B ASN* 1.3 74.9 + - - +
240B GLN 3.1 0.2 - - - -
241B GLY* 3.0 17.3 + - - -
244B ALA* 3.8 8.5 - - - +
248B GLY* 3.9 22.2 - - - -
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Residues in contact with ASN 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LYS* 3.5 25.4 - - - +
35B ILE* 3.3 24.7 - - - +
40B GLY 4.4 1.4 - - - +
41B ILE* 3.6 13.2 - - + +
42B HIS* 2.8 48.8 + - - +
235B ILE* 2.8 35.5 + - + +
236B GLN* 4.0 4.7 - - - +
238B VAL* 1.3 77.3 - - - +
240B GLN* 1.3 62.9 + - - +
241B GLY 3.2 0.4 + - - -
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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