Contacts of the helix formed by residues 235 - 250 (chain B) in PDB entry 2XWU
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 PRO 235 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B ARG* 6.0 0.2 - - - +
195B ALA* 6.5 1.3 - - + -
233B GLU 3.6 3.8 - - - +
234B VAL* 1.3 95.7 - - + +
236B LEU* 1.3 67.0 + - - +
237B GLN* 3.0 2.7 + - + +
238B ASP* 3.1 33.8 + - - +
239B CYS* 3.7 5.7 - - - -
271B ASP* 5.2 0.4 - - - +
275B TYR* 3.1 37.7 - - + +
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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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234B VAL 3.3 5.0 + - - -
235B PRO* 1.3 70.5 - - - +
237B GLN* 1.3 61.4 + - - +
239B CYS* 3.1 18.3 + - + +
240B GLU 3.5 4.5 + - - -
243B ILE* 3.4 27.4 - - + -
266B ALA* 4.0 20.9 - - + +
267B ILE* 5.2 0.7 - - - -
269B GLN* 4.5 4.8 + - - +
272B ALA* 3.8 22.4 - - + +
275B TYR* 3.3 23.6 - - + +
278B THR* 3.8 23.6 - - + +
279B LEU* 3.3 34.8 - - + -
282B LEU* 4.7 4.7 - - + -
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Residues in contact with GLN 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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235B PRO* 3.0 2.3 + - + -
236B LEU* 1.3 74.5 - - - +
238B ASP* 1.3 68.0 + - - +
239B CYS 3.0 5.6 + - - -
240B GLU* 3.3 34.6 + - - +
275B TYR* 4.2 19.8 - - + -
278B THR* 3.7 15.3 + - - +
281B LYS* 5.4 4.0 - - - +
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Residues in contact with ASP 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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198B CYS* 6.2 0.2 - - - -
202B PHE* 3.4 27.6 - - + +
206B GLU* 5.1 2.4 - - - +
234B VAL* 4.0 16.5 - - + +
235B PRO* 3.1 26.6 + - - +
237B GLN* 1.3 83.7 - - - +
239B CYS* 1.3 60.4 + - - +
240B GLU 3.5 0.4 + - - -
241B ALA* 4.6 8.4 + - - +
242B LEU 5.1 0.7 + - - -
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Residues in contact with CYS 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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202B PHE* 3.7 13.9 - - - -
226B PHE* 3.9 16.4 - - + -
230B VAL* 4.7 5.2 - - - -
234B VAL* 3.7 31.4 - - - -
235B PRO 3.7 8.3 - - - -
236B LEU* 3.3 15.7 - - + +
237B GLN 3.0 0.8 - - - -
238B ASP* 1.3 78.7 - - - +
240B GLU* 1.3 54.2 + - - +
241B ALA 3.2 3.1 - - - -
242B LEU* 2.9 4.9 + - - +
243B ILE* 2.6 53.9 + - + +
266B ALA* 5.4 0.7 - - - -
269B GLN* 4.8 4.3 - - - -
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Residues in contact with GLU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B LEU 3.5 1.2 + - - -
237B GLN* 3.3 27.5 + - - +
239B CYS* 1.3 75.8 - - - +
241B ALA* 1.3 56.3 + - - +
243B ILE* 3.8 7.6 - - - +
244B GLN* 2.9 34.9 + - - +
278B THR* 3.2 40.8 + - + +
281B LYS* 3.1 39.2 + - + +
282B LEU* 5.3 2.5 - - + -
285B LEU* 5.9 0.2 - - - +
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Residues in contact with ALA 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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206B GLU* 3.4 32.9 - - + +
237B GLN 5.0 0.2 + - - -
238B ASP 4.6 6.8 + - - +
239B CYS 3.2 0.6 - - - -
240B GLU* 1.3 76.9 - - - +
242B LEU* 1.3 62.7 + - - +
244B GLN* 3.6 8.6 + - - +
245B ALA* 3.3 21.7 + - - +
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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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202B PHE* 3.9 20.4 - - + +
205B LEU* 3.8 28.7 - - + -
206B GLU* 3.9 29.8 - - + +
209B LEU* 3.8 28.6 - - + +
222B VAL* 4.8 2.7 - - + -
223B LEU* 5.7 0.3 - - - +
226B PHE* 3.3 46.0 - - + -
238B ASP 5.1 0.4 + - - -
239B CYS* 2.9 5.9 + - - +
241B ALA* 1.3 78.1 - - - +
243B ILE* 1.3 60.0 + - - +
245B ALA* 3.3 4.1 + - + +
246B ALA* 2.9 29.5 + - - +
