Contacts of the helix formed by residues 235 - 256 (chain B) in PDB entry 3ZXR
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 LEU 235 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ALA* 3.7 29.6 - - + +
115B ALA* 4.2 6.1 - - + -
116B GLU* 3.3 13.3 + - + +
128B ALA* 3.0 11.8 + - + +
130B PHE* 3.7 35.2 - - + -
234B SER* 1.3 73.4 - - - +
236B LEU* 1.3 66.7 + - - +
238B ALA* 3.1 3.9 + - - +
239B ALA* 3.0 21.0 + - + +
377B TYR 4.5 1.1 - - - +
380B PHE* 3.8 29.9 - - + +
381B SER* 3.8 13.2 - - - +
384B LEU* 3.7 27.8 - - + -
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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
----------------------------------------------------------
74B ASP* 4.7 4.5 - - - +
94B PHE* 4.4 19.3 - - + -
109B ARG* 4.1 17.7 - - - +
112B ALA* 3.7 24.5 - - + -
113B ARG* 4.6 14.8 - - + -
116B GLU* 3.1 26.2 + - - +
235B LEU* 1.3 82.8 - - - +
237B HIS* 1.3 75.3 + - + +
239B ALA* 3.1 3.7 + - - +
240B ASP* 3.0 33.2 + - - +
377B TYR* 4.0 14.4 - - + -
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Residues in contact with HIS 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ASP* 6.1 0.2 - - - -
76B GLU* 3.3 39.8 + - + +
77B THR* 6.3 0.4 - - - +
233B ASN* 3.5 27.4 - - - +
234B SER* 3.1 26.0 + - - +
236B LEU* 1.3 88.3 - - + +
238B ALA* 1.3 52.2 + - - +
240B ASP* 3.4 10.0 + - - +
241B ASP* 2.8 42.0 + - - +
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Residues in contact with ALA 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B PHE* 3.9 19.5 - - + +
132B ALA* 6.2 0.4 - - + +
230B TYR* 4.3 5.1 + - + -
233B ASN* 3.8 17.9 - - + +
234B SER 2.8 12.0 + - - +
235B LEU 3.1 9.4 + - - +
237B HIS* 1.3 78.4 - - - +
239B ALA* 1.3 56.3 + - - +
241B ASP* 3.3 11.0 + - - +
242B MET* 2.9 28.2 + - - +
380B PHE* 3.7 16.8 - - + -
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Residues in contact with ALA 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B LEU* 3.0 13.5 + - + +
236B LEU* 3.1 7.4 + - - +
238B ALA* 1.3 73.1 - - - +
240B ASP* 1.3 64.8 + - - +
242B MET* 3.3 3.5 + - - +
243B GLN* 3.2 27.0 + - - +
376B PRO* 3.9 4.7 - - - +
377B TYR* 3.4 47.6 - - + +
380B PHE* 3.6 16.1 - - + -
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Residues in contact with ASP 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ASP* 4.5 0.2 - - - +
77B THR* 3.6 12.3 - - + +
92B ASN* 3.1 16.5 + - - +
109B ARG* 2.8 37.0 + - - -
236B LEU* 3.0 21.0 + - - +
237B HIS* 3.6 13.0 + - - +
239B ALA* 1.3 73.9 - - - +
241B ASP* 1.3 67.4 + - - +
243B GLN* 3.3 4.0 + - - +
244B LEU* 3.0 24.2 + - - +
377B TYR* 2.4 31.3 + - - -
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Residues in contact with ASP 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ARG* 4.8 11.4 + - - -
211B PHE* 3.5 22.9 - - + -
230B TYR* 3.7 24.9 - - + -
231B GLN 4.6 2.9 - - - +
233B ASN* 4.1 22.0 + - - +
237B HIS* 2.8 28.3 + - - +
238B ALA* 3.4 7.8 - - - +
240B ASP* 1.3 74.6 - - - +
242B MET* 1.3 51.8 + - - +
244B LEU* 3.2 3.7 + - - +
245B TYR* 2.8 35.9 + - - +
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Residues in contact with MET 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ALA* 3.3 35.0 - - + -
134B ALA* 3.6 34.1 - - + +
230B TYR* 3.2 17.5 + - + +
238B ALA 2.9 13.9 + - - +
239B ALA* 3.6 8.7 - - - +
240B ASP 3.3 0.4 - - - -
241B ASP* 1.3 75.1 - - - +
243B GLN* 1.3 57.6 + - - +
245B TYR* 3.3 11.1 + - + +
