Contacts of the helix formed by residues 222 - 242 (chain E) in PDB entry 3HB8
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 GLY 222 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E ASP* 3.7 4.9 - - - -
221E LEU* 1.3 76.1 - - - +
223E VAL* 1.3 54.8 + - - +
224E PRO* 3.3 6.4 - - - +
225E PHE* 2.9 14.1 + - - +
226E ASN* 2.6 47.4 + - - -
614E EDO 4.4 10.9 + - - -
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Residues in contact with VAL 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E TYR* 4.0 11.9 - - + -
36E GLN* 5.4 1.1 - - - +
214E GLN* 4.5 1.6 - - - +
217E GLY* 3.8 16.2 - - - -
218E ASP 3.2 20.3 + - - +
219E MET* 3.5 31.2 - - + -
222E GLY* 1.3 71.7 - - - +
224E PRO* 1.4 63.4 - - + +
226E ASN* 3.0 9.1 + - - -
227E ILE* 2.7 49.8 + - + +
250E HIS* 3.4 24.2 - - + +
252E LEU* 4.1 6.5 - - + -
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Residues in contact with PRO 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E TYR* 3.4 17.9 - - + +
72E PRO 5.0 1.0 - - - +
73E LEU* 5.2 0.3 - - - +
74E LEU* 3.3 39.2 - - + +
77E LYS* 5.8 3.4 - - + +
79E VAL* 4.1 19.5 - - + +
219E MET 3.5 11.0 - - - +
220E GLY 3.9 7.6 - - - +
222E GLY 3.5 9.2 - - - +
223E VAL* 1.4 94.0 - - + +
225E PHE* 1.3 59.2 + - - +
227E ILE* 3.7 5.5 + - + +
228E ALA* 3.3 21.3 + - - +
268E GLN* 6.1 0.2 - - - +
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Residues in contact with PHE 225 (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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79E VAL* 3.9 13.4 - - + +
80E PHE* 3.8 20.6 - + + -
83E GLY* 3.7 11.9 - - - -
84E VAL* 3.4 44.5 - - + +
87E GLU* 3.6 30.5 - - - -
108E ILE* 4.2 11.7 - - + -
222E GLY* 2.9 12.1 + - - +
224E PRO* 1.3 75.7 - - - +
226E ASN* 1.3 68.9 + - - +
228E ALA* 3.1 5.0 + - - +
229E SER* 2.8 40.1 + - - -
614E EDO 3.8 33.4 - - - +
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Residues in contact with ASN 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196E HIS* 3.1 35.9 + - + -
212E LEU* 5.2 4.3 - - + -
214E GLN* 3.2 29.8 + - - +
217E GLY* 5.4 0.9 - - - -
218E ASP 5.6 0.3 + - - -
222E GLY* 2.6 34.8 + - - +
223E VAL* 3.3 9.3 + - - +
225E PHE* 1.3 83.9 - - - +
227E ILE* 1.3 66.2 + - - +
229E SER* 3.2 8.0 + - - -
230E TYR* 3.2 25.2 + - - +
250E HIS* 4.9 2.2 - - - +
614E EDO 5.2 3.2 + - - -
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Residues in contact with ILE 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E TYR* 4.2 10.3 - - + -
65E TYR* 3.4 41.7 - - + +
72E PRO* 3.8 25.1 - - + +
74E LEU* 4.5 7.9 - - + -
223E VAL* 2.7 38.3 + - + +
224E PRO* 3.8 8.7 - - + +
226E ASN* 1.3 74.3 - - - +
228E ALA* 1.3 65.3 + - - +
230E TYR* 3.4 0.9 + - - -
231E ALA* 3.0 21.7 + - - +
248E PHE* 3.9 24.8 - - + -
250E HIS* 3.9 18.4 - - + +
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Residues in contact with ALA 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E PHE* 3.4 24.4 - - + -
72E PRO 4.3 4.9 + - - +
73E LEU* 4.0 24.5 - - + -
79E VAL* 4.6 0.7 - - + -
81E TRP* 4.6 1.1 - - + -
84E VAL* 4.0 18.2 - - + -
224E PRO 3.3 11.0 + - - +
225E PHE* 3.1 8.8 + - - +
227E ILE* 1.3 78.4 - - - +
229E SER* 1.3 64.1 + - - +
231E ALA* 3.1 1.9 + - - -
232E LEU* 2.9 22.0 + - - +
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Residues in contact with SER 229 (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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84E VAL* 3.5 19.7 + - - +
87E GLU* 4.0 12.5 + - - -
