Contacts of the helix formed by residues 235 - 256 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F ALA* 3.7 29.2 - - + +
115F ALA* 4.2 6.1 - - + -
116F GLU* 3.2 14.1 + - + +
128F ALA* 3.0 11.8 + - + +
130F PHE* 3.7 36.1 - - + -
234F SER* 1.3 73.0 - - - +
236F LEU* 1.3 66.3 + - - +
238F ALA* 3.1 4.0 + - - +
239F ALA* 2.9 21.3 + - + +
377F TYR 4.7 0.9 - - - +
380F PHE* 3.8 28.3 - - + +
381F SER* 3.9 15.7 - - - +
384F LEU* 3.7 27.4 - - + -
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Residues in contact with LEU 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F ASP* 4.7 4.0 - - - +
94F PHE* 4.4 19.5 - - + -
109F ARG* 4.1 17.9 - - - +
112F ALA* 3.7 23.8 - - + -
113F ARG* 4.6 14.1 - - + -
116F GLU* 3.1 25.3 + - + +
235F LEU* 1.3 82.8 - - - +
237F HIS* 1.3 75.0 + - + +
239F ALA* 3.1 3.4 + - - +
240F ASP* 2.9 35.6 + - - +
377F TYR* 4.0 13.7 - - + -
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Residues in contact with HIS 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F ASP* 6.1 0.2 - - - -
76F GLU* 3.3 40.4 + - + +
77F THR* 6.2 0.6 - - - +
233F ASN* 3.6 28.3 - - - +
234F SER* 3.1 25.0 + - - +
236F LEU* 1.3 88.7 - - + +
238F ALA* 1.3 52.3 + - - +
240F ASP* 3.3 11.0 + - - +
241F ASP* 2.8 42.4 + - - +
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Residues in contact with ALA 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F PHE* 3.8 18.6 - - + +
230F TYR* 4.3 4.4 + - + -
233F ASN* 3.7 17.6 - - + +
234F SER 2.8 12.6 + - - +
235F LEU 3.3 8.7 - - - +
237F HIS* 1.3 73.3 - - - +
239F ALA* 1.3 60.4 + - - +
241F ASP* 3.3 11.5 + - - +
242F MET* 2.9 27.9 + - - +
380F PHE* 3.7 17.2 - - + -
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Residues in contact with ALA 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235F LEU* 2.9 14.6 + - + +
236F LEU* 3.1 6.5 + - - +
238F ALA* 1.3 72.7 - - - +
240F ASP* 1.3 65.6 + - - +
242F MET* 3.2 3.5 + - - +
243F GLN* 3.1 26.9 + - - +
376F PRO* 4.1 3.6 - - - +
377F TYR* 3.3 49.8 - - + +
380F PHE* 3.6 15.4 - - + -
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Residues in contact with ASP 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F ASP* 4.5 0.3 - - - +
77F THR* 3.6 13.1 - - + +
92F ASN* 3.0 16.9 + - - +
109F ARG* 2.8 37.9 + - - -
236F LEU* 2.9 22.2 + - - +
237F HIS* 3.5 13.4 + - - +
239F ALA* 1.3 75.9 - - - +
241F ASP* 1.3 63.0 + - - +
243F GLN* 3.4 4.0 + - - +
244F LEU* 3.1 24.0 + - - +
377F TYR* 2.4 30.4 + - - -
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Residues in contact with ASP 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F ARG* 4.8 11.1 + - - -
211F PHE* 3.5 22.6 - - + -
230F TYR* 3.7 26.4 - - + -
231F GLN 4.6 2.8 - - - +
233F ASN* 4.1 19.7 + - - +
237F HIS* 2.8 30.9 + - - +
238F ALA* 3.4 7.5 - - - +
240F ASP* 1.3 73.8 - - - +
242F MET* 1.3 56.7 + - - +
244F LEU* 3.3 2.5 + - - +
245F TYR* 2.8 31.5 + - - +
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Residues in contact with MET 242 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F ALA* 3.3 34.3 - - + -
134F ALA* 3.5 33.2 - - + +
230F TYR* 3.2 16.8 + - + +
238F ALA 2.9 14.3 + - - +
239F ALA 3.5 8.5 - - - +
241F ASP* 1.3 75.7 - - - +
243F GLN* 1.3 62.6 + - - +
