Contacts of the helix formed by residues 229 - 246 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C HIS* 3.3 42.7 - - + +
172C VAL* 3.9 17.7 - - + -
228C GLY* 1.3 79.7 - - - +
230C GLU* 1.3 65.1 + - - +
231C VAL 3.0 1.8 - - - -
232C ASP* 3.0 7.1 + - - +
233C VAL* 2.9 28.5 + - - +
91D SER* 3.9 13.5 - - - +
95D GLN* 4.9 1.1 - - - +
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Residues in contact with GLU 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C GLU* 4.5 2.9 - - - +
228C GLY* 3.1 28.8 + - - -
229C PRO* 1.3 80.2 - - - +
231C VAL* 1.3 62.9 + - + +
233C VAL* 3.2 10.2 + - - +
234C TRP 3.0 19.4 + - - -
289C PRO* 3.7 35.0 - - + +
290C SER* 5.9 0.8 - - - -
292C ARG* 3.2 34.2 + - + +
293C GLY 5.5 0.9 - - - +
91D SER* 5.1 2.6 + - - -
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Residues in contact with VAL 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C VAL* 5.3 0.4 - - + -
174C ARG* 4.4 12.1 - - + -
217C ALA* 4.4 3.4 - - + +
219C GLU* 3.5 19.1 - - + +
225C LYS 5.1 0.4 - - - +
226C TYR* 3.0 68.9 - - + +
227C ASP 4.5 0.9 - - - +
228C GLY 3.0 15.9 + - - +
230C GLU* 1.3 78.6 - - + +
232C ASP* 1.3 74.0 + - - +
234C TRP* 3.5 3.5 + - - +
235C SER* 3.2 22.2 + - - +
292C ARG* 4.2 4.5 - - - +
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Residues in contact with ASP 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C VAL* 4.1 3.2 - - + +
167C HIS* 2.9 33.9 + - + +
172C VAL* 3.3 7.1 - - - -
173C HIS* 2.5 36.3 + - - +
174C ARG* 2.8 27.5 + - - -
175C ASP 4.6 0.2 + - - -
176C LEU* 3.7 17.3 - - + +
228C GLY 4.2 0.2 + - - -
229C PRO 3.0 5.2 + - - +
231C VAL* 1.3 77.9 - - - +
233C VAL* 1.3 63.0 + - - +
235C SER* 3.1 6.9 + - - -
236C LEU* 3.0 26.2 + - - +
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Residues in contact with VAL 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C HIS* 4.8 2.2 - - + +
229C PRO* 2.9 19.3 + - + +
230C GLU* 3.2 12.3 + - + +
232C ASP* 1.3 74.1 - - - +
234C TRP* 1.3 64.8 + - - +
236C LEU* 3.0 16.1 + - - +
283C LYS 4.6 2.2 - - - +
284C PHE* 3.2 44.8 - - + +
292C ARG* 4.7 6.3 - - + +
293C GLY 3.7 20.9 - - - +
294C THR* 5.0 0.7 - - - -
295C LEU* 3.9 27.4 - - + +
298C ILE* 4.0 13.0 - - + -
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Residues in contact with TRP 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C TYR 3.5 17.0 + - - -
216C ALA 3.2 12.5 + - - -
217C ALA* 3.5 26.9 - - + -
218C PRO* 3.6 31.4 - - + -
230C GLU 3.0 6.5 + - - -
231C VAL 3.8 2.5 - - - +
233C VAL* 1.3 74.3 - - - +
235C SER* 1.3 66.7 + - - +
237C GLY* 3.0 12.1 + - - -
238C VAL* 3.4 17.8 + - + +
250C PHE* 3.5 35.3 - + - -
262C VAL* 4.2 16.6 - - + -
265C GLY* 4.9 2.2 - - - -
284C PHE 3.9 10.3 - - - -
285C LEU* 3.5 37.9 - - + +
286C ILE 3.5 30.1 - - - -
287C LEU* 4.0 7.2 - - + -
292C ARG* 3.8 11.3 - - - +
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Residues in contact with SER 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ARG 5.8 2.8 - - - -
176C LEU* 4.0 31.0 + - - -
215C TYR* 2.8 30.6 + - - +
216C ALA* 4.8 0.2 - - - -
226C TYR* 4.7 5.4 + - - -
231C VAL* 3.2 11.2 + - - +
232C ASP* 3.1 12.6 + - - -
234C TRP* 1.3 78.5 - - - +
236C LEU* 1.3 57.1 + - - +
238C VAL* 3.1 7.7 + - - +
239C ILE* 2.9 30.3 + - - +
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Residues in contact with LEU 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C PHE* 3.5 13.8 - - + -
159C ILE* 3.3 32.5 - - + -
160C VAL* 5.0 6.5 - - + +
163C VAL* 3.9 31.2 - - + -
176C LEU* 4.1 5.8 - - + -
232C ASP 3.0 18.5 + - - +
233C VAL 3.0 7.3 + - - +
235C SER* 1.3 76.3 - - - +
237C GLY* 1.3 57.7 + - - +
239C ILE* 3.4 20.0 - - + +
240C LEU* 2.9 29.6 + - - +
284C PHE* 3.9 12.8 - - + -
295C LEU* 3.9 27.1 - - + -
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Residues in contact with GLY 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C VAL 3.2 6.9 + - - -
234C TRP 3.0 4.2 + - - -
236C LEU* 1.3 76.6 - - - +
238C VAL* 1.3 55.5 + - - +
240C LEU 3.4 0.9 + - - -
241C TYR* 3.0 25.3 + - - +
281C LEU* 3.3 14.1 - - - +
284C PHE* 3.3 32.4 - - - -
285C LEU* 3.6 13.6 - - - +
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Residues in contact with VAL 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C PRO 3.6 22.2 - - - +
