Contacts of the helix formed by residues 229 - 246 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C SER* 4.2 10.3 - - - +
95C GLN* 4.5 1.8 - - - +
167D HIS* 3.5 41.2 - - + +
170D PHE* 5.6 11.9 - - + -
172D VAL* 4.1 16.3 - - + -
228D GLY* 1.3 80.6 - - - +
230D GLU* 1.3 74.5 + - - +
231D VAL 3.0 2.7 - - - -
232D ASP* 2.8 18.5 + - - +
233D VAL* 3.1 14.2 + - + +
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Residues in contact with GLU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C SER* 4.2 8.5 + - - -
219D GLU* 4.1 6.1 - - - +
225D LYS 5.7 1.4 - - - +
227D ASP 5.5 0.2 + - - -
228D GLY* 3.4 22.5 + - - +
229D PRO* 1.3 89.9 - - - +
231D VAL* 1.3 65.1 + - + +
233D VAL* 3.2 12.0 + - - +
234D TRP 3.1 18.9 + - - -
289D PRO* 3.6 33.4 - - + +
290D SER* 6.2 0.4 - - - -
292D ARG* 3.2 31.5 + - + +
293D GLY 5.5 1.1 - - - +
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Residues in contact with VAL 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D VAL* 5.4 0.7 - - + -
174D ARG* 4.3 12.6 - - + -
217D ALA* 4.2 7.7 - - + +
219D GLU* 3.6 18.8 - - - +
226D TYR* 3.0 68.9 - - + +
227D ASP 4.6 0.9 - - - +
228D GLY 3.1 15.0 + - - +
229D PRO 2.9 1.2 + - - -
230D GLU* 1.3 83.9 - - + +
232D ASP* 1.3 72.7 + - - +
234D TRP* 3.3 4.5 + - - +
235D SER* 3.2 22.0 + - - +
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Residues in contact with ASP 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D VAL* 4.1 5.7 - - + +
167D HIS* 2.9 28.1 + - + +
172D VAL* 3.4 7.7 - - - +
173D HIS* 2.8 23.3 + - - +
174D ARG* 2.8 26.7 + - - -
175D ASP 4.2 0.5 + - - -
176D LEU* 3.2 27.0 + - + +
194D PHE* 5.1 0.2 - - - -
229D PRO 2.8 12.1 + - - +
231D VAL* 1.3 77.8 - - - +
233D VAL* 1.3 53.4 + - - +
235D SER* 3.0 7.5 + - - -
236D LEU* 2.7 39.8 + - - +
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Residues in contact with VAL 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D HIS* 4.6 4.3 - - + -
229D PRO* 3.1 14.5 + - + +
230D GLU* 3.2 14.6 + - - +
232D ASP* 1.3 75.8 - - - +
234D TRP* 1.3 61.8 + - - +
236D LEU* 3.2 5.4 + - - -
237D GLY 3.0 6.2 + - - -
283D LYS 4.5 0.2 - - - +
284D PHE* 2.9 53.7 - - + +
292D ARG* 4.3 12.1 - - + -
293D GLY 3.8 24.9 - - - +
294D THR* 5.1 0.4 - - - -
295D LEU* 4.0 24.5 - - + +
298D ILE* 4.2 6.1 - - + -
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Residues in contact with TRP 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D PRO 5.1 0.6 + - - -
215D TYR 3.4 15.1 + - - -
216D ALA 3.3 12.7 + - - -
217D ALA* 3.3 24.5 - - + -
218D PRO* 3.6 34.5 - - + -
230D GLU 3.1 10.4 + - - +
231D VAL 3.3 8.0 + - - +
233D VAL* 1.3 76.2 - - - +
235D SER* 1.3 58.1 + - - +
237D GLY* 2.9 17.5 + - - -
238D VAL* 3.1 21.9 + - + +
250D PHE* 3.4 36.0 - + - -
262D VAL* 4.1 16.3 - - + +
265D GLY* 4.8 3.1 - - - -
284D PHE 4.1 9.6 - - - -
285D LEU* 3.5 43.9 - - + +
