Contacts of the helix formed by residues 235 - 256 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E ALA* 3.6 30.1 - - + +
115E ALA* 4.3 5.8 - - + -
116E GLU* 3.3 13.8 + - + +
128E ALA* 3.0 12.8 + - + +
130E PHE* 3.6 40.2 - - + -
234E SER* 1.3 72.7 - - - +
236E LEU* 1.3 66.0 - - - +
238E ALA* 3.2 3.0 + - - +
239E ALA* 2.9 21.6 + - + +
377E TYR 4.6 1.3 - - - +
380E PHE* 3.9 26.7 - - + +
381E SER* 3.8 13.5 - - - +
384E LEU* 3.7 27.6 - - + -
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Residues in contact with LEU 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E ASP* 4.7 3.8 - - - +
94E PHE* 4.4 18.6 - - + -
109E ARG* 4.0 19.1 - - - +
112E ALA* 3.7 23.6 - - + -
113E ARG* 4.6 14.8 - - + -
116E GLU* 3.1 28.2 + - + +
235E LEU* 1.3 81.5 - - - +
237E HIS* 1.3 75.5 + - + +
239E ALA* 3.1 4.1 + - - +
240E ASP* 3.0 34.9 + - - +
377E TYR* 4.1 13.0 - - + -
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Residues in contact with HIS 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E ASP* 6.1 0.7 - - - -
76E GLU* 3.4 39.6 + - + +
116E GLU* 5.9 0.2 - - - -
233E ASN* 3.6 25.8 - - - +
234E SER* 3.1 26.0 + - - +
236E LEU* 1.3 89.3 - - + +
238E ALA* 1.3 52.5 + - - +
240E ASP* 3.4 11.8 + - - +
241E ASP* 2.8 41.9 + - - +
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Residues in contact with ALA 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E PHE* 3.8 19.7 - - + +
230E TYR* 4.4 4.8 + - + -
233E ASN* 3.8 18.1 - - + +
234E SER 2.8 17.0 + - - +
235E LEU 3.4 4.9 - - - +
236E LEU 3.2 0.2 - - - -
237E HIS* 1.3 76.9 - - - +
239E ALA* 1.3 56.3 + - - +
241E ASP* 3.4 11.2 - - - +
242E MET* 2.9 27.7 + - - +
380E PHE* 3.7 15.8 - - + -
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Residues in contact with ALA 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235E LEU* 2.9 15.5 + - + +
236E LEU* 3.1 6.9 + - - +
238E ALA* 1.3 71.7 - - - +
240E ASP* 1.3 65.2 + - - +
242E MET* 3.2 3.0 + - - +
243E GLN* 3.1 28.2 + - - +
376E PRO* 4.0 3.7 - - - +
377E TYR* 3.3 48.2 - - + +
380E PHE* 3.6 15.8 - - + -
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Residues in contact with ASP 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E ASP* 4.6 0.2 - - - +
77E THR* 3.6 12.7 - - + +
92E ASN* 3.0 16.5 + - - +
109E ARG* 2.9 36.5 + - - -
236E LEU* 3.0 24.1 + - - +
237E HIS* 3.6 13.5 + - - +
239E ALA* 1.3 73.2 - - - +
241E ASP* 1.3 66.6 + - - +
242E MET 3.3 0.2 + - - -
243E GLN* 3.3 3.6 + - - +
244E LEU* 3.0 24.4 + - - +
377E TYR* 2.4 30.8 + - - -
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Residues in contact with ASP 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E ARG* 4.8 11.3 + - - -
211E PHE* 3.5 22.0 - - + -
230E TYR* 3.7 25.2 - - + -
231E GLN 4.6 3.1 - - - +
233E ASN* 4.2 20.1 + - - +
237E HIS* 2.8 28.0 + - - +
238E ALA* 3.4 10.3 - - - +
240E ASP* 1.3 74.1 - - - +
242E MET* 1.3 57.0 + - - +
244E LEU* 3.3 3.5 + - - +
245E TYR* 2.8 31.4 + - - +
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Residues in contact with MET 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E ALA* 3.4 33.2 - - + -
134E ALA* 3.6 34.3 - - + +
230E TYR* 3.3 20.9 - - + +
238E ALA 2.9 14.2 + - - +
239E ALA* 3.6 8.7 - - - +
240E ASP 3.2 0.6 - - - -
241E ASP* 1.3 74.8 - - - +
