Contacts of the helix formed by residues 229 - 246 (chain B) in PDB entry 2WZJ
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 229 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A SER* 4.1 10.3 - - - +
95A GLN* 6.0 0.9 - - + -
167B HIS* 3.2 51.1 - - + +
170B PHE* 5.3 17.9 - - + -
172B VAL* 4.2 13.6 - - + -
228B GLY* 1.3 79.3 - - - +
230B GLU* 1.3 72.9 + - - +
231B VAL 3.1 2.0 - - - -
232B ASP 3.1 11.8 + - - +
233B VAL* 3.1 12.8 + - + +
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Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A SER* 3.1 24.2 + - - -
219B GLU* 4.4 3.4 - - - +
228B GLY* 3.4 9.2 + - - -
229B PRO* 1.3 96.2 - - - +
231B VAL* 1.3 70.7 + - + +
233B VAL* 3.1 10.9 + - - +
234B TRP 3.0 19.4 + - - -
289B PRO* 3.8 35.7 - - + +
290B SER* 5.6 1.2 - - - -
292B ARG* 3.2 32.3 + - + +
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Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ARG* 4.4 12.6 - - + +
217B ALA* 4.6 2.3 - - - +
219B GLU* 3.9 12.3 - - - +
225B LYS 4.9 0.2 - - - +
226B TYR* 3.0 74.0 - - + +
227B ASP 4.4 0.7 - - - +
228B GLY 3.1 15.6 + - - +
229B PRO 3.1 0.4 - - - -
230B GLU* 1.3 83.4 - - + +
232B ASP* 1.3 71.3 + - - +
234B TRP* 3.4 4.3 + - - +
235B SER* 3.1 25.7 + - - +
292B ARG* 4.0 4.7 - - - +
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Residues in contact with ASP 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B VAL* 4.0 4.5 - - + +
167B HIS* 3.0 33.0 + - + +
172B VAL* 3.6 6.4 - - - -
173B HIS* 2.7 28.9 + - - +
174B ARG* 2.9 26.7 + - - -
176B LEU* 3.5 23.8 + - + +
194B PHE* 5.0 0.2 - - - -
229B PRO 3.1 3.9 + - - +
231B VAL* 1.3 81.1 - - - +
233B VAL* 1.3 57.1 + - - +
235B SER* 3.2 7.2 + - - -
236B LEU* 2.9 34.1 + - - +
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Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B HIS* 4.7 2.2 - - + +
229B PRO 3.1 15.1 + - - +
230B GLU* 3.1 15.1 + - - +
232B ASP* 1.3 72.9 - - - +
234B TRP* 1.3 70.6 + - - +
236B LEU* 3.1 14.7 + - - -
283B LYS 4.5 0.4 - - - +
284B PHE* 3.2 46.1 - - + -
292B ARG* 4.3 12.1 - - + -
293B GLY 3.7 25.1 - - - +
294B THR* 5.2 1.3 - - - -
295B LEU* 3.7 22.9 - - + +
298B ILE* 4.2 7.2 - - + -
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Residues in contact with TRP 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B PRO 5.1 0.4 + - - -
215B TYR 3.5 12.5 - - - -
216B ALA 3.4 11.1 + - - -
217B ALA* 3.4 29.8 - - + -
218B PRO* 3.6 31.9 - - + -
230B GLU 3.0 6.7 + - - -
231B VAL 3.7 4.3 - - - +
233B VAL* 1.3 78.1 - - - +
235B SER* 1.3 65.6 + - - +
237B GLY* 3.0 11.1 + - - -
238B VAL* 3.3 22.5 + - + +
250B PHE* 3.4 37.0 - + - -
262B VAL* 4.2 15.5 - - + +
265B GLY* 4.8 2.5 - - - -
284B PHE 4.0 10.3 - - - -
285B LEU* 3.6 46.6 - - + +
286B ILE 3.7 21.5 - - - -
287B LEU* 4.1 6.5 - - + -
292B ARG* 3.9 11.7 - - - +
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Residues in contact with SER 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ARG 6.0 1.4 - - - -
176B LEU* 3.8 31.7 + - - -
215B TYR* 3.0 27.1 + - - +
226B TYR* 4.4 6.4 + - - -
231B VAL* 3.1 15.1 + - - +
232B ASP* 3.2 10.1 + - - -
234B TRP* 1.3 78.3 - - - +
236B LEU* 1.3 56.0 + - - +
238B VAL* 3.2 6.8 + - - +
239B ILE* 2.9 32.9 + - - +
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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
----------------------------------------------------------
156B PHE* 3.5 16.8 - - + -
159B ILE* 3.5 32.3 - - + +
160B VAL* 5.1 5.2 - - + -
163B VAL* 4.2 18.8 - - + -
176B LEU* 4.6 5.6 - - + -
232B ASP 2.9 24.0 + - - +
233B VAL* 3.1 6.7 + - - +
234B TRP 3.0 0.2 + - - -
235B SER* 1.3 76.8 - - - +
237B GLY* 1.3 51.0 + - - +
239B ILE* 3.0 17.4 + - + +
240B LEU 2.8 31.2 + - - -
284B PHE* 3.8 10.1 - - + -
295B LEU* 3.7 42.4 - - + -
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Residues in contact with GLY 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 VAL 3.3 4.0 + - - -
234B TRP 3.0 6.7 + - - -
236B LEU* 1.3 75.3 - - - +
238B VAL* 1.3 63.4 + - - +
240B LEU* 3.3 2.7 + - - -
241B TYR* 3.1 19.6 + - - +
281B LEU* 3.4 12.7 - - - +
284B PHE* 3.4 33.7 - - - -
285B LEU* 4.1 10.2 - - - +
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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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214B PRO 3.7 21.8 - - - +