286D ILE 3.8 10.8 - - - -
287D LEU* 4.2 7.0 - - + -
292D ARG* 3.7 15.2 - - - +
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Residues in contact with SER 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D ARG 5.8 0.5 - - - -
175D ASP* 5.7 1.6 + - - -
176D LEU* 4.0 32.1 + - - -
215D TYR* 2.9 27.6 + - - -
226D TYR* 4.4 6.1 + - - -
231D VAL* 3.2 14.3 + - - +
232D ASP* 3.0 12.1 + - - -
234D TRP* 1.3 76.9 - - - +
236D LEU* 1.3 59.1 + - - +
238D VAL* 3.2 6.6 + - - +
239D ILE* 2.8 33.2 + - - +
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Residues in contact with LEU 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D PHE* 3.7 13.8 - - + -
159D ILE* 3.6 31.9 - - + -
160D VAL* 4.6 6.3 - - + -
163D VAL* 4.3 17.5 - - + -
176D LEU* 5.0 4.9 - - + -
232D ASP 2.7 21.6 + - - +
233D VAL* 3.3 12.1 - - - +
235D SER* 1.3 73.0 - - - +
237D GLY* 1.3 55.4 + - - +
239D ILE* 3.2 14.2 + - + +
240D LEU* 2.9 31.4 + - - +
284D PHE* 3.5 14.8 - - + -
295D LEU* 3.5 42.0 - - + -
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Residues in contact with GLY 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D VAL 3.0 7.1 + - - -
234D TRP 2.9 9.9 + - - -
236D LEU* 1.3 76.5 - - - +
238D VAL* 1.3 61.8 + - - +
240D LEU* 4.7 0.2 - - - -
241D TYR* 3.2 18.4 + - - +
281D LEU* 3.3 14.0 - - - +
284D PHE* 3.4 28.4 - - - -
285D LEU* 3.7 12.7 - - - +
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Residues in contact with VAL 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D PRO 3.6 22.4 - - - +
215D TYR* 3.4 31.6 - - + -
234D TRP* 3.1 32.4 + - - +
235D SER 3.5 5.6 - - - +
237D GLY* 1.3 74.1 - - - +
239D ILE* 1.3 56.0 + - - +
241D TYR* 3.2 3.6 + - - +
242D THR* 2.6 36.0 + - + +
248D LEU* 4.6 2.9 - - + -
249D PRO* 3.7 26.2 - - + -
250D PHE* 4.3 9.0 - - + -
285D LEU* 3.8 7.1 - - + +
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Residues in contact with ILE 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D PHE* 4.4 10.5 - - + -
159D ILE* 4.5 4.5 - - + -
176D LEU* 3.7 30.3 - - + +
177D LYS 4.2 8.7 - - - +
178D ALA* 4.7 2.0 - - + +
181D LEU* 3.7 33.4 - - + -
215D TYR* 3.6 22.0 - - + -
235D SER 2.8 23.9 + - - +
236D LEU* 3.2 18.1 + - + +
238D VAL* 1.3 72.2 - - - +
240D LEU* 1.3 65.9 + - - +
242D THR* 3.1 6.3 + - - +
243D LEU* 2.9 35.2 + - + +
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Residues in contact with LEU 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D ALA* 5.5 0.2 - - + -
156D PHE* 3.6 28.2 - - + -
236D LEU 2.9 15.8 + - - +
237D GLY* 3.7 3.8 - - - +
238D VAL 3.3 0.2 - - - -
239D ILE* 1.3 77.3 - - - +
241D TYR* 1.3 64.2 + - - +
243D LEU* 3.1 11.9 + - + +
244D VAL* 3.0 37.5 + - + +
277D CYS* 4.4 5.8 - - - -
280D LEU* 3.5 31.2 - - + -
281D LEU* 3.6 26.9 - - + +
284D PHE* 4.4 6.1 - - + -
303D TRP* 3.9 28.0 - - + -