245F TYR* 3.3 10.4 + - - +
246F LYS* 3.0 37.3 + - + +
275F MET* 3.9 18.6 - - - +
372F SER* 5.2 0.2 - - - -
376F PRO* 4.1 25.1 - - + -
380F PHE* 4.7 3.8 - - + -
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Residues in contact with GLN 243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F CYS* 3.5 12.7 - - - -
30F GLY 3.0 27.1 + - - +
32F MET* 3.4 42.0 - - + +
92F ASN* 5.6 0.9 - - - +
239F ALA 3.1 9.9 + - - +
240F ASP 3.4 7.2 + - - +
242F MET* 1.3 74.3 - - - +
244F LEU* 1.3 63.3 + - - +
246F LYS* 3.4 20.8 + - - +
247F TYR* 3.2 20.1 + - - +
376F PRO* 3.5 22.8 - - + +
377F TYR* 3.5 27.0 - - + +
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Residues in contact with LEU 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F ARG* 4.9 5.6 - - - +
77F THR 5.8 0.2 - - - +
79F ARG* 3.8 35.9 - - + +
82F PRO* 6.0 1.6 - - + -
90F ASN* 5.0 9.2 - - + +
209F SER* 4.5 6.5 - - - -
211F PHE* 3.6 26.2 - - + -
240F ASP 3.1 16.3 + - - +
241F ASP* 3.8 5.6 - - - +
243F GLN* 1.3 73.1 - - - +
245F TYR* 1.3 60.7 + - - +
247F TYR* 3.2 27.4 + - + +
248F ILE* 2.9 36.5 + - + +
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Residues in contact with TYR 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F ALA* 2.9 39.9 + - + -
136F PHE* 3.4 14.9 - - - -
206F LEU* 3.9 18.8 - - + -
211F PHE* 3.7 10.4 - - + -
228F ILE* 3.2 40.2 + - + -
230F TYR* 3.5 27.6 - + + -
241F ASP 2.8 18.0 + - - +
242F MET* 3.4 18.6 - - - +
244F LEU* 1.3 76.7 - - - +
246F LYS* 1.3 60.6 + - + +
248F ILE* 3.3 1.0 + - - +
249F ILE* 2.9 53.0 + - + +
262F PHE* 3.8 12.6 - + - -
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Residues in contact with LYS 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F GLY 5.2 3.6 + - - -
31F ILE* 5.9 4.2 - - - +
242F MET* 3.0 30.3 + - + +
243F GLN* 3.8 23.8 + - - +
244F LEU 3.2 0.2 - - - -
245F TYR* 1.3 78.0 - - + +
247F TYR* 1.3 54.7 + - - +
249F ILE* 3.2 1.2 + - - +
250F LYS* 2.8 58.2 + - + +
262F PHE* 3.9 47.5 - - + +
372F SER* 2.8 32.7 + - - +
374F GLY 4.5 10.1 + - - -
376F PRO* 5.7 1.4 - - + +
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Residues in contact with TYR 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A VAL* 4.0 15.9 - - + -
190A ALA* 3.5 23.3 - - + +
24F ARG* 3.0 41.0 + - - +
32F MET* 6.5 0.7 - - + -
81F ASP* 2.5 33.4 + - - -
82F PRO* 4.7 3.1 - - + -
83F PHE* 3.8 22.5 - + - +
84F ARG* 4.9 5.5 - - - +
90F ASN* 4.1 4.3 - - - -
243F GLN 3.2 10.9 + - - +
244F LEU* 3.2 21.0 + - + +
246F LYS* 1.3 78.3 - - - +
248F ILE* 1.3 63.7 + - + +
250F LYS* 4.7 4.2 - - - +
251F ASN* 2.8 59.6 + - - +
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Residues in contact with ILE 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F PRO* 4.3 5.4 - - + -
83F PHE* 3.5 16.6 - - + -
202F MET 4.4 2.5 - - - +
205F ASN* 3.8 28.9 - - + +
206F LEU* 3.9 31.6 - - + -
209F SER* 3.2 35.9 - - - +
211F PHE* 3.9 8.1 - - + -
244F LEU* 2.9 30.1 + - + +
245F TYR 3.9 3.4 - - - +
247F TYR* 1.3 73.7 - - + +
249F ILE* 1.3 61.0 + - + +
252F THR* 2.7 40.3 + - - +
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Residues in contact with ILE 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F PHE* 3.5 41.5 - - + -