88E LEU* 3.9 21.8 - - - +
91E PHE* 5.1 2.8 - - - -
196E HIS* 5.8 0.8 + - - -
225E PHE* 2.8 27.5 + - - -
226E ASN* 3.4 13.9 - - - -
228E ALA* 1.3 74.6 - - - +
230E TYR* 1.3 73.3 + - - +
232E LEU* 3.4 5.0 + - - +
233E LEU* 3.3 15.6 + - - +
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Residues in contact with TYR 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E LEU* 6.4 0.9 - - + -
91E PHE* 5.9 3.7 - + - -
135E TYR* 4.5 3.3 - - - -
139E TRP* 3.5 27.9 + + - -
196E HIS* 3.6 45.2 + + - +
199E CYS* 4.0 26.1 - - + +
210E CYS* 4.8 5.4 - - - -
212E LEU* 3.7 33.3 - - + +
226E ASN 3.2 13.6 + - - +
229E SER* 1.3 85.6 - - - +
231E ALA* 1.3 63.9 + - - +
232E LEU 3.2 1.8 - - - -
233E LEU* 3.2 25.5 + - + +
234E THR* 2.9 27.8 + - - -
248E PHE* 3.7 23.7 - - + -
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Residues in contact with ALA 231 (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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67E LEU* 4.1 10.2 - - + +
71E PHE* 3.8 9.9 - - + -
72E PRO* 3.4 31.6 - - + -
227E ILE 3.0 18.1 + - - +
228E ALA 3.5 4.3 - - - +
230E TYR* 1.3 77.1 - - - +
232E LEU* 1.3 62.0 + - - +
234E THR* 3.4 8.7 + - - -
235E TYR* 3.2 28.9 + - - -
248E PHE* 4.8 8.6 - - + -
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Residues in contact with LEU 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E PHE* 3.7 11.4 - - + -
81E TRP* 3.8 20.9 - - + -
84E VAL* 4.2 7.6 - - + -
85E LEU* 3.9 31.2 - - + -
88E LEU* 3.5 22.2 - - + -
228E ALA 2.9 11.4 + - - +
229E SER 3.5 7.4 - - - +
231E ALA* 1.3 75.9 - - - +
233E LEU* 1.3 63.6 + - - +
234E THR 3.1 0.4 - - - -
235E TYR* 3.2 3.2 + - + +
236E MET* 3.0 30.1 + - + +
279E LEU* 3.5 24.7 - - + -
296E PHE* 4.1 25.6 - - + -
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Residues in contact with LEU 233 (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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88E LEU* 3.7 16.1 - - + +
92E ILE* 4.3 23.6 - - + -
139E TRP* 3.8 23.8 - - + -
161E LEU* 4.6 3.8 - - + -
179E MET* 4.3 9.9 - - + -
199E CYS* 5.0 0.4 - - - -
201E PHE* 4.3 15.7 - - + -
229E SER 3.3 10.2 + - - +
230E TYR* 3.2 31.5 + - + +
232E LEU* 1.3 80.0 - - - +
234E THR* 1.3 61.1 + - - +
236E MET* 3.6 3.8 + - - -
237E ILE* 3.2 45.0 + - + +
288E ILE* 4.4 5.6 - - + -
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Residues in contact with THR 234 (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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67E LEU* 3.9 21.3 - - + +
201E PHE* 4.2 6.6 - - + -
208E LEU* 3.6 34.6 - - + +
209E SER 4.6 0.4 - - - -
210E CYS* 3.3 32.8 - - + +
230E TYR 2.9 14.1 + - - -
231E ALA* 3.6 9.4 - - - -
232E LEU 3.1 0.6 - - - -
233E LEU* 1.3 76.9 - - - +
235E TYR* 1.3 55.8 + - - +
237E ILE* 3.4 1.4 + - - -
238E ALA* 2.7 36.6 + - - +
245E PRO* 5.2 4.3 - - + -
248E PHE* 4.9 1.2 - - - -
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Residues in contact with TYR 235 (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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67E LEU* 2.6 47.1 + - + -
69E ASP* 4.5 1.7 + - - -
70E GLU 2.7 19.9 + - - -
71E PHE* 4.0 20.1 - + - +
231E ALA 3.2 21.6 + - - +
232E LEU* 3.2 9.7 + - + +
234E THR* 1.3 79.6 - - - +
236E MET* 1.3 53.7 + - - +
238E ALA* 3.6 6.8 - - - +
239E HIS* 2.7 36.7 + - - +
245E PRO* 3.8 20.8 - - + +
279E LEU* 3.9 42.5 + - + +
281E ILE* 4.1 16.3 - - + +
296E PHE* 5.8 0.2 - - + -