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Residues in contact with TYR 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D GLY 3.2 9.9 + - - +
238D VAL 3.2 8.4 + - - +
240D LEU* 1.3 81.6 - - - +
242D THR* 1.3 56.4 + - - +
244D VAL* 3.4 4.1 + - - +
245D SER* 2.8 51.2 + - - -
247D SER* 3.4 17.9 + - - -
248D LEU 3.7 5.5 + - - -
249D PRO* 3.3 41.3 - - + +
267D TYR* 4.1 16.8 - + + -
268D ARG* 2.7 40.7 + - - +
269D ILE* 5.0 0.9 - - - -
270D PRO* 4.3 6.3 - - + +
273D MET* 4.2 13.9 - - + -
281D LEU* 3.7 30.3 - - + -
285D LEU* 5.2 0.4 - - + -
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Residues in contact with THR 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D LEU* 3.6 21.2 - - - +
178D ALA* 4.7 2.8 - - - +
215D TYR* 4.0 13.7 + - - +
238D VAL* 2.6 44.1 + - + +
239D ILE* 3.6 7.1 + - - +
241D TYR* 1.3 73.1 - - - +
243D LEU* 1.3 64.1 + - - +
246D GLY* 2.9 28.3 + - - -
247D SER 3.3 25.1 - - - +
248D LEU* 4.1 13.7 - - + -
249D PRO* 4.2 3.1 - - + -
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Residues in contact with LEU 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D VAL* 3.8 30.5 - - + -
141D LEU* 4.1 7.6 - - + +
146D ARG* 3.9 1.9 - - - -
147D MET* 3.0 47.2 + - + +
152D ALA* 4.1 33.7 - - + +
155D LYS* 4.8 5.2 - - + -
156D PHE* 4.1 28.9 - - + +
159D ILE* 4.6 6.7 - - + -
178D ALA* 6.4 0.2 - - + -
181D LEU* 5.4 2.0 - - + -
239D ILE* 2.9 27.0 + - + +
240D LEU* 3.3 9.0 - - + +
242D THR* 1.3 82.0 + - - +
244D VAL* 1.3 60.2 + - - +
245D SER 3.6 0.2 + - - -
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Residues in contact with VAL 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ARG* 3.2 29.5 + - - +
147D MET 3.7 9.4 - - - +
149D GLU* 4.5 15.9 - - + +
152D ALA* 4.4 9.0 - - + -
240D LEU* 3.0 38.0 + - + +
241D TYR* 4.5 2.0 - - - +
243D LEU* 1.3 79.1 - - + +
245D SER* 1.3 58.4 + - - +
246D GLY 3.7 0.2 - - - -
272D TYR* 3.5 4.5 - - + -
273D MET* 3.6 34.1 - - + -
277D CYS* 4.0 15.3 - - - -
303D TRP* 4.9 2.7 - - + -
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Residues in contact with SER 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D ARG* 3.7 8.3 + - - +
241D TYR* 2.8 42.0 + - - -
244D VAL* 1.3 80.6 - - - +
246D GLY* 1.3 63.5 + - - +
247D SER* 3.2 16.3 + - - -
270D PRO* 4.2 17.5 - - - -
272D TYR* 3.4 25.5 + - - -
273D MET* 4.9 1.1 - - - -
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Residues in contact with GLY 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D LEU* 4.8 11.7 - - - +
145D GLY* 4.8 1.6 - - - -
146D ARG* 3.6 21.8 - - - +
242D THR* 2.9 19.0 + - - -
245D SER* 1.3 78.8 - - - +
247D SER* 1.3 59.6 + - - +
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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
------------------------------------------------------------
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