Contacts of the helix formed by residues 231 - 247 (chain B) in PDB entry 2WA2
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 ILE 231 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B LEU* 4.1 12.1 - - + -
197B LEU* 3.9 31.9 - - + +
198B MET* 4.1 17.2 - - - +
201B GLN* 3.6 46.9 + - + +
207B GLY* 4.5 5.2 - - - -
208B LEU* 3.9 43.7 - - + +
223B PHE* 4.6 7.6 - - + -
229B ASN* 3.4 3.3 + - - +
230B ASN* 1.3 69.5 + - - +
232B MET* 1.3 66.9 + - - +
234B ASN* 3.0 4.3 + - - +
235B VAL* 2.9 23.0 + - - +
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Residues in contact with MET 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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194B LEU* 4.2 39.3 - - + -
198B MET* 4.0 32.9 - - + +
230B ASN* 3.4 6.3 + - - +
231B ILE* 1.3 73.3 - - - +
233B GLY* 1.3 62.8 - - - +
235B VAL* 3.4 2.6 + - - +
236B THR* 3.1 28.5 + - - +
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Residues in contact with GLY 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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230B ASN* 2.9 21.9 + - - -
232B MET* 1.3 79.8 - - - +
234B ASN* 1.3 60.8 + - - +
236B THR* 3.5 5.5 + - - -
237B ALA* 3.1 22.6 + - - +
240B ARG* 5.0 1.6 + - - -
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Residues in contact with ASN 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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208B LEU* 2.6 30.2 + - + +
209B ILE* 3.6 9.9 - - - +
210B ARG* 3.9 5.0 - - - +
221B MET* 3.3 15.4 - - + +
229B ASN* 3.7 10.7 - - - +
230B ASN 2.9 19.0 + - - +
231B ILE 3.0 3.1 + - - +
233B GLY* 1.3 74.2 - - - +
235B VAL* 1.3 64.9 + - - +
237B ALA* 3.4 11.3 + - - +
238B VAL* 3.0 28.4 + - - +
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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
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188B PRO* 3.5 27.6 - - + +
189B TYR* 3.7 23.6 - - + +
194B LEU* 3.8 16.8 - - + -
208B LEU* 3.2 33.4 - - + -
219B HIS* 3.6 7.2 - - + -
221B MET* 4.0 9.2 - - - -
231B ILE 2.9 15.4 + - - +
232B MET 3.8 4.5 - - - +
233B GLY 3.3 0.2 - - - -
234B ASN* 1.3 76.1 - - - +
236B THR* 1.3 58.6 + - - +
238B VAL* 3.2 5.4 + - - +
239B SER* 3.0 30.1 + - - +
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Residues in contact with THR 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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9B LEU* 4.1 22.2 - - + -
232B MET 3.1 17.2 + - - -
233B GLY* 3.9 5.6 - - - -
234B ASN 3.3 0.2 - - - -
235B VAL* 1.3 76.1 - - - +
237B ALA* 1.3 60.0 + - - +
239B SER* 3.2 7.7 + - - -
240B ARG* 2.9 39.9 + - + +
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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 GLY 3.1 18.3 + - - +
234B ASN* 3.6 16.4 - - - +
235B VAL 3.4 0.2 - - - -
236B THR* 1.3 73.6 - - - +
238B VAL* 1.3 64.0 + - - +
240B ARG* 3.4 31.8 + - - +
241B GLN* 3.0 22.0 + - - +
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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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210B ARG* 3.6 39.3 - - + +
219B HIS* 3.4 24.2 - - + +
221B MET* 3.6 21.3 - - + -
234B ASN* 3.0 20.0 + - - +
235B VAL 3.2 6.7 + - - +
237B ALA* 1.3 73.1 - - - +
239B SER* 1.3 66.5 + - - +
241B GLN* 3.0 9.4 + - - +
242B LEU* 2.9 39.0 + - + +
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Residues in contact with SER 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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9B LEU* 3.5 27.4 - - - -
10B GLY* 3.5 14.1 + - - -
13B TRP* 5.0 1.7 - - - +
189B TYR* 4.6 4.3 - - - +
219B HIS* 2.8 28.6 + - - -
235B VAL* 3.0 13.2 + - - +