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Residues in contact with MET 236 (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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85E LEU* 4.8 4.7 - - + -
88E LEU* 3.3 35.2 - - + -
89E LEU* 4.2 16.4 - - + -
92E ILE* 4.9 5.4 - - + -
232E LEU* 3.0 17.7 + - + +
233E LEU* 3.8 10.1 - - - +
235E TYR* 1.3 75.2 - - - +
237E ILE* 1.3 53.1 + - - +
239E HIS* 3.0 4.9 + - - +
240E ILE* 2.7 36.6 + - - +
281E ILE* 4.9 1.1 - - - -
288E ILE* 4.7 13.5 - - + -
291E PHE* 3.5 44.8 - - + -
296E PHE* 3.4 39.0 - - + -
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Residues in contact with ILE 237 (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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161E LEU* 4.3 12.3 - - + -
164E VAL* 4.8 5.4 - - + -
165E ILE* 4.2 16.8 - - + -
168E ILE* 4.7 10.3 - - + -
201E PHE* 3.5 34.5 - - + -
208E LEU* 3.9 15.7 - - + -
233E LEU* 3.2 35.5 + - + +
234E THR* 4.0 2.5 - - - +
236E MET* 1.3 74.6 - - - +
238E ALA* 1.3 51.5 + - - +
240E ILE* 4.2 7.2 - - - -
241E THR* 2.7 50.7 + - + +
288E ILE* 4.5 11.7 - - + -
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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
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208E LEU* 3.7 13.2 - - + +
234E THR 2.7 23.4 + - - +
235E TYR 3.6 4.5 - - - +
237E ILE* 1.3 72.9 - - - +
239E HIS* 1.3 58.0 + - - +
241E THR* 3.3 6.2 + - - -
242E GLY* 2.9 10.0 + - - -
243E LEU 2.9 46.6 + - - +
244E LYS 4.5 0.7 - - - -
245E PRO* 4.0 24.5 - - + -
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Residues in contact with HIS 239 (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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235E TYR 2.7 17.1 + - - +
236E MET* 3.4 2.7 - - - +
238E ALA* 1.3 79.8 - - - +
240E ILE* 1.3 63.2 + - + +
241E THR 3.4 0.3 + - - -
242E GLY* 3.7 7.2 + - - -
243E LEU 5.0 0.4 - - - -
281E ILE* 3.5 26.5 - - + +
283E ARG 3.4 18.1 + - - -
284E LYS* 3.7 23.6 + - + -
285E VAL* 2.8 36.8 + - + +
291E PHE* 3.4 26.2 - + - -
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Residues in contact with ILE 240 (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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165E ILE* 3.7 39.7 - - + -
169E LYS* 4.5 11.8 + - + +
236E MET 2.7 17.3 + - - +
237E ILE* 3.8 9.4 - - - +
239E HIS* 1.3 75.6 - - + +
241E THR* 1.3 58.1 + - + +
242E GLY 3.6 0.2 - - - -
285E VAL* 3.7 22.7 - - + +
286E GLU* 3.2 28.4 - - - +
287E LYS* 3.6 19.5 - - - +
288E ILE* 3.8 12.8 - - + +
291E PHE* 3.7 26.0 - - + -
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Residues in contact with THR 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E ILE* 4.1 5.8 - - + +
168E ILE* 3.9 26.2 - - + +
169E LYS* 3.9 31.0 - - + +
208E LEU* 4.4 1.0 - - - +
237E ILE* 2.7 32.5 + - + +
238E ALA* 3.4 7.4 + - - -
240E ILE* 1.3 90.8 - - + +
242E GLY* 1.3 59.6 + - - +
243E LEU* 3.4 24.0 + - - +
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Residues in contact with GLY 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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206E SER* 5.8 0.9 - - - -
238E ALA 2.9 5.6 + - - -
239E HIS* 3.7 7.0 + - - -
240E ILE 3.6 2.4 - - - -
241E THR* 1.3 79.0 - - - +
243E LEU* 1.3 66.4 + - - +
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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
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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