Contacts of the helix formed by residues 232 - 246 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230B THR 4.1 3.6 - - - +
231B ALA* 1.3 71.2 - - - +
233B ARG* 1.3 66.6 + - - +
234B ASP* 3.3 2.5 - - + +
235B ILE* 3.1 37.0 + - + +
236B LEU* 3.0 26.1 + - - +
285B GLN* 4.0 12.0 + - - +
288B ARG* 3.0 40.2 + - - +
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Residues in contact with ARG 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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231B ALA* 3.4 7.7 + - - +
232B ASP* 1.3 71.7 - - - +
234B ASP* 1.3 58.3 + - - +
236B LEU* 3.3 10.7 + - - +
237B ALA* 2.9 31.1 + - - +
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Residues in contact with ASP 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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232B ASP* 3.3 1.3 - - + -
233B ARG* 1.3 78.6 - - - +
235B ILE* 1.3 58.7 - - + +
237B ALA* 3.3 6.9 + - - +
238B ARG* 2.8 48.7 + - - +
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Residues in contact with ILE 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 ASP* 3.1 39.3 + - + +
234B ASP* 1.3 76.3 - - + +
236B LEU* 1.3 61.4 + - + +
238B ARG* 3.1 5.4 + - - +
239B LEU* 2.8 28.2 + - + +
278B VAL* 4.3 5.9 - - + +
279B GLN* 3.5 25.4 - - - +
281B LEU* 3.6 33.0 - - + -
285B GLN* 3.8 23.3 - - + +
289B LEU* 4.6 23.8 - - + -
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Residues in contact with LEU 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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231B ALA* 4.2 23.1 - - + -
232B ASP 3.0 20.5 + - - +
233B ARG* 3.7 9.4 - - - +
235B ILE* 1.3 76.0 - - + +
237B ALA* 1.3 59.2 + - - +
239B LEU* 3.3 5.9 + - - +
240B HIS* 3.0 28.1 + - - +
289B LEU* 3.5 28.7 - - + -
292B GLU* 4.4 20.2 - - + -
310B PHE* 4.0 27.5 - - + -
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Residues in contact with ALA 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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233B ARG 2.9 17.1 + - - +
234B ASP* 3.6 7.4 - - - +
236B LEU* 1.3 76.2 - - - +
238B ARG* 1.3 60.6 + - - +
240B HIS* 3.3 8.1 + - - +
241B LYS* 3.0 27.9 + - - +
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Residues in contact with ARG 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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234B ASP* 2.8 37.4 + - - +
235B ILE* 3.1 6.4 + - - +
237B ALA* 1.3 75.3 - - - +
239B LEU* 1.3 57.4 + - - +
241B LYS* 3.4 8.1 + - + +
242B ALA* 2.9 27.3 + - + +
277B ARG 5.1 1.6 - - - +
278B VAL* 3.5 31.6 - - + +
279B GLN* 2.7 34.2 + - - +
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Residues in contact with LEU 239 (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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235B ILE* 2.8 18.0 + - + +
236B LEU* 3.5 5.8 - - - +
237B ALA 3.2 0.2 - - - -
238B ARG* 1.3 73.9 - - - +
240B HIS* 1.3 65.2 + - - +
242B ALA* 3.2 4.2 + - + +
243B VAL* 3.0 31.6 + - + +
270B PHE* 4.6 1.3 - - + -
274B CYS* 4.7 11.4 - - - -
277B ARG* 6.2 0.7 - - + -
278B VAL* 3.8 26.6 - - + +
289B LEU* 3.9 29.6 - - + -
293B MET* 4.2 2.9 - - + -
306B PHE* 3.8 32.8 - - + -
310B PHE* 3.7 27.8 - - + -
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Residues in contact with HIS 240 (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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236B LEU 3.0 13.8 + - - +
237B ALA* 3.3 12.1 + - - +
239B LEU* 1.3 78.1 - - - +
241B LYS* 1.3 62.4 + - - +
243B VAL 3.4 0.3 + - - -
244B THR* 3.1 41.3 + - + +
309B ARG 3.9 9.5 + - - -
310B PHE* 3.5 46.7 + + + +
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Residues in contact with LYS 241 (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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237B ALA 3.0 16.3 + - - +
238B ARG* 3.7 9.2 - - + +
239B LEU 3.3 0.2 - - - -
240B HIS* 1.3 76.8 - - - +
242B ALA* 1.3 57.5 + - - +
244B THR* 3.0 7.2 + - - -
245B SER* 2.9 38.2 + - - +
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Residues in contact with ALA 242 (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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238B ARG 2.9 17.7 + - - +
239B LEU* 3.5 6.7 - - + +
241B LYS* 1.3 78.8 - - - +
243B VAL* 1.3 59.6 + - + +
245B SER* 3.8 3.1 - - - -
246B HIS* 3.0 32.3 + - + +
250B ILE* 3.5 11.0 - - + +
277B ARG* 3.6 38.1 - - + +
278B VAL* 4.3 4.7 - - + -
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Residues in contact with VAL 243 (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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239B LEU* 3.0 18.8 + - + +
240B HIS 3.8 0.2 - - - +
242B ALA* 1.3 78.3 - - - +
244B THR* 1.3 57.4 + - + +
247B TYR* 2.9 51.5 + - + +
250B ILE* 3.8 14.1 - - + -
306B PHE* 3.7 31.6 - - + -
307B LEU* 4.0 20.2 - - + +
310B PHE* 3.3 34.1 - - + +
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Residues in contact with THR 244 (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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240B HIS* 3.1 34.4 + - + +
241B LYS* 3.0 17.5 + - - -
243B VAL* 1.3 78.4 - - + +
245B SER* 1.3 61.8 + - - +
247B TYR* 4.3 10.7 + - - +
310B PHE 3.8 8.5 - - - +
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Residues in contact with SER 245 (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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241B LYS* 2.9 26.5 + - - +
242B ALA* 4.1 1.1 - - - -
244B THR* 1.3 81.0 + - - +
246B HIS* 1.3 83.5 + - - +
247B TYR 3.7 0.7 - - - -
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Residues in contact with HIS 246 (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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242B ALA* 3.0 20.3 + - + +
243B VAL 3.6 2.0 - - - -
245B SER* 1.3 95.2 + - - +
247B TYR* 1.3 66.6 + - - +
248B HIS 3.4 1.8 - - - -
249B ALA* 3.2 12.1 + - + +
250B ILE* 2.9 28.0 + - + +
277B ARG* 3.8 34.6 + - - +
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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