243E GLN* 1.3 65.1 + - - +
245E TYR* 3.3 10.5 + - + +
246E LYS* 3.0 37.3 + - + +
275E MET* 3.9 17.5 - - + +
372E SER* 5.0 0.9 - - - -
376E PRO* 4.1 24.9 - - + -
380E PHE* 4.7 3.1 - - + -
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Residues in contact with GLN 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E CYS* 3.6 13.1 - - - -
30E GLY 3.0 27.4 + - - +
32E MET* 3.5 42.4 - - + +
92E ASN* 5.6 1.6 - - - +
239E ALA 3.1 13.7 + - - +
240E ASP 3.7 5.8 - - - +
242E MET* 1.3 77.5 - - - +
244E LEU* 1.3 62.7 + - - +
246E LYS* 3.2 20.9 + - - +
247E TYR* 3.2 21.3 + - - +
376E PRO* 3.4 24.3 - - + +
377E TYR* 3.5 21.0 - - + +
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Residues in contact with LEU 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E ARG* 5.0 4.3 - - - +
77E THR 5.8 0.2 - - - +
79E ARG* 3.8 36.6 - - + +
82E PRO* 6.0 2.0 - - + -
90E ASN* 5.0 11.4 - - + +
209E SER* 4.5 4.9 - - - -
211E PHE* 3.6 26.7 - - + -
240E ASP 3.0 17.0 + - - +
241E ASP* 3.9 4.7 - - - +
243E GLN* 1.3 72.9 - - - +
245E TYR* 1.3 60.8 + - - +
247E TYR* 3.1 26.7 + - + +
248E ILE* 2.9 37.5 + - + +
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Residues in contact with TYR 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E ALA* 2.8 42.2 + - + -
136E PHE* 3.4 14.0 - - - -
206E LEU* 3.9 18.8 - - + -
211E PHE* 3.7 9.5 - - + -
228E ILE* 3.2 39.4 + - + -
230E TYR* 3.5 28.0 - + + -
241E ASP 2.8 18.0 + - - +
242E MET* 3.4 19.5 - - - +
244E LEU* 1.3 77.7 - - - +
246E LYS* 1.3 60.9 + - + +
248E ILE* 3.3 1.4 + - - +
249E ILE* 2.8 53.3 + - + +
262E PHE* 3.9 11.2 - + - -
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Residues in contact with LYS 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E GLY 5.2 3.8 + - - -
31E ILE* 5.8 4.4 - - - +
242E MET* 3.0 37.5 + - + +
243E GLN* 3.7 22.9 + - - +
244E LEU 3.2 0.4 - - - -
245E TYR* 1.3 75.7 - - + +
247E TYR* 1.3 58.1 + - - +
249E ILE* 3.4 0.5 + - - +
250E LYS* 2.8 54.1 + - - +
262E PHE* 4.0 49.2 - - + +
372E SER* 2.8 32.2 + - - +
373E SER 5.4 0.2 - - - -
374E GLY 4.4 9.9 + - - -
376E PRO* 5.8 1.0 - - + +
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Residues in contact with TYR 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E ARG* 3.1 40.3 + - - +
32E MET* 6.4 1.8 - - + -
81E ASP* 2.6 32.2 + - - -
82E PRO* 4.8 3.4 - - + -
83E PHE* 3.7 24.1 - + - +
84E ARG* 4.9 5.2 - - - +
90E ASN* 4.1 4.0 - - - -
243E GLN 3.2 11.6 + - - +
244E LEU* 3.1 22.4 + - + +
246E LYS* 1.3 77.7 - - - +
248E ILE* 1.3 59.4 + - + +
250E LYS* 4.7 3.8 - - - -
251E ASN* 2.8 62.1 + - - +
189F VAL* 4.1 16.2 - - + -
190F ALA* 3.5 23.8 - - + +
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Residues in contact with ILE 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E PRO* 4.3 5.2 - - + -
83E PHE* 3.4 17.1 - - + -
202E MET 4.4 2.5 - - - +
205E ASN* 3.8 21.5 - - + +
206E LEU* 3.8 32.1 - - + -
209E SER* 3.3 34.3 - - - +
211E PHE* 3.9 8.1 - - + -
244E LEU* 2.9 29.0 + - + +
245E TYR 3.8 3.1 - - - +
247E TYR* 1.3 75.5 - - + +
249E ILE* 1.3 59.6 - - + +
252E THR* 2.6 49.1 + - - +
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Residues in contact with ILE 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E PHE* 3.5 37.0 - - + -
202E MET* 3.7 36.3 - - + +