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Residues in contact with ILE 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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226B PHE* 4.0 13.2 - - + -
236B LEU* 3.4 33.4 - - + +
239B CYS* 2.6 38.4 + - + +
240B GLU* 3.8 7.4 - - - +
242B LEU* 1.3 72.3 - - - +
244B GLN* 1.3 58.6 + - - +
246B ALA* 3.2 7.5 + - - +
247B PHE* 3.0 52.2 + - + -
263B ILE* 4.8 10.3 - - + -
266B ALA* 4.1 12.8 - - + -
267B ILE* 5.5 1.1 - - + -
278B THR* 5.2 0.2 - - + -
282B LEU* 4.4 23.6 - - + -
285B LEU* 5.1 1.6 - - + -
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Residues in contact with GLN 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 GLU 2.9 19.9 + - - +
241B ALA* 3.9 7.6 - - - +
242B LEU 3.2 0.2 - - - -
243B ILE* 1.3 78.7 - - - +
245B ALA* 1.3 60.7 + - - +
247B PHE* 3.4 4.4 + - - +
248B ALA* 3.2 21.1 + - - +
285B LEU* 4.3 33.9 - - + +
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Residues in contact with ALA 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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206B GLU* 6.3 1.1 - - - -
209B LEU* 3.6 34.7 - - + +
241B ALA 3.3 12.2 + - - +
242B LEU* 3.6 8.3 - - + +
243B ILE 3.3 0.4 - - - -
244B GLN* 1.3 76.2 - - - +
246B ALA* 1.3 63.5 + - - +
248B ALA* 3.3 8.7 + - - +
249B ALA* 3.1 21.5 + - - +
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Residues in contact with ALA 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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209B LEU* 5.0 0.4 - - - +
223B LEU* 4.0 25.1 - - + -
226B PHE* 5.2 2.9 - - + -
242B LEU 2.9 17.4 + - - +
243B ILE* 3.2 8.3 + - - +
245B ALA* 1.3 76.0 - - - +
247B PHE* 1.3 64.6 + - - +
249B ALA* 3.1 10.7 + - - +
250B LEU* 3.4 2.8 + - - +
259B SER* 3.3 24.6 + - - -
262B ALA* 4.8 5.6 - - + -
263B ILE* 3.8 19.5 - - + -
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Residues in contact with PHE 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 ILE* 3.0 45.1 + - + -
244B GLN* 3.5 9.4 - - - +
245B ALA 3.3 0.2 - - - -
246B ALA* 1.3 76.0 - - - +
248B ALA* 1.3 63.7 + - - +
250B LEU* 3.1 39.3 + - + +
251B GLN 4.4 0.3 + - - -
263B ILE* 3.7 25.8 - - + -
267B ILE* 5.0 2.5 - - + -
282B LEU* 4.8 6.5 - - + -
285B LEU* 3.6 56.5 - - + -
286B VAL* 3.9 18.8 - - + -
289B LEU* 3.8 21.7 - - + +
311B ILE* 4.0 8.7 - - + -
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Residues in contact with ALA 248 (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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244B GLN 3.2 10.1 + - - +
245B ALA* 3.4 12.6 - - - +
246B ALA 3.2 0.2 - - - -
247B PHE* 1.3 79.8 - - - +
249B ALA* 1.3 59.7 + - - +
250B LEU 3.1 1.4 + - - -
251B GLN* 3.4 19.8 + - - +
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Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 6.3 1.6 - - + -
219B ARG* 6.2 0.2 - - - +
223B LEU* 4.7 5.6 - - + -
245B ALA 3.1 12.9 + - - +
246B ALA* 3.1 13.8 + - - +
248B ALA* 1.3 71.6 - - - +
250B LEU* 1.3 57.5 - - - +
251B GLN 2.9 11.3 + - - -
252B ASP* 3.0 25.8 + - - +
255B LEU* 3.6 33.0 - - + +
256B PHE 4.2 0.3 + - - -
259B SER* 4.2 7.6 - - - +
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Residues in contact with LEU 250 (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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246B ALA 3.6 3.4 - - - +
247B PHE* 3.1 32.8 + - + +
249B ALA* 1.3 77.5 - - - +
251B GLN* 1.3 58.9 + - - +
252B ASP 3.4 2.5 + - - +
256B PHE* 3.5 26.5 - - + +
259B SER* 3.1 25.1 - - - +
260B VAL* 3.7 31.2 - - + +
263B ILE* 3.6 20.4 - - + -
289B LEU* 3.8 20.4 - - + -
292B GLN* 3.0 32.5 + - - +
308B ILE* 5.8 0.9 - - + -
311B ILE* 3.9 5.2 - - + -
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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