202F MET* 3.7 34.4 - - + +
206F LEU* 4.2 9.6 - - + -
228F ILE* 4.1 11.2 - - + -
245F TYR* 2.9 56.4 + - + +
246F LYS 3.7 2.7 - - - +
248F ILE* 1.3 75.9 - - - +
250F LYS* 1.3 64.6 + - - +
253F ALA* 3.1 22.7 + - - +
260F VAL* 3.9 10.5 - - + -
262F PHE* 4.0 5.6 - - + -
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Residues in contact with LYS 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A TYR* 3.3 39.0 + - + +
190A ALA 5.5 0.4 - - - +
191A PRO* 3.9 23.4 - - + +
31F ILE* 5.0 13.9 - - - +
246F LYS* 2.8 40.3 + - + +
247F TYR* 4.0 4.0 - - - +
249F ILE* 1.3 74.8 - - - +
251F ASN* 1.3 58.1 + - - +
253F ALA* 3.5 3.8 + - - +
254F TRP* 2.9 26.9 + - - +
259F THR* 5.8 0.2 - - - -
260F VAL* 4.3 15.0 + - + +
262F PHE* 3.7 34.0 - - + +
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Residues in contact with ASN 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ALA* 3.0 34.1 + - - +
191A PRO* 3.3 26.3 - - - +
83F PHE* 3.6 26.7 - - + -
247F TYR* 2.8 45.7 + - - +
250F LYS* 1.3 73.9 - - - +
252F THR* 1.3 65.4 + - - +
254F TRP* 3.7 7.4 - - - +
255F GLN* 3.0 30.0 + - + +
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Residues in contact with THR 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F PHE* 3.4 9.8 - - - -
198F LEU* 4.1 3.6 - - + -
201F LYS* 4.0 8.1 - - + -
202F MET* 3.6 36.5 - - + +
205F ASN* 2.8 31.5 + - - +
248F ILE* 2.7 26.7 + - - +
249F ILE 3.9 0.2 - - - -
251F ASN* 1.3 76.8 - - - +
253F ALA* 1.3 61.7 + - - +
255F GLN* 3.4 1.5 + - - +
256F ASN* 2.7 41.9 + - - +
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Residues in contact with ALA 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198F LEU* 4.5 6.3 - - + -
202F MET* 4.0 10.4 - - + +
249F ILE 3.1 7.8 + - - +
250F LYS 3.5 6.5 - - - +
252F THR* 1.3 77.5 - - - +
254F TRP* 1.3 62.8 + - - +
256F ASN 3.0 9.5 + - - -
257F GLY 3.3 0.2 + - - -
258F LYS* 2.9 41.5 + - + +
260F VAL* 3.4 35.0 - - + +
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Residues in contact with TRP 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ILE* 6.1 2.7 - - + -
176A ARG* 2.6 86.1 + - + +
177A GLY 3.8 15.0 - - - -
178A TYR* 3.9 18.6 - + + -
191A PRO* 3.7 29.1 + - + +
194A GLN* 3.9 26.8 + - - +
250F LYS 2.9 16.5 + - - +
251F ASN* 3.7 11.9 - - - +
252F THR 3.3 0.6 - - - -
253F ALA* 1.3 74.9 - - - +
255F GLN* 1.3 66.6 + - + +
257F GLY 3.1 3.5 + - - -
258F LYS 3.5 13.2 - - - -
259F THR* 4.5 4.0 - - - -
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Residues in contact with GLN 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ASP* 5.5 3.8 + - - -
82F PRO 5.1 1.0 - - - +
83F PHE* 3.4 53.7 + - + +
205F ASN* 5.8 0.2 + - - -
251F ASN* 3.0 18.4 + - + +
252F THR* 3.9 5.3 - - - +
254F TRP* 1.3 80.0 - - + +
256F ASN* 1.3 67.5 + - - +
257F GLY 3.4 1.1 + - - -
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Residues in contact with ASN 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198F LEU* 3.8 26.4 - - + +
201F LYS* 3.1 33.3 + - - +
252F THR* 2.7 34.6 + - - +
253F ALA 3.0 3.9 + - - +
255F GLN* 1.3 87.0 - - - +
257F GLY* 1.3 60.5 + - - +
258F LYS* 3.3 12.9 + - - +
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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