246B LYS* 3.0 42.8 + - + +
275B MET* 4.0 17.9 - - + +
372B SER* 5.2 0.2 - - - -
376B PRO* 4.1 24.5 - - + -
380B PHE* 4.7 2.7 - - + -
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Residues in contact with GLN 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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26B CYS* 3.6 12.5 - - - -
30B GLY 2.9 27.9 + - - +
32B MET* 3.5 41.4 - - + +
92B ASN* 5.6 0.9 - - - +
239B ALA 3.2 13.8 + - - +
240B ASP 3.7 6.3 - - - +
242B MET* 1.3 78.6 - - - +
244B LEU* 1.3 63.3 + - - +
246B LYS* 3.4 21.4 + - - +
247B TYR* 3.2 21.3 + - - +
376B PRO* 3.5 24.0 - - + +
377B TYR* 3.5 21.9 - - + +
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Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ARG* 4.9 6.3 - - - +
77B THR 5.8 0.4 - - - +
79B ARG* 3.8 35.2 - - + +
82B PRO* 6.1 2.0 - - + -
90B ASN* 5.0 9.0 - - + +
92B ASN* 6.4 0.2 - - - +
209B SER* 4.6 6.1 - - - -
211B PHE* 3.6 26.0 - - + -
240B ASP 3.0 16.9 + - - +
241B ASP* 3.8 5.6 - - - +
243B GLN* 1.3 71.9 - - - +
245B TYR* 1.3 61.0 + - - +
247B TYR* 3.2 24.9 + - + +
248B ILE* 2.9 39.3 + - + +
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Residues in contact with TYR 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ALA* 2.9 40.9 + - + -
136B PHE* 3.4 14.7 - - - -
206B LEU* 3.8 19.3 - - + -
211B PHE* 3.6 10.2 - - + -
228B ILE* 3.3 38.3 + - + -
230B TYR* 3.5 27.8 - + + -
241B ASP 2.8 20.9 + - - +
242B MET* 3.4 19.1 - - - +
244B LEU* 1.3 73.1 - - - +
246B LYS* 1.3 60.4 + - + +
248B ILE* 3.2 2.3 + - - +
249B ILE* 2.8 53.4 + - + +
262B PHE* 3.9 11.7 - + - -
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Residues in contact with LYS 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLY 5.3 2.8 + - - -
31B ILE* 5.9 4.9 - - - +
242B MET* 3.0 33.0 + - + +
243B GLN* 3.8 22.1 + - - +
244B LEU 3.3 0.2 - - - -
245B TYR* 1.3 78.4 - - + +
247B TYR* 1.3 57.5 + - - +
249B ILE* 3.8 0.5 - - - +
250B LYS* 2.9 52.2 + - - +
262B PHE* 3.9 51.7 - - + +
372B SER* 2.8 31.6 + - - +
374B GLY 4.5 9.7 + - - -
376B PRO* 5.8 1.6 - - + +
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Residues in contact with TYR 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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24B ARG* 3.0 42.2 + - - +
32B MET* 6.4 1.1 - - + -
81B ASP* 2.5 33.5 + - - -
82B PRO* 4.8 3.1 - - + -
83B PHE* 3.8 21.4 - + - +
84B ARG* 4.9 5.7 - - - +
90B ASN* 4.2 4.0 - - - -
243B GLN 3.2 10.5 + - - +
244B LEU* 3.2 22.1 + - + +
246B LYS* 1.3 79.0 - - - +
248B ILE* 1.3 59.9 + - + +
250B LYS* 4.7 4.0 - - - -
251B ASN* 2.8 62.9 + - - +
189C VAL* 4.0 16.2 - - + -
190C ALA* 3.5 23.4 - - + +
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Residues in contact with ILE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PRO* 4.4 6.1 - - + -
83B PHE* 3.8 16.4 - - + -
202B MET 4.3 2.5 - - - +
205B ASN* 3.8 29.4 - - + +
206B LEU* 3.8 22.2 - - + -
209B SER* 3.4 33.2 - - - +
211B PHE* 3.9 19.5 - - + -
244B LEU* 2.9 30.3 + - + +
245B TYR 3.7 3.6 - - - +
247B TYR* 1.3 76.2 - - + +
249B ILE* 1.3 66.4 + - + +
252B THR* 2.8 32.9 + - - +
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Residues in contact with ILE 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PHE* 3.5 37.7 - - + -
202B MET* 3.8 34.9 - - + +
206B LEU* 4.1 13.7 - - + -
228B ILE* 4.1 6.7 - - + -
245B TYR* 2.8 60.0 + - + +
246B LYS 3.8 2.9 - - - +
248B ILE* 1.3 73.7 - - + +
