Contacts of the helix formed by residues 233 - 244 (chain A) in PDB entry 2WJZ
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 ASP 233 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ILE* 5.5 6.4 - - - +
232A ILE* 1.3 76.6 - - - +
234A VAL* 1.3 66.3 + - - +
235A ARG* 3.7 13.1 + - - +
236A GLU* 3.4 46.7 + - - +
237A LEU* 3.0 30.0 + - - +
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Residues in contact with VAL 234 (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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6A ILE* 5.0 6.1 - - + -
39A TYR* 5.5 0.4 - - + -
42A ILE* 3.8 31.4 - - + +
43A GLY* 3.7 32.1 - - - +
44A ILE* 3.7 27.1 - - + +
227A PHE* 4.3 20.4 - - + -
232A ILE 4.8 1.3 - - - +
233A ASP* 1.3 75.2 + - - +
235A ARG* 1.3 67.1 + - - +
237A LEU* 3.3 7.3 + - + +
238A LYS* 3.0 33.3 + - + +
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Residues in contact with ARG 235 (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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42A ILE 4.3 8.7 + - - +
233A ASP* 3.5 12.2 + - - +
234A VAL* 1.3 78.6 - - - +
236A GLU* 1.3 58.4 + - + +
238A LYS* 3.3 7.9 + - - +
239A GLU* 2.9 63.1 + - + +
250A LEU* 3.5 24.3 - - + +
251A GLU* 3.4 32.5 - - - +
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Residues in contact with GLU 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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207A MET* 4.1 14.2 - - - +
233A ASP* 3.4 34.4 + - - +
234A VAL 3.2 0.6 - - - -
235A ARG* 1.3 78.0 - - + +
237A LEU* 1.3 56.9 + - - +
239A GLU* 3.3 9.4 + - + +
240A TYR* 2.9 30.5 + - - +
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Residues in contact with LEU 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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6A ILE* 4.1 22.2 - - + -
207A MET* 3.7 47.3 - - + +
210A PHE* 3.9 43.3 - - + -
227A PHE* 4.2 11.7 - - + -
232A ILE* 4.0 6.7 - - + -
233A ASP 3.0 18.5 + - - +
234A VAL* 3.5 6.3 - - - +
236A GLU* 1.3 75.9 - - - +
238A LYS* 1.3 56.9 + - - +
240A TYR* 3.3 3.0 + - + +
241A LEU* 3.0 43.2 + - + +
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Residues in contact with LYS 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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6A ILE* 3.9 23.3 - - + -
43A GLY* 2.8 25.3 + - - +
45A ASP* 2.7 39.1 + - - -
234A VAL* 3.0 24.2 + - + +
235A ARG* 3.7 5.4 - - - +
237A LEU* 1.3 75.0 - - + +
239A GLU* 1.3 64.5 + - - +
241A LEU* 4.4 3.8 - - - +
242A LYS* 2.9 26.2 + - - +
248A VAL* 3.4 18.2 - - + +
249A ARG* 3.0 37.2 + - - +
250A LEU* 4.0 16.4 - - + -
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Residues in contact with GLU 239 (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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235A ARG* 2.9 64.5 + - + +
236A GLU* 3.3 7.8 + - - +
238A LYS* 1.3 75.2 - - - +
240A TYR* 1.3 64.4 + - - +
242A LYS* 3.5 2.5 + - - +
243A LYS* 3.0 24.5 + - - +
250A LEU* 3.6 19.7 - - + +
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Residues in contact with TYR 240 (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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207A MET* 3.8 52.3 - - + -
208A GLU* 3.2 32.0 - - + +
211A LEU* 3.9 24.2 - - + +
236A GLU 2.9 16.9 + - - +
237A LEU 3.4 5.2 - - - +
238A LYS 3.2 0.2 - - - -
239A GLU* 1.3 77.4 - - - +
241A LEU* 1.3 71.6 + - + +
243A LYS* 3.4 9.3 + - + +
244A HIS* 2.9 63.8 + + - -
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Residues in contact with LEU 241 (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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6A ILE* 3.9 15.7 - - + -
210A PHE* 4.2 5.2 - - + -
211A LEU* 3.7 40.4 - - + +
214A PHE* 3.9 19.5 - - + -
237A LEU* 3.0 31.8 + - + +
238A LYS* 3.3 2.2 + - - +
240A TYR* 1.3 81.8 - - + +
242A LYS* 1.3 65.8 + - - +
244A HIS* 3.1 10.8 + - - +
245A GLY 3.3 0.3 + - - -
246A VAL* 2.9 37.5 + - + +
248A VAL* 3.8 28.9 - - + -
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Residues in contact with LYS 242 (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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238A LYS 2.9 18.4 + - - +
239A GLU* 3.6 4.7 - - - +
241A LEU* 1.3 78.4 - - - +
243A LYS* 1.3 62.6 + - - +
245A GLY* 3.1 13.2 + - - -
246A VAL 3.5 16.5 + - - +
247A ASN* 4.1 16.2 + - - +
248A VAL* 4.1 20.8 + - + +
250A LEU* 4.3 25.4 - - + -
136B TYR* 5.0 4.9 + - - -
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Residues in contact with LYS 243 (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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239A GLU 3.0 14.8 + - - +
240A TYR* 3.4 15.5 - - + +
241A LEU 3.2 0.2 - - - -
242A LYS* 1.3 77.9 - - - +
244A HIS* 1.3 81.8 + - + +
245A GLY 3.3 2.6 + - - -
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Residues in contact with HIS 244 (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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211A LEU* 4.1 32.9 - - + +
215A LEU* 6.0 0.5 - - - +
240A TYR* 2.9 61.0 + + - +
241A LEU 3.1 5.1 + - - +
242A LYS 3.1 0.8 - - - -
243A LYS* 1.3 101.3 + - + +
245A GLY* 1.3 58.6 + - - +
246A VAL* 3.4 3.3 + - - +
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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