Contacts of the helix formed by residues 232 - 243 (chain B) in PDB entry 5YWB
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 TRP 232 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216B ARG 3.8 6.1 - - - -
217B PHE* 3.4 39.0 - + - -
218B LEU* 3.4 59.9 - - + -
219B GLN* 2.9 32.1 + - - -
222B VAL* 4.5 11.2 - - + -
226B SER* 3.8 8.1 + - - -
227B LYS* 5.9 0.2 - - - -
230B TYR* 3.4 27.9 - + + +
231B TRP* 1.3 79.1 - - - +
233B MET* 1.3 90.5 + - + +
234B ASN 3.1 1.4 + - - -
235B ALA* 3.7 14.4 + - - +
236B PHE* 4.3 5.2 + - + +
1240B PHE* 4.0 14.4 - + - -
1243B ALA* 4.5 6.7 - - + -
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Residues in contact with MET 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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230B TYR* 3.2 19.3 + - + +
231B TRP 3.0 1.0 + - - -
232B TRP* 1.3 121.3 - - + +
234B ASN* 1.3 63.7 + - - +
236B PHE* 2.9 44.3 + - + +
237B ILE* 2.9 32.5 + - + +
1240B PHE* 4.8 5.2 - - - +
1243B ALA* 4.6 10.5 - - + +
1244B ALA* 3.8 33.2 - - + +
1247B TRP* 4.3 18.8 - - + -
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Residues in contact with ASN 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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231B TRP* 2.9 68.5 + - - +
232B TRP 3.1 0.2 - - - -
233B MET* 1.3 75.6 - - - +
235B ALA* 1.3 65.7 + - - +
237B ILE* 3.0 10.4 - - - +
238B LYS* 2.8 30.4 + - - +
1247B TRP* 3.7 12.0 + - - -
1251B ARG* 3.6 19.5 + - - -
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Residues in contact with ALA 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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232B TRP 3.7 8.8 + - - +
233B MET 3.4 0.4 - - - -
234B ASN* 1.3 78.5 - - - +
236B PHE* 1.3 52.8 + - - +
238B LYS* 3.0 12.1 + - - +
239B THR* 2.6 43.6 + - - +
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Residues in contact with PHE 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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216B ARG* 6.2 1.8 - - + -
232B TRP* 4.3 4.4 + - + +
233B MET* 2.9 45.2 + - + +
235B ALA* 1.3 76.5 - - - +
237B ILE* 1.3 68.3 + - + +
239B THR* 2.9 10.1 + - - -
240B ALA* 2.9 24.2 + - + +
245B ILE* 3.9 39.5 - - + -
249B ALA* 6.5 0.2 - - + -
250B ILE* 5.5 4.7 - - + -
1185B ALA* 5.5 5.4 - - + -
1189B LEU* 4.4 16.2 - - + -
1240B PHE* 3.4 42.0 - + + -
1244B ALA* 5.5 0.2 - - + -
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Residues in contact with ILE 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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233B MET* 2.9 23.1 + - + +
234B ASN* 3.0 24.0 - - - +
236B PHE* 1.3 83.0 - - + +
238B LYS* 1.3 62.8 + - + +
240B ALA* 3.4 12.5 + - - +
241B HIS* 3.7 10.7 + - - +
1181B TYR* 4.4 33.4 - - + +
1182B PHE* 5.0 0.9 - - - -
1185B ALA* 4.5 18.2 - - + +
1247B TRP* 3.4 46.0 - - + -
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Residues in contact with LYS 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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234B ASN* 2.8 16.8 + - - +
235B ALA* 3.4 13.7 - - - +
237B ILE* 1.3 81.2 - - - +
239B THR* 1.3 63.1 + - - +
241B HIS* 3.6 10.8 + - - +
242B LYS* 3.7 33.1 + - + +
1181B TYR* 5.9 8.3 - - + -
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Residues in contact with THR 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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235B ALA* 2.6 32.9 + - - +
236B PHE* 3.4 10.9 - - + -
238B LYS* 1.3 73.6 - - - +
240B ALA* 1.3 66.0 + - - +
242B LYS* 2.9 22.7 + - + +
243B LYS* 3.1 19.1 + - + +
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Residues in contact with ALA 240 (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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236B PHE* 2.9 19.1 + - + +
237B ILE* 3.8 9.4 - - - +
238B LYS 3.3 0.4 - - - -
239B THR* 1.3 76.9 - - - +
241B HIS* 1.3 61.0 + - - +
243B LYS 2.8 26.3 - - - +
244B PRO* 4.0 4.0 - - - +
245B ILE* 3.6 33.0 - - + +
1184B VAL* 6.2 1.1 - - + -
1185B ALA* 4.5 14.1 - - + -
1188B ASP* 5.2 0.7 - - - +
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Residues in contact with HIS 241 (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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237B ILE 3.7 7.1 + - - +
238B LYS* 3.6 9.0 + - - +
239B THR 3.1 0.8 + - - -
240B ALA* 1.3 80.5 - - - +
242B LYS* 1.3 63.4 + - + +
243B LYS* 3.6 0.3 + - - -
244B PRO* 5.7 0.9 - - - +
1180B LYS* 5.7 8.1 - - + -
1181B TYR* 5.0 30.5 - + + -
1184B VAL* 3.4 39.4 - - + +
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Residues in contact with LYS 242 (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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238B LYS* 3.9 30.4 - - + +
239B THR* 2.9 14.5 + - + +
241B HIS* 1.3 81.3 - - + +
243B LYS* 1.3 61.5 + - + +
244B PRO* 4.6 1.8 - - - +
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Residues in contact with LYS 243 (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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239B THR* 3.1 13.9 + - + +
240B ALA* 2.8 25.5 - - - +
241B HIS 4.9 0.2 - - - -
242B LYS* 1.3 80.0 - - + +
244B PRO* 1.3 89.0 - - + +
245B ILE* 4.5 0.3 - - - +
246B ASP* 5.7 5.9 - - - +
248B ARG* 4.7 14.8 - - - +
249B ALA* 5.1 14.1 - - - +
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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