Contacts of the helix formed by residues 235 - 256 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C ALA* 3.7 28.7 - - + +
115C ALA* 4.2 6.3 - - + -
116C GLU* 3.2 15.0 + - + +
128C ALA* 3.1 11.4 + - + +
130C PHE* 3.7 36.6 - - + -
234C SER* 1.3 72.4 - - - +
236C LEU* 1.3 65.9 - - - +
238C ALA* 3.2 3.3 + - - +
239C ALA* 3.0 21.8 + - + +
377C TYR 4.6 0.7 - - - +
380C PHE* 3.9 28.4 - - + +
381C SER* 3.9 13.9 - - - +
384C LEU* 3.7 28.0 - - + -
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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
----------------------------------------------------------
74C ASP* 4.6 4.0 - - - +
94C PHE* 4.4 19.5 - - + -
109C ARG* 4.1 17.9 - - - +
112C ALA* 3.7 25.1 - - + +
113C ARG* 4.6 14.1 - - + -
116C GLU* 3.1 25.7 + - - +
235C LEU* 1.3 84.2 - - - +
237C HIS* 1.3 70.8 + - + +
239C ALA* 3.1 2.9 + - - +
240C ASP* 2.9 40.4 + - - +
377C TYR* 4.1 13.2 - - + -
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Residues in contact with HIS 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ASP* 6.1 0.9 - - - -
76C GLU* 3.4 39.3 + - + +
77C THR* 6.2 0.8 - - - +
116C GLU* 4.8 0.6 + - - -
233C ASN* 3.6 28.5 - - - +
234C SER* 3.1 24.1 + - - +
236C LEU* 1.3 88.0 - - + +
238C ALA* 1.3 52.5 + - - +
240C ASP* 3.2 9.7 + - - +
241C ASP* 2.7 42.7 + - - +
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Residues in contact with ALA 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C PHE* 3.8 19.1 - - + +
230C TYR* 4.3 5.1 + - + -
233C ASN* 3.7 19.0 - - + +
234C SER 2.8 15.9 + - - +
235C LEU 3.5 4.9 - - - +
237C HIS* 1.3 77.6 - - - +
239C ALA* 1.3 56.6 + - - +
241C ASP* 3.3 11.3 + - - +
242C MET* 2.8 28.2 + - - +
380C PHE* 3.7 17.4 - - + -
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Residues in contact with ALA 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C LEU* 3.0 14.1 + - + +
236C LEU* 3.1 6.0 + - - +
238C ALA* 1.3 73.6 - - - +
240C ASP* 1.3 64.9 + - - +
242C MET* 3.3 3.5 + - - +
243C GLN* 3.2 26.7 + - - +
376C PRO* 4.1 4.0 - - - +
377C TYR* 3.4 43.7 - - + +
380C PHE* 3.7 19.2 - - + -
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Residues in contact with ASP 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ASP* 4.6 0.3 - - - +
77C THR* 3.7 13.7 - - + +
92C ASN* 3.0 21.8 + - - +
109C ARG* 2.9 31.0 + - - -
236C LEU* 2.9 22.5 + - - +
237C HIS* 3.5 12.8 + - - +
239C ALA* 1.3 74.1 - - - +
241C ASP* 1.3 67.0 + - - +
243C GLN* 3.2 3.6 + - - +
244C LEU* 3.1 23.4 + - - +
377C TYR* 2.5 30.2 + - - -
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Residues in contact with ASP 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ARG* 4.7 11.8 + - - -
211C PHE* 3.5 21.7 - - + -
230C TYR* 3.7 26.4 - - + -
231C GLN 4.6 3.6 - - - +
233C ASN* 4.2 17.3 + - - +
237C HIS* 2.7 26.4 + - - +
238C ALA* 3.3 12.1 + - - +
240C ASP* 1.3 74.9 - - - +
242C MET* 1.3 56.0 + - - +
244C LEU* 3.4 2.5 + - - +
245C TYR* 2.8 32.1 + - - +
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Residues in contact with MET 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ALA* 3.4 32.5 - - + -
134C ALA* 3.6 34.5 - - + +
230C TYR* 3.2 17.0 + - + +
238C ALA 2.8 17.4 + - - +
239C ALA 3.6 8.1 - - - +
240C ASP 3.2 0.4 - - - -
241C ASP* 1.3 73.8 - - - +
243C GLN* 1.3 56.9 + - - +
245C TYR* 3.2 11.5 + - - +
246C LYS* 3.0 42.4 + - + +