250B LYS* 1.3 64.8 + - - +
252B THR* 3.9 0.2 - - - -
253B ALA* 3.0 22.3 + - - +
260B VAL* 4.0 9.0 - - + -
262B PHE* 4.0 11.2 - - + -
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Residues in contact with LYS 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ILE* 5.1 12.9 - - - +
246B LYS* 2.9 36.9 + - + +
247B TYR* 4.0 4.5 - - - +
249B ILE* 1.3 78.4 - - - +
251B ASN* 1.3 58.5 + - - +
253B ALA* 3.6 3.6 + - - +
254B TRP* 3.1 26.3 + - - +
259B THR* 5.8 0.2 - - - -
260B VAL* 4.2 14.9 + - + +
262B PHE* 3.7 33.6 - - + +
178C TYR* 3.2 39.3 + - + +
190C ALA 5.4 0.7 - - - +
191C PRO* 3.8 22.4 - - + +
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Residues in contact with ASN 251 (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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83B PHE* 3.5 26.0 - - + -
247B TYR* 2.8 44.8 + - - +
250B LYS* 1.3 73.7 - - - +
252B THR* 1.3 67.2 + - - +
253B ALA 3.2 0.9 - - - -
254B TRP* 3.7 7.2 - - - +
255B GLN* 3.0 29.9 + - + +
190C ALA* 3.1 31.4 + - - +
191C PRO* 3.4 27.1 - - - +
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Residues in contact with THR 252 (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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83B PHE* 3.5 9.3 - - - -
198B LEU* 4.1 3.4 - - + -
201B LYS* 4.0 7.4 - - + -
202B MET* 3.7 35.9 - - + +
205B ASN* 2.7 34.8 + - - +
248B ILE* 2.8 27.5 + - - +
249B ILE 3.9 0.2 - - - -
251B ASN* 1.3 77.2 - - - +
253B ALA* 1.3 61.2 + - - +
255B GLN* 3.4 1.7 + - - +
256B ASN* 2.7 42.3 + - - +
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Residues in contact with ALA 253 (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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138B ILE* 5.1 0.4 - - + -
198B LEU* 4.4 5.2 - - - -
202B MET* 4.0 11.8 - - + +
249B ILE 3.0 11.3 + - - +
250B LYS 3.6 4.0 - - - +
252B THR* 1.3 76.9 - - - +
254B TRP* 1.3 61.3 + - - +
256B ASN* 3.1 9.9 + - - +
257B GLY 3.3 0.2 + - - -
258B LYS* 2.9 42.7 + - + +
260B VAL* 3.4 35.0 - - + +
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Residues in contact with TRP 254 (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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250B LYS 3.1 18.4 + - - +
251B ASN* 3.7 11.9 - - - +
252B THR 3.3 0.2 - - - -
253B ALA* 1.3 75.8 - - - +
255B GLN* 1.3 68.7 + - + +
257B GLY 3.2 3.1 + - - -
258B LYS 3.5 16.6 - - - -
259B THR* 4.5 4.9 - - - +
158C ILE* 6.1 2.7 - - + -
176C ARG* 2.6 84.7 + - + +
177C GLY 3.7 14.6 - - - -
178C TYR* 3.9 18.8 - + + -
191C PRO* 3.8 28.2 - - + +
194C GLN* 4.0 26.0 - - + +
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Residues in contact with GLN 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PRO 5.1 1.2 - - - +
83B PHE* 3.5 54.7 + - + +
205B ASN* 5.8 0.5 + - - -
251B ASN* 3.0 19.1 + - + +
252B THR* 3.9 4.8 - - - +
253B ALA 3.3 0.2 - - - -
254B TRP* 1.3 82.0 - - + +
256B ASN* 1.3 65.0 + - - +
257B GLY 3.4 1.0 + - - -
197C ASP* 5.4 4.2 + - - -
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Residues in contact with ASN 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 3.8 27.2 - - + +
201B LYS* 3.2 33.7 + - - +
252B THR* 2.7 34.8 + - - +
253B ALA 3.1 3.9 + - - +
255B GLN* 1.3 85.5 - - - +
257B GLY* 1.3 59.9 + - - +
258B LYS* 3.3 14.1 + - - +
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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