215C TYR* 3.4 30.1 - - + -
234C TRP* 3.4 30.9 + - + +
235C SER 3.1 7.1 + - - +
237C GLY* 1.3 72.3 - - - +
239C ILE* 1.3 70.0 + - - +
241C TYR* 3.2 2.1 + - - +
242C THR* 3.1 27.6 + - + +
248C LEU* 4.6 2.2 - - + -
249C PRO* 3.7 26.0 - - + -
250C PHE* 4.3 10.8 - - + -
285C LEU* 3.7 7.2 - - + +
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Residues in contact with ILE 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C PHE* 3.9 17.7 - - + -
159C ILE* 4.3 3.6 - - + -
176C LEU* 3.9 26.2 - - + -
177C LYS* 4.3 6.7 - - - +
178C ALA* 4.7 1.8 - - + +
181C LEU* 4.0 33.2 - - + -
215C TYR* 3.9 20.4 - - + -
235C SER 2.9 16.6 + - - +
236C LEU* 3.4 29.6 - - + +
238C VAL* 1.3 78.4 - - - +
240C LEU* 1.3 63.5 + - - +
242C THR* 3.1 8.2 + - - +
243C LEU* 3.1 31.4 + - + +
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Residues in contact with LEU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C PHE* 3.5 38.1 - - + -
236C LEU 2.9 13.8 + - - +
237C GLY* 3.5 7.4 - - - +
239C ILE* 1.3 75.9 - - - +
241C TYR* 1.3 64.2 + - - +
243C LEU* 2.8 21.7 + - + +
244C VAL* 3.2 19.7 + - + +
277C CYS* 4.6 10.1 - - - -
280C LEU* 3.6 28.9 - - + -
281C LEU* 3.2 28.5 - - + -
284C PHE* 4.4 3.1 - - + -
303C TRP* 3.9 21.5 - - + -
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Residues in contact with TYR 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C GLY 3.0 14.8 + - - +
238C VAL 3.2 5.8 + - - +
240C LEU* 1.3 79.8 - - - +
242C THR* 1.3 56.6 + - - +
244C VAL* 3.7 4.2 + - - +
245C SER* 2.9 53.8 + - - -
247C SER* 3.2 17.5 + - - -
248C LEU 3.7 5.5 + - - -
249C PRO* 3.5 34.9 - - + +
267C TYR* 3.7 21.1 - + + -
268C ARG* 2.6 43.0 + - - +
269C ILE* 5.2 0.2 - - - -
270C PRO* 4.2 5.2 - - + +
273C MET* 4.2 12.8 - - + -
281C LEU* 3.6 26.7 - - + +
285C LEU* 5.3 1.3 - - + -
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Residues in contact with THR 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B LEU* 4.1 12.6 - - + -
141C LEU* 3.6 21.8 - - - +
178C ALA* 4.8 3.3 - - - +
215C TYR* 4.4 10.8 + - - +
238C VAL* 3.1 22.6 + - + +
239C ILE* 3.1 8.8 + - - -
241C TYR* 1.3 73.8 - - - +
243C LEU* 1.3 65.6 + - - +
246C GLY* 2.8 27.5 + - - -
247C SER 3.4 20.6 - - - +
248C LEU* 3.8 26.9 - - + -
249C PRO* 4.4 0.4 - - + -
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Residues in contact with LEU 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C VAL* 4.0 28.3 - - + -
141C LEU* 4.2 8.1 - - + +
146C ARG* 3.9 0.5 - - - -
147C MET* 2.9 56.0 + - + +
152C ALA* 4.2 28.9 - - + +
155C LYS* 4.8 4.5 - - + -
156C PHE* 4.0 28.7 - - + +
159C ILE* 4.3 11.9 - - + -
181C LEU* 5.9 0.2 - - + -
239C ILE* 3.1 21.1 + - + +
240C LEU* 2.8 10.1 + - + +
242C THR* 1.3 85.3 + - - +
244C VAL* 1.3 58.2 + - + +
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Residues in contact with VAL 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C ARG* 3.5 26.3 + - - +
147C MET 4.0 9.4 - - - +
149C GLU* 4.9 13.5 - - + +
152C ALA* 3.7 25.4 - - + -
240C LEU* 3.2 21.6 + - + +
241C TYR* 4.3 4.0 - - - +
243C LEU* 1.3 77.9 - - - +
245C SER* 1.3 60.1 + - - +
246C GLY 3.6 0.2 - - - -
272C TYR* 3.9 6.3 - - + -
273C MET* 3.6 34.5 - - + -
277C CYS* 3.8 22.0 - - - -
303C TRP* 4.6 4.9 - - + -
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Residues in contact with SER 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C ARG* 3.8 7.4 - - - +
241C TYR* 2.9 38.5 + - - -
244C VAL* 1.3 81.9 - - - +
246C GLY* 1.3 62.9 + - - +
247C SER* 3.0 28.4 + - - -
270C PRO* 4.3 15.0 - - - -
272C TYR* 3.4 19.8 + - - -
273C MET* 4.8 1.1 - - - -
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Residues in contact with GLY 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B ASN 4.4 3.5 - - - +
205B LYS* 5.0 1.7 - - - -
206B LEU* 4.1 16.7 - - - +
141C LEU* 4.7 8.0 - - - +
145C GLY* 4.9 1.3 - - - -
146C ARG* 3.6 23.2 - - - +
242C THR 2.8 18.3 + - - -
244C VAL 3.6 1.4 - - - -
245C SER* 1.3 77.3 - - - +
247C SER* 1.3 59.7 + - - +
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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
------------------------------------------------------------
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