275C MET* 3.8 19.1 - - + +
372C SER* 5.3 0.7 - - - -
376C PRO* 4.1 25.6 - - + -
380C PHE* 4.7 3.4 - - + -
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Residues in contact with GLN 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C CYS* 3.6 13.5 - - - -
30C GLY 3.1 25.4 + - - +
32C MET* 3.4 42.3 - - + +
92C ASN* 5.6 1.3 - - - +
239C ALA 3.2 14.6 + - - +
240C ASP 3.8 6.1 - - - +
242C MET* 1.3 76.9 - - - +
244C LEU* 1.3 62.9 + - - +
246C LYS* 3.4 20.6 + - - +
247C TYR* 3.2 21.0 + - - +
376C PRO* 3.5 23.9 - - + +
377C TYR* 3.5 22.0 - - + +
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Residues in contact with LEU 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ARG* 4.9 6.3 - - - +
77C THR 5.8 0.4 - - - +
79C ARG* 3.8 35.7 - - + +
82C PRO* 6.1 1.8 - - + -
90C ASN* 5.0 9.0 - - + +
209C SER* 4.6 6.3 - - - -
211C PHE* 3.6 26.0 - - + -
240C ASP 3.1 15.2 + - - +
241C ASP* 3.8 4.0 - - - +
243C GLN* 1.3 75.5 - - - +
245C TYR* 1.3 65.0 + - - +
247C TYR* 3.3 26.8 + - + +
248C ILE* 2.9 30.3 + - + +
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Residues in contact with TYR 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C ALA* 3.0 40.1 + - + -
136C PHE* 3.4 15.5 - + - -
206C LEU* 3.9 19.1 - - + -
211C PHE* 3.7 9.5 - - + -
228C ILE* 3.2 39.9 + - + +
230C TYR* 3.5 26.9 - + + -
241C ASP 2.8 22.6 + - - +
242C MET* 3.3 19.5 - - - +
244C LEU* 1.3 73.6 - - - +
246C LYS* 1.3 60.7 + - + +
248C ILE* 3.1 1.9 + - - +
249C ILE* 2.8 53.1 + - + +
262C PHE* 3.9 12.1 - + - -
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Residues in contact with LYS 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C GLY 5.1 3.4 + - - -
31C ILE* 5.9 4.2 - - - +
242C MET* 3.0 29.4 + - + +
243C GLN* 3.7 26.5 + - - +
244C LEU 3.2 0.2 - - - -
245C TYR* 1.3 79.5 - - + +
247C TYR* 1.3 58.9 + - - +
249C ILE* 3.8 0.5 - - - +
250C LYS* 2.8 52.6 + - - +
262C PHE* 4.0 47.0 - - + +
372C SER* 2.8 34.1 + - - +
374C GLY 4.4 11.1 + - - -
376C PRO* 5.7 1.8 - - + +
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Residues in contact with TYR 247 (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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24C ARG* 3.0 41.2 + - - +
32C MET* 6.5 0.7 - - + -
81C ASP* 2.6 32.1 + - - -
82C PRO* 4.7 2.9 - - + -
83C PHE* 3.8 23.0 - + - +
84C ARG* 4.9 5.0 - - - +
90C ASN* 4.1 4.3 - - - -
243C GLN 3.2 10.8 + - - +
244C LEU* 3.4 21.8 - - + +
246C LYS* 1.3 78.5 - - - +
248C ILE* 1.3 59.9 + - + +
250C LYS* 4.7 3.8 - - - -
251C ASN* 2.8 63.7 + - - +
189D VAL* 4.1 15.7 - - + -
190D ALA* 3.5 23.2 - - + +
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Residues in contact with ILE 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C PRO* 4.3 5.6 - - + -
83C PHE* 3.5 13.6 - - + -
202C MET 4.4 2.2 - - - +
205C ASN* 3.8 28.3 - - + +
206C LEU* 3.8 31.2 - - + -
209C SER* 3.2 35.7 - - - +
211C PHE* 4.0 6.1 - - + -
244C LEU* 2.9 31.8 + - + +
245C TYR 3.7 3.1 - - - +
247C TYR* 1.3 78.5 - - + +
249C ILE* 1.3 65.6 + - + +
252C THR* 2.7 35.6 + - - +
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Residues in contact with ILE 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C PHE* 3.5 38.4 - - + -
202C MET* 3.7 35.3 - - + +
206C LEU* 4.1 9.9 - - + -
228C ILE* 4.1 10.8 - - + -
245C TYR* 2.8 59.4 + - + +
246C LYS 3.8 3.1 - - - +
248C ILE* 1.3 73.6 - - - +