215B TYR* 3.6 26.7 - - + -
234B TRP* 3.3 34.8 + - + +
235B SER 3.2 8.5 + - - +
237B GLY* 1.3 74.0 - - - +
239B ILE* 1.3 63.6 + - - +
241B TYR* 3.3 8.4 + - - +
242B THR* 3.0 30.1 + - + +
248B LEU* 4.8 2.0 - - + -
249B PRO* 3.8 28.7 - - + -
250B PHE* 4.4 3.6 - - + -
285B LEU* 4.1 8.1 - - + -
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Residues in contact with ILE 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B PHE* 4.0 14.8 - - + -
159B ILE* 4.3 4.0 - - + -
176B LEU* 4.0 26.9 - - + -
177B LYS* 4.2 7.4 - - - +
178B ALA* 4.8 1.6 - - + +
181B LEU* 3.6 35.0 - - + -
215B TYR* 3.8 18.2 - - + -
235B SER 2.9 17.6 + - - +
236B LEU* 3.1 22.4 - - + +
238B VAL* 1.3 77.3 - - - +
240B LEU* 1.3 64.9 + - - +
242B THR* 2.9 21.6 + - - +
243B LEU* 3.0 24.9 + - + +
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Residues in contact with LEU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ALA* 5.2 0.2 - - + -
156B PHE* 3.7 25.1 - - + -
236B LEU 2.8 15.2 + - - +
237B GLY* 3.3 8.3 + - - +
239B ILE* 1.3 72.3 - - - +
241B TYR* 1.3 63.8 + - - +
243B LEU* 3.1 17.5 + - + +
244B VAL* 3.1 32.9 + - + +
277B CYS* 4.5 7.2 - - - +
280B LEU* 3.4 31.9 - - + -
281B LEU* 3.6 26.0 - - + -
284B PHE* 4.1 6.7 - - + -
303B TRP* 3.7 32.3 - - + -
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Residues in contact with TYR 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 GLY 3.1 10.5 + - - +
238B VAL* 3.4 10.3 - - - +
240B LEU* 1.3 80.3 - - - +
242B THR* 1.3 57.4 + - - +
244B VAL* 4.5 3.8 - - - +
245B SER* 2.9 56.3 + - - -
247B SER* 3.4 16.0 + - - -
248B LEU 3.9 3.7 + - - -
249B PRO* 3.7 36.6 - - + +
267B TYR* 3.8 18.4 - + - -
268B ARG* 2.5 45.3 + - - +
269B ILE* 5.2 0.7 - - - -
270B PRO* 4.1 5.5 - - + +
273B MET* 4.5 12.3 - - + -
281B LEU* 4.0 25.5 - - + +
285B LEU* 5.4 1.6 - - + -
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Residues in contact with THR 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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141B LEU* 3.3 29.6 - - - +
178B ALA* 4.5 4.5 - - - +
215B TYR* 4.3 10.9 + - - +
238B VAL* 3.0 23.1 - - + +
239B ILE* 2.9 13.5 + - - +
241B TYR* 1.3 77.6 - - - +
243B LEU* 1.3 59.2 + - - +
244B VAL 3.5 0.2 - - - -
246B GLY* 3.0 20.8 + - - -
247B SER 3.4 20.2 - - - +
248B LEU* 3.7 26.7 - - + -
249B PRO* 4.5 0.4 - - + -
206C LEU* 4.2 9.4 - - - -
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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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137B VAL* 3.8 29.2 - - + -
141B LEU* 4.4 8.9 - - + +
146B ARG* 3.8 1.9 - - - -
147B MET* 3.1 50.3 + - + +
152B ALA* 4.3 22.2 - - + +
155B LYS* 4.8 7.2 - - + -
156B PHE* 4.1 35.0 - - + -
159B ILE* 4.5 9.4 - - + -
181B LEU* 5.7 0.2 - - + -
239B ILE* 3.0 25.2 + - + +
240B LEU* 3.1 8.7 + - + +
242B THR* 1.3 81.8 - - - +
244B VAL* 1.3 59.9 + - - +
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Residues in contact with VAL 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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146B ARG* 3.3 15.5 + - - +
147B MET 4.0 10.4 - - - +
149B GLU* 4.9 12.6 - - + +
152B ALA* 4.1 15.3 - - + -
240B LEU* 3.1 34.3 + - + +
241B TYR* 4.5 3.4 - - - +
243B LEU* 1.3 77.0 - - - +
245B SER* 1.3 60.5 + - - +
272B TYR* 3.4 17.0 - - + -
273B MET* 3.2 40.6 - - + -
277B CYS* 4.0 14.8 - - - -
303B TRP* 4.8 3.6 - - + -
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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
----------------------------------------------------------
146B ARG* 3.7 10.5 - - - +
241B TYR* 2.9 38.6 + - - -
244B VAL* 1.3 80.9 - - - +
246B GLY* 1.3 59.1 + - - +
247B SER* 3.1 27.5 + - - -
270B PRO* 4.1 13.5 - - - -
272B TYR* 3.2 23.5 + - - -
273B MET* 5.0 0.2 - - - -
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Residues in contact with GLY 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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141B LEU* 5.0 5.8 - - - +
145B GLY* 4.8 3.6 - - - -
146B ARG* 3.8 21.0 - - - +
242B THR 3.0 18.5 + - - -
245B SER* 1.3 77.3 + - - +
247B SER* 1.3 59.4 + - - +
204C ASN 4.6 3.9 - - - +
205C LYS* 5.1 0.9 - - - -
206C LEU* 3.7 23.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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