Contacts of the helix formed by residues 230 - 237 (chain B) in PDB entry 1WNY
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 230 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B THR* 3.1 13.4 + - - +
229B THR* 1.3 93.6 + - - +
231B PRO* 1.3 66.8 - - - +
232B TRP* 3.0 30.8 + - + +
233B THR* 3.0 31.6 + - - +
234B LEU* 4.3 0.3 + - - +
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Residues in contact with PRO 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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203B PRO 4.7 6.3 - - - +
205B VAL* 3.8 23.1 - - + -
228B THR* 4.1 5.4 - - + +
229B THR 3.5 9.4 - - - +
230B THR* 1.3 88.1 - - - +
232B TRP* 1.3 55.6 + - - +
233B THR 3.0 1.6 - - - -
234B LEU* 2.9 43.0 + - + +
363B ASN* 3.3 24.5 - - - +
366B ILE* 3.6 26.6 - - + +
367B LEU* 4.3 16.6 - - + -
370B LEU* 5.2 0.7 - - + -
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Residues in contact with TRP 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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230B THR* 3.0 24.9 + - + +
231B PRO* 1.3 76.5 - - - +
233B THR* 1.3 68.2 + - + +
234B LEU 3.3 0.4 - - - -
235B PRO* 3.3 15.4 - - - +
324B PHE* 3.5 38.6 - + - -
342B THR* 4.6 0.5 - - - +
343B VAL* 4.5 13.5 - - + -
349B LEU* 4.1 15.6 - - + +
359B PHE* 3.4 66.0 - + + +
362B ALA* 4.7 2.5 - - + -
363B ASN* 3.0 36.8 + - + +
366B ILE* 3.6 11.6 - - + +
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Residues in contact with THR 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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228B THR* 4.7 0.3 + - - -
230B THR* 3.0 25.8 + - - +
231B PRO 3.0 0.6 + - - -
232B TRP* 1.3 98.1 - - + +
234B LEU* 1.3 59.9 + - - +
235B PRO* 3.3 3.4 - - - -
236B GLY* 2.8 23.9 + - - +
319B HIS* 2.9 29.7 + - - -
321B ALA* 4.1 1.6 - - - +
324B PHE* 3.9 39.7 - - + -
342B THR* 4.9 0.4 - - - -
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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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207B VAL* 4.2 15.7 - - + -
209B PHE* 4.1 22.0 - - + -
226B ILE* 4.3 9.0 - - + -
228B THR* 4.5 4.7 - - + -
231B PRO* 2.9 30.0 + - + +
233B THR* 1.3 78.0 + - - +
235B PRO* 1.4 65.8 - - + +
237B ASN* 2.9 21.3 + - - +
291B PRO* 5.9 0.2 - - - +
292B PRO* 4.1 18.6 - - + +
293B TYR* 4.2 7.6 + - + +
319B HIS* 3.7 32.1 - - + +
366B ILE* 4.3 2.2 - - + -
370B LEU* 3.9 28.9 - - + -
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Residues in contact with PRO 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 3.3 17.7 - - - +
233B THR 3.3 1.3 - - - -
234B LEU* 1.4 94.5 - - + +
236B GLY* 1.4 55.9 + - - +
237B ASN 3.3 1.9 + - - +
293B TYR* 3.8 27.7 - - + +
295B GLN* 3.9 14.4 - - - +
340B LEU* 3.7 12.5 - - - +
342B THR* 5.3 0.2 - - + -
349B LEU* 4.2 7.9 - - + -
351B VAL* 3.5 28.9 - - + +
352B GLU 4.8 0.7 - - - +
354B PHE* 3.8 26.5 - - + -
366B ILE* 3.9 10.5 - - + -
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Residues in contact with GLY 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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233B THR 2.8 13.5 + - - -
235B PRO* 1.4 76.4 - - - +
237B ASN* 1.3 67.2 + - - +
238B VAL* 3.5 8.5 + - - +
321B ALA* 3.4 22.2 - - - +
322B PRO* 4.1 1.4 - - - +
340B LEU* 3.7 12.0 - - - +
342B THR* 3.2 27.7 + - - +
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Residues in contact with ASN 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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209B PHE* 3.6 16.3 - - + -
233B THR 3.6 2.0 + - - -
234B LEU* 2.9 17.1 + - - +
235B PRO 3.3 1.9 - - - +
236B GLY* 1.3 80.1 - - - +
238B VAL* 1.3 63.8 + - - +
239B ALA 2.9 21.3 - - - +
289B TYR* 2.6 30.3 + - - -
291B PRO* 3.8 6.5 - - + +
292B PRO* 5.2 0.9 - - + -
301B TYR* 3.2 33.5 + - + -
319B HIS* 2.9 26.9 - - + -
320B GLN 3.4 5.8 - - - -
340B LEU* 3.5 8.1 - - - +
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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