250C LYS* 1.3 63.1 + - - +
253C ALA* 3.1 23.0 + - - +
260C VAL* 3.9 11.4 - - + -
262C PHE* 4.0 5.2 - - + -
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Residues in contact with LYS 250 (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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31C ILE* 5.1 13.5 - - - +
246C LYS* 2.8 40.4 + - + +
247C TYR* 4.0 4.0 - - - +
249C ILE* 1.3 74.1 - - - +
251C ASN* 1.3 59.6 + - - +
253C ALA* 3.3 5.2 + - - +
254C TRP* 3.0 25.5 + - - +
259C THR* 5.7 0.3 - - - -
260C VAL* 4.3 14.3 + - + +
262C PHE* 3.7 34.0 - - + +
178D TYR* 3.2 39.3 + - + +
190D ALA 5.5 0.4 - - - +
191D PRO* 3.8 23.0 - - + +
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Residues in contact with ASN 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C PHE* 3.5 24.9 - - + -
247C TYR* 2.8 46.7 + - - +
250C LYS* 1.3 72.8 - - - +
252C THR* 1.3 66.2 + - - +
253C ALA 3.2 1.3 - - - -
254C TRP* 3.7 7.3 - - - +
255C GLN* 3.0 30.4 + - + +
190D ALA* 3.1 33.6 + - - +
191D PRO* 3.3 26.2 - - - +
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Residues in contact with THR 252 (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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83C PHE* 3.5 9.3 - - - -
198C LEU* 4.1 4.0 - - + -
201C LYS* 4.0 7.2 - - + -
202C MET* 3.7 38.1 - - + +
205C ASN* 2.9 30.3 + - - +
248C ILE* 2.7 30.8 + - - +
249C ILE 3.8 0.2 - - - -
251C ASN* 1.3 79.0 - - - +
253C ALA* 1.3 61.1 + - - +
255C GLN* 3.4 1.8 + - - +
256C ASN* 2.8 40.8 + - - +
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Residues in contact with ALA 253 (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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198C LEU* 4.5 6.5 - - + -
202C MET* 4.0 9.7 - - + +
249C ILE 3.1 7.9 + - - +
250C LYS 3.4 7.2 - - - +
252C THR* 1.3 78.0 - - - +
254C TRP* 1.3 59.3 + - - +
256C ASN 3.1 9.4 + - - -
257C GLY 3.3 0.2 + - - -
258C LYS* 2.8 44.7 + - + +
259C THR 4.3 0.2 - - - +
260C VAL* 3.4 35.7 - - + +
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Residues in contact with TRP 254 (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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250C LYS 3.0 15.7 + - - +
251C ASN* 3.7 12.8 - - - +
252C THR 3.2 0.4 - - - -
253C ALA* 1.3 76.0 - - - +
255C GLN* 1.3 68.2 + - + +
256C ASN 3.1 0.9 + - - -
257C GLY 3.2 1.7 + - - -
258C LYS 3.5 16.2 - - - -
259C THR* 4.5 3.8 - - - -
158D ILE* 6.0 3.6 - - + -
176D ARG* 2.6 81.3 + - + +
177D GLY 3.7 17.5 - - - -
178D TYR* 3.9 16.2 - + + -
191D PRO* 3.8 28.4 - - + +
194D GLN* 4.0 29.4 + - - +
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Residues in contact with GLN 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C PRO 5.1 1.0 - - - +
83C PHE* 3.5 53.6 + - + +
251C ASN* 3.0 18.9 + - + +
252C THR* 3.9 5.1 - - - +
254C TRP* 1.3 81.7 - - + +
256C ASN* 1.3 64.9 + - - +
257C GLY 3.5 0.8 + - - -
197D ASP* 5.3 5.1 + - - -
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Residues in contact with ASN 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C LEU* 3.8 26.8 - - + +
201C LYS* 3.0 36.8 + - - +
252C THR* 2.8 32.3 + - - +
253C ALA 3.1 4.1 + - - +
255C GLN* 1.3 86.6 - - - +
257C GLY* 1.3 59.7 + - - -
258C LYS* 3.3 14.3 + - - +
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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