Contacts of the helix formed by residues 232 - 246 (chain A) in PDB entry 1WLZ
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 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A THR 3.5 3.5 + - - +
231A ALA* 1.3 71.0 - - - +
233A ARG* 1.3 59.0 + - - +
234A ASP* 2.8 37.4 + - - +
235A ILE* 3.0 41.3 + - + +
236A LEU* 3.0 32.2 + - - +
285A GLN* 4.6 6.1 + - + -
288A ARG* 6.0 0.2 - - - +
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Residues in contact with ARG 233 (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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231A ALA* 3.6 9.0 + - + +
232A ASP* 1.3 71.5 + - - +
234A ASP* 1.3 58.7 + - - +
236A LEU* 3.8 15.1 - - + +
237A ALA* 2.8 30.3 + - - +
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Residues in contact with ASP 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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232A ASP* 2.8 14.3 + - - +
233A ARG* 1.3 77.0 - - - +
235A ILE* 1.3 57.6 + - - +
237A ALA* 3.3 5.4 + - - +
238A ARG* 2.8 70.8 + - - +
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Residues in contact with ILE 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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232A ASP* 3.0 41.0 + - + +
234A ASP* 1.3 76.6 - - - +
236A LEU* 1.3 57.9 + - - +
238A ARG* 3.4 12.3 + - - +
239A LEU* 2.9 28.7 + - + +
278A VAL* 4.4 11.2 - - + +
279A GLN* 3.6 18.8 - - - +
281A LEU* 3.6 32.8 - - + -
285A GLN* 3.9 23.6 - - + +
289A LEU* 4.6 25.6 - - + -
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Residues in contact with LEU 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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231A ALA* 4.5 16.8 - - + -
232A ASP 3.0 24.6 + - - +
233A ARG* 3.9 11.9 - - + +
235A ILE* 1.3 78.4 - - + +
237A ALA* 1.3 61.7 + - - +
239A LEU* 3.3 5.6 + - - +
240A HIS* 3.1 31.1 + - + -
289A LEU* 3.7 27.4 - - + -
292A GLU* 4.6 14.1 - - + -
293A MET* 4.6 2.5 - - + -
309A ARG* 4.4 12.3 - - - +
310A PHE* 4.0 23.2 - - + -
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Residues in contact with ALA 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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233A ARG 2.8 20.3 + - - +
234A ASP* 3.7 6.1 - - - +
236A LEU* 1.3 76.7 - - - +
238A ARG* 1.3 61.4 + - + +
240A HIS* 3.2 12.0 + - - +
241A LYS* 3.1 24.3 + - - +
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Residues in contact with ARG 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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234A ASP* 2.8 52.1 + - - +
235A ILE* 3.8 13.0 - - - +
237A ALA* 1.3 76.5 - - + +
239A LEU* 1.3 60.7 + - - +
241A LYS* 3.6 9.2 - - + +
242A ALA* 2.9 28.6 + - - +
277A ARG 5.2 0.5 - - - +
278A VAL* 3.5 32.6 + - + +
279A GLN* 2.6 36.3 + - - +
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Residues in contact with LEU 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 ILE* 2.9 19.1 + - + +
236A LEU* 3.5 6.5 - - + +
237A ALA 3.2 0.2 - - - -
238A ARG* 1.3 73.8 - - - +
240A HIS* 1.3 64.9 + - - +
242A ALA* 3.3 3.1 + - + +
243A VAL* 3.0 34.3 + - + +
250A ILE* 6.4 0.4 - - + -
270A PHE* 4.6 2.9 - - + -
273A ILE* 6.5 0.2 - - + -
274A CYS* 4.7 11.9 - - - -
277A ARG* 5.8 2.0 - - + -
278A VAL* 3.5 26.7 - - + +
289A LEU* 4.1 31.0 - - + -
293A MET* 4.6 0.4 - - + -
306A PHE* 3.9 29.8 - - + -
310A PHE* 3.8 27.1 - - + -
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Residues in contact with HIS 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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236A LEU* 3.1 21.5 + - + -
237A ALA* 3.3 12.8 - - - +
239A LEU* 1.3 79.0 - - - +
241A LYS* 1.3 62.5 + - - +
243A VAL 3.3 0.3 + - - -
244A THR* 3.1 31.7 + - + +
309A ARG* 3.1 33.1 + - + -
310A PHE* 3.3 44.9 + + - +
311A SER 5.5 1.7 - - - -
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Residues in contact with LYS 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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237A ALA 3.1 9.8 + - - +
238A ARG* 3.6 13.5 - - + +
240A HIS* 1.3 81.2 - - - +
242A ALA* 1.3 56.1 + - - +
244A THR* 3.0 8.7 + - - -
245A SER* 2.9 36.7 + - - +
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Residues in contact with ALA 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 ARG 2.9 18.2 + - - +
239A LEU* 3.6 10.1 - - + +
240A HIS 3.3 0.2 - - - -
241A LYS* 1.3 77.0 - - - +
243A VAL* 1.3 57.1 + - - +
245A SER* 4.6 0.7 - - - -
246A HIS* 2.8 45.0 + - + +
250A ILE* 3.6 3.8 - - + +
277A ARG* 3.6 37.5 - - + +
278A VAL* 4.4 2.2 - - + -
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Residues in contact with VAL 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 LEU* 3.0 26.4 + - + +
242A ALA* 1.3 75.4 - - - +
244A THR* 1.3 58.6 + - - +
247A TYR* 2.9 49.9 + - + +
250A ILE* 3.9 15.7 - - + -
306A PHE* 3.7 32.1 - - + -
307A LEU* 4.2 16.4 - - + +
310A PHE* 3.6 31.6 - - + +
311A SER* 4.1 3.4 - - - +
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Residues in contact with THR 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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240A HIS* 3.1 16.5 + - + +
241A LYS* 3.0 17.5 + - - -
243A VAL* 1.3 79.3 - - - +
245A SER* 1.3 61.8 + - - +
247A TYR* 3.8 12.1 + - - +
310A PHE 3.6 13.5 - - - +
311A SER* 3.8 22.4 - - - +
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Residues in contact with SER 245 (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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241A LYS* 2.9 22.6 + - - +
242A ALA* 4.6 0.4 - - - -
244A THR* 1.3 80.3 + - - +
246A HIS* 1.3 83.0 + - - +
247A TYR 3.6 0.6 + - - -
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Residues in contact with HIS 246 (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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242A ALA* 2.8 27.6 + - + +
243A VAL 3.6 2.7 - - - -
245A SER* 1.3 94.4 + - - +
247A TYR* 1.3 59.6 + - - +
248A HIS 3.4 2.4 + - - -
249A ALA* 3.4 7.4 + - + +
250A ILE* 2.9 35.1 + - + +
277A ARG* 3.6 37.7 + - - +
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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