236B THR* 3.2 10.3 + - - -
238B VAL* 1.3 74.7 - - - +
240B ARG* 1.3 57.8 + - - +
242B LEU* 3.3 3.1 + - - +
243B LEU* 2.9 36.0 + - - +
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Residues in contact with ARG 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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9B LEU* 3.8 21.7 - - + +
233B GLY 5.0 1.4 + - - -
236B THR* 2.9 27.8 + - + +
237B ALA* 3.5 42.6 + - - +
239B SER* 1.3 76.1 - - - +
241B GLN* 1.3 56.9 + - - +
243B LEU* 3.3 6.2 + - - +
244B LYS* 2.9 30.1 + - - +
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Residues in contact with GLN 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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210B ARG* 4.6 17.7 + - - +
237B ALA 3.0 14.2 + - - +
238B VAL* 3.5 11.7 - - - +
240B ARG* 1.3 76.0 - - - +
242B LEU* 1.3 69.0 + - - +
244B LYS* 3.2 8.3 + - + +
245B ARG* 2.9 71.7 + - + +
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Residues in contact with LEU 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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13B TRP* 3.5 34.3 - - + +
28B TYR* 2.6 20.6 + - - +
210B ARG* 3.7 16.2 - - - +
216B ASN* 3.5 30.7 - - + +
218B THR 3.9 19.7 - - - +
219B HIS* 3.9 20.2 - - + -
238B VAL* 2.9 26.9 + - + +
239B SER 3.8 2.7 - - - +
241B GLN* 1.3 90.0 - - - +
243B LEU* 1.3 62.6 + - - +
245B ARG* 3.6 3.3 + - - +
246B MET* 3.5 13.3 + - - +
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Residues in contact with LEU 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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9B LEU* 3.7 44.0 - - + +
12B ILE* 4.0 8.7 - - + -
13B TRP* 3.6 33.4 - - + +
16B LYS* 3.8 25.1 - - + -
239B SER 2.9 21.0 + - - +
240B ARG* 3.7 4.9 - - - +
242B LEU* 1.3 75.8 - - - +
244B LYS* 1.3 64.5 + - - +
246B MET* 3.1 23.7 + - - +
247B GLU* 3.7 12.3 - - - +
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Residues in contact with LYS 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 ARG 2.9 18.3 + - - +
241B GLN* 3.5 8.5 - - - +
243B LEU* 1.3 75.5 - - - +
245B ARG* 1.3 61.6 + - + +
247B GLU* 3.0 29.3 + - - +
248B GLU* 3.3 37.4 - - + +
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Residues in contact with ARG 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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28B TYR* 3.7 15.5 - - + -
31B ARG* 2.9 38.6 + - - -
32B PHE* 3.8 30.9 + - + +
33B VAL* 4.2 4.8 - - - +
210B ARG* 5.9 0.4 - - - +
212B PRO* 5.4 6.7 + - - +
214B SER 5.5 1.2 + - - -
216B ASN* 2.9 35.1 + - - +
241B GLN* 2.9 59.9 + - + +
242B LEU* 3.9 3.7 - - - +
243B LEU 3.3 0.2 - - - -
244B LYS* 1.3 76.5 - - + +
246B MET* 1.3 60.5 + - - +
248B GLU* 3.3 23.7 + - - +
253B ARG* 3.8 21.2 - - - +
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Residues in contact with MET 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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13B TRP* 3.6 21.3 - - + +
16B LYS* 3.6 31.2 - - + +
17B LEU* 3.5 33.2 - - - +
20B LEU* 4.6 8.5 - - + -
28B TYR* 3.1 47.8 - - + -
31B ARG* 4.2 5.9 + - - -
242B LEU 3.5 6.7 + - - +
243B LEU* 3.1 16.7 + - - +
244B LYS 3.1 1.0 - - - -
245B ARG* 1.3 78.8 - - - +
247B GLU* 1.3 59.5 + - + +
248B GLU 3.4 1.5 + - - +
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Residues in contact with GLU 247 (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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243B LEU* 3.7 17.3 - - - +
244B LYS* 3.0 18.8 + - - +
246B MET* 1.3 77.6 - - + +
248B GLU* 1.3 64.6 + - - +
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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