Contacts of the helix formed by residues 231 - 238 (chain B) in PDB entry 1WZ2
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 ARG 231 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B THR* 3.1 15.0 + - - +
230B LEU* 1.3 97.1 - - + +
232B PRO* 1.3 58.0 - - - +
233B GLU* 2.9 38.3 + - - +
234B THR* 2.4 40.8 + - - +
235B VAL 4.5 0.3 + - - -
328B HIS* 3.2 17.4 - - - +
329B ALA* 3.2 43.4 - - - +
397B THR* 4.2 8.1 + - - +
398B LYS* 5.8 1.7 - - - +
400B ILE* 3.5 26.5 - - - +
401B TYR* 3.4 36.0 - - + +
424B LYS* 4.7 0.9 - - - -
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Residues in contact with PRO 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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210B ILE* 4.1 22.7 - - + -
212B ILE* 4.9 2.0 - - + -
229B THR* 4.1 7.8 - - + -
230B LEU 3.2 13.2 - - - +
231B ARG* 1.3 83.5 - - - +
233B GLU* 1.3 55.8 + - - +
234B THR 3.3 0.2 - - - -
235B VAL* 3.0 35.2 - - + +
424B LYS* 3.8 21.8 - - + +
427B ILE* 3.3 9.1 - - + +
428B ALA* 3.5 42.4 - - + +
431B MET* 5.2 0.9 - - - -
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Residues in contact with GLU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ARG* 3.1 38.7 + - + +
232B PRO* 1.3 76.6 - - - +
234B THR* 1.3 96.5 + - - +
235B VAL* 3.1 12.3 + - - +
236B TYR* 3.7 6.8 + - - +
355B ILE* 2.8 22.1 - - + +
401B TYR* 4.0 8.8 - - - -
410B PHE* 4.9 5.1 - - + -
420B VAL* 4.7 11.4 - - + +
423B VAL* 3.5 27.4 - - + -
424B LYS* 3.9 24.9 - - + +
427B ILE* 3.3 13.2 - - + +
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Residues in contact with THR 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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229B THR* 4.0 5.7 + - - +
231B ARG* 2.4 53.1 + - - +
233B GLU* 1.3 91.0 + - - +
235B VAL* 1.3 55.8 + - - +
236B TYR 3.3 0.4 - - - -
237B GLY* 2.7 23.5 + - - -
323B MET* 3.9 5.2 - - - -
325B VAL* 3.0 53.4 - - + +
328B HIS* 4.8 5.2 - - + -
329B ALA* 5.3 3.1 - - + +
355B ILE* 3.4 9.0 - - + -
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Residues in contact with VAL 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ILE* 2.9 39.5 - - + -
232B PRO* 3.0 20.8 + - + +
233B GLU 3.8 0.2 - - - +
234B THR* 1.3 75.6 + - - +
236B TYR* 1.3 69.9 + - + +
237B GLY 2.7 10.0 + - - -
238B VAL* 3.0 10.2 + - - +
298B ASN* 3.0 22.0 - - - +
300B VAL* 3.6 19.3 - - + -
323B MET* 3.5 12.7 - - - +
427B ILE* 3.5 26.2 - - + -
431B MET* 3.6 11.7 - - + -
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Residues in contact with TYR 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 GLU 3.7 5.6 + - - +
234B THR 3.3 0.8 - - - -
235B VAL* 1.3 88.8 - - + +
237B GLY* 1.3 55.4 + - - +
238B VAL* 3.7 1.1 - - - -
298B ASN* 4.9 2.0 - - - -
300B VAL* 3.4 32.1 - - + +
301B SER* 4.9 13.2 - - - -
353B PRO* 5.2 6.8 - - - +
354B ARG 5.9 0.5 + - - -
355B ILE* 4.4 9.8 - - + +
410B PHE* 4.6 11.0 - + - -
412B VAL* 4.7 14.0 - - + +
413B PRO* 5.4 6.9 - - + +
414B PRO* 3.4 34.9 - - + +
415B TYR* 2.9 33.8 + + - -
427B ILE* 3.8 25.0 - - + +
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Residues in contact with GLY 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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234B THR 2.7 9.8 + - - -
236B TYR* 1.3 80.4 - - - +
238B VAL* 1.3 65.0 + - - +
239B THR* 3.1 14.9 - - - +
325B VAL* 2.8 32.1 - - - +
327B ALA* 5.2 0.5 - - - +
353B PRO* 4.6 10.4 - - - +
354B ARG* 5.6 2.5 - - - -
355B ILE* 4.0 10.4 - - - +
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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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214B PHE* 3.6 26.5 - - + -
234B THR 3.4 1.4 + - - -
235B VAL 3.0 1.4 + - - +
236B TYR 3.7 0.8 - - - -
237B GLY* 1.3 77.6 - - - +
239B THR* 1.3 61.1 + - - +
240B ASN 3.8 15.3 - - - +
241B MET* 5.3 0.4 - - - -
298B ASN* 2.8 39.0 - - + +
303B ASP* 4.0 9.8 - - - +
305B VAL* 4.1 14.2 - - + +
323B MET* 3.4 19.3 - - + -
324B SER 3.2 12.3 - - - +
325B VAL* 3.5 2.9 - - - -
353B PRO* 5.0 3.5 - - - +
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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