206E LEU* 4.1 10.8 - - + -
228E ILE* 4.1 9.0 - - + -
245E TYR* 2.8 57.9 + - + +
246E LYS 3.9 2.9 - - - +
248E ILE* 1.3 71.9 - - - +
250E LYS* 1.3 63.5 + - - +
252E THR* 3.8 1.5 - - - -
253E ALA* 3.1 22.7 + - - +
260E VAL* 4.0 6.7 - - + -
262E PHE* 4.0 10.8 - - + -
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Residues in contact with LYS 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E ILE* 5.0 14.3 - - - +
246E LYS* 2.8 39.9 + - + +
247E TYR* 3.9 3.6 - - - +
249E ILE* 1.3 73.4 - - - +
251E ASN* 1.3 58.0 + - - +
253E ALA* 3.5 3.5 + - - +
254E TRP* 3.0 27.3 + - - +
260E VAL* 4.3 15.0 + - + +
262E PHE* 3.7 32.9 - - + +
178F TYR* 3.3 40.0 + - + +
190F ALA 5.4 0.7 - - - +
191F PRO* 3.8 22.7 - - + +
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Residues in contact with ASN 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E PHE* 3.5 27.8 - - + -
247E TYR* 2.8 45.6 + - - +
250E LYS* 1.3 74.6 - - - +
252E THR* 1.3 67.4 + - - +
253E ALA 3.2 0.2 - - - -
254E TRP* 3.7 7.0 - - - +
255E GLN* 3.0 30.5 + - + +
190F ALA* 3.0 34.0 + - - +
191F PRO* 3.4 24.5 - - - +
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Residues in contact with THR 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E PHE* 3.5 9.1 - - - -
198E LEU* 4.2 3.6 - - + -
201E LYS* 3.9 7.4 - - + -
202E MET* 3.6 38.3 - - + +
205E ASN* 2.9 29.8 + - - +
248E ILE* 2.6 35.7 + - - +
249E ILE 3.8 0.4 - - - -
251E ASN* 1.3 75.5 - - - +
253E ALA* 1.3 61.5 + - - +
255E GLN* 3.5 1.7 + - - +
256E ASN* 2.8 40.1 + - - +
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Residues in contact with ALA 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E ILE* 5.1 0.2 - - + -
198E LEU* 4.4 5.4 - - + -
202E MET* 4.0 11.3 - - + +
249E ILE 3.1 7.8 + - - +
250E LYS 3.6 6.7 - - - +
252E THR* 1.3 78.0 - - - +
254E TRP* 1.3 60.3 + - - +
256E ASN* 3.0 9.7 + - - +
258E LYS* 2.9 43.7 + - + +
260E VAL* 3.3 35.2 - - + +
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Residues in contact with TRP 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250E LYS 3.0 17.4 + - - +
251E ASN* 3.7 11.4 - - - +
252E THR 3.3 0.4 - - - -
253E ALA* 1.3 76.7 - - - +
255E GLN* 1.3 67.7 + - + +
256E ASN 3.1 1.4 + - - -
257E GLY 3.2 2.4 + - - -
258E LYS 3.5 8.5 - - - -
259E THR* 4.5 4.0 - - - -
158F ILE* 6.0 3.8 - - + -
176F ARG* 2.6 92.0 + - + +
177F GLY 3.7 14.8 - - - -
178F TYR* 3.9 18.2 - + + -
191F PRO* 3.8 29.1 - - + +
194F GLN* 4.0 26.1 - - + +
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Residues in contact with GLN 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E PRO 5.0 1.0 - - - +
83E PHE* 3.4 52.6 + - + +
205E ASN* 5.8 0.2 + - - -
251E ASN* 3.0 19.7 + - + +
252E THR* 4.0 4.3 - - - +
254E TRP* 1.3 81.8 - - + +
256E ASN* 1.3 65.4 + - - +
257E GLY 3.5 1.0 + - - -
197F ASP* 5.3 4.8 + - - -
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Residues in contact with ASN 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198E LEU* 3.8 25.5 - - + +
201E LYS* 3.1 34.7 + - - +
252E THR* 2.8 31.1 + - - +
253E ALA 3.0 5.3 + - - +
255E GLN* 1.3 87.1 + - - +
257E GLY* 1.3 59.4 + - - -
258E LYS* 3.2 13.4 + - - +
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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