Contacts of the helix formed by residues 230 - 250 (chain B) in PDB entry 4CZ8
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 PRO 230 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A MSE 3.9 28.7 - - + -
25A ARG* 3.7 16.8 - - - +
296A THR* 4.9 4.8 - - + +
299A ALA* 3.9 19.1 - - + -
1426A TAM 4.9 7.2 - - - +
229B PHE* 1.3 113.6 - - + +
231B GLU* 1.3 59.8 + - + +
233B GLU* 2.9 21.0 - - - +
234B ALA* 3.5 18.3 + - + +
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Residues in contact with GLU 231 (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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18A VAL* 4.8 1.7 - - - +
21A MSE 4.3 19.6 - - + +
22A LEU* 3.4 22.6 - - + +
25A ARG* 3.3 32.3 - - - +
26A ARG* 2.4 38.8 + - - -
225B GLY 4.1 1.2 - - - +
226B ILE* 3.6 14.7 - - + +
228B ASP* 2.9 31.2 + - - +
230B PRO* 1.3 79.0 - - + +
232B ILE* 1.3 58.8 + - - +
234B ALA* 3.9 1.5 - - - +
235B PHE* 2.9 33.8 + - - +
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Residues in contact with ILE 232 (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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221B ILE* 3.9 27.8 - - + -
226B ILE* 3.6 26.8 - - + +
227B PHE 4.3 11.0 - - - +
228B ASP 3.6 12.4 + - - +
231B GLU* 1.3 76.6 - - - +
233B GLU* 1.3 78.4 - - + +
235B PHE* 3.9 1.5 - - + +
236B SER* 2.9 34.3 + - - -
286B ALA* 3.6 34.5 - - + +
287B ILE* 5.0 7.2 - - + -
289B LYS* 4.4 6.7 - - + -
290B GLU* 3.8 15.5 - - + -
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Residues in contact with GLU 233 (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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292A HIS* 2.6 34.9 + - + +
296A THR* 3.6 20.6 - - + -
229B PHE* 3.3 17.1 - - - +
230B PRO* 2.9 27.6 - - - +
232B ILE* 1.3 86.7 - - - +
234B ALA* 1.3 62.8 + - - +
236B SER* 2.5 23.4 + - - -
237B LEU* 2.9 12.4 + - - +
289B LYS* 4.0 2.0 - - - +
290B GLU* 4.3 12.6 - - - +
293B PHE* 3.9 26.5 - - + -
294B ASN* 4.6 1.6 + - - +
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Residues in contact with ALA 234 (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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14A LEU* 4.8 0.7 - - - +
18A VAL* 3.7 22.4 - - + +
21A MSE 5.1 3.1 - - - -
296A THR* 5.0 1.5 - - + +
300A LEU* 3.8 28.3 - - + -
303A ILE* 5.1 5.2 - - + -
230B PRO* 3.5 15.2 + - + +
231B GLU* 4.1 2.2 - - - +
233B GLU* 1.3 78.8 - - - +
235B PHE* 1.3 54.4 + - - +
237B LEU* 3.5 6.3 + - - +
238B SER* 2.5 39.3 + - - -
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Residues in contact with PHE 235 (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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15A PHE* 5.5 9.2 - + - -
18A VAL* 4.0 16.9 - - + +
19A ILE* 5.4 7.6 - - + -
22A LEU* 4.5 9.2 - - + -
217B GLY* 4.1 15.9 - - - -
220B PHE* 3.5 40.2 - + + -
221B ILE* 3.8 33.7 - - + -
226B ILE* 4.2 16.2 - - + -
231B GLU 2.9 20.4 + - - +
232B ILE* 3.9 4.5 - - - +
234B ALA* 1.3 77.6 - - - +
236B SER* 1.3 60.3 + - - +
238B SER* 3.3 6.3 + - - -
239B LEU* 2.9 43.8 + - + +
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Residues in contact with SER 236 (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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71B PHE* 4.1 9.8 - - - -
221B ILE* 6.2 0.9 - - - -
232B ILE* 2.9 20.0 + - - -
233B GLU 2.5 21.5 + - - -
235B PHE* 1.3 77.3 - - - +
237B LEU* 1.3 61.5 + - - +
239B LEU* 3.1 11.4 + - - +
240B ALA* 2.9 29.2 + - - +
265B LEU* 5.0 6.7 - - - -
290B GLU* 3.1 35.6 - - - +
294B ASN* 3.4 5.1 + - - -
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Residues in contact with LEU 237 (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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14A LEU* 3.7 24.9 - - + -
300A LEU* 4.3 24.9 - - + -
1424A PTY 6.2 1.6 - - + -
64B PHE* 5.3 4.9 - - + -
68B ILE* 4.0 12.8 - - + -
71B PHE* 5.6 