Contacts of the helix formed by residues 231 - 238 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A THR* 3.0 15.0 + - - +
230A LEU* 1.3 95.6 - - + +
232A PRO* 1.3 57.4 - - - +
233A GLU* 2.9 47.0 + - - +
234A THR* 2.4 39.9 + - - +
235A VAL 4.5 0.3 + - - -
328A HIS* 4.1 16.2 - - - +
329A ALA* 3.5 30.1 - - - +
397A THR 5.0 2.4 + - - -
398A LYS* 6.2 0.7 - - - +
400A ILE* 3.5 32.4 + - - +
401A TYR* 3.8 34.1 - - + +
404A GLU 5.9 0.8 + - - -
420A VAL* 6.2 1.2 - - - +
424A LYS* 4.6 1.1 - - - +
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Residues in contact with PRO 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ILE* 3.1 33.0 - - + -
212A ILE* 4.7 3.6 - - + -
229A THR* 4.1 7.6 - - + -
230A LEU 3.2 14.1 - - - +
231A ARG* 1.3 83.2 - - - +
233A GLU* 1.3 54.4 + - - +
234A THR 3.3 0.2 - - - -
235A VAL* 3.0 28.7 - - - +
424A LYS* 3.7 21.8 - - + +
427A ILE* 3.1 13.7 - - + +
428A ALA* 3.4 34.5 - - + +
431A MET* 5.1 0.4 - - - -
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Residues in contact with GLU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ARG* 2.9 46.8 + - - +
232A PRO* 1.3 76.4 - - - +
234A THR* 1.3 87.4 + - - +
235A VAL* 3.0 13.2 + - - +
236A TYR* 3.7 11.4 + - - -
355A ILE* 4.2 15.8 - - + +
401A TYR* 4.4 0.7 - - - -
410A PHE* 5.3 3.2 - - + -
420A VAL* 4.3 8.0 - - + +
423A VAL* 3.3 26.7 - - + -
424A LYS* 3.1 47.4 + - + +
427A ILE* 3.3 14.0 - - + +
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Residues in contact with THR 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A THR* 3.8 6.1 + - - -
231A ARG* 2.4 50.4 + - - +
233A GLU* 1.3 86.9 + - - +
235A VAL* 1.3 58.3 + - - +
236A TYR 3.3 0.7 - - - -
237A GLY* 2.8 19.4 + - - +
323A MET* 3.4 8.2 - - - +
325A VAL* 2.9 53.4 - - + +
328A HIS* 4.6 14.4 - - + -
329A ALA* 5.3 3.6 - - + +
355A ILE* 4.8 3.8 - - + -
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Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ILE* 3.0 39.0 - - + -
214A PHE* 5.8 1.1 - - + -
232A PRO 3.0 18.4 + - - +
234A THR* 1.3 75.2 + - - +
236A TYR* 1.3 84.4 + - + +
237A GLY 2.7 10.7 + - - -
238A VAL* 3.0 7.6 + - - +
298A ASN* 2.9 24.3 + - - +
300A VAL* 3.5 17.3 - - + -
323A MET* 3.3 12.8 - - + +
427A ILE* 3.7 11.9 - - + -
431A MET* 3.3 14.8 - - + -
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Residues in contact with TYR 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A GLU 4.1 3.6 - - - +
234A THR 3.3 1.0 - - - -
235A VAL* 1.3 87.4 - - + +
237A GLY* 1.3 54.7 + - - +
238A VAL* 3.7 1.1 - - - -
298A ASN* 5.1 0.2 - - - +
300A VAL* 3.4 35.5 - - + +
301A SER* 5.1 13.2 - - - -
353A PRO* 5.2 6.4 - - - +
355A ILE* 3.5 24.3 - - + +
410A PHE* 4.6 11.4 - + - -
412A VAL* 4.7 6.3 - - + -
413A PRO* 5.4 5.6 - - + +
414A PRO* 3.5 35.4 - - + +
415A TYR* 3.8 21.3 + + - -
427A ILE* 3.3 34.0 - - + +
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Residues in contact with GLY 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A THR 2.8 9.4 + - - -
235A VAL 2.7 0.2 + - - -
236A TYR* 1.3 80.7 - - - +
238A VAL* 1.3 59.9 + - - +
239A THR* 2.9 24.1 - - - +
325A VAL* 3.1 26.0 - - - +
327A ALA* 5.2 1.4 - - - +
353A PRO* 4.5 12.5 - - - +
354A ARG 5.6 1.3 - - - -
355A ILE* 3.9 11.1 - - - +
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Residues in contact with VAL 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A PHE* 3.6 25.6 - - + -
235A VAL 3.0 5.1 + - - +
236A TYR 3.7 0.8 - - - -
237A GLY* 1.3 78.2 - - - +
239A THR* 1.3 61.4 + - - +
240A ASN 3.9 15.3 - - - +
241A MET* 4.7 0.7 - - - -
298A ASN* 2.8 42.8 - - + +
303A ASP* 3.8 13.1 - - - +
305A VAL* 4.0 13.3 - - + +
323A MET* 3.7 13.5 - - + -
324A SER 3.2 12.1 - - - +
325A VAL* 3.4 4.3 - - - +
353A PRO* 5.0 4.5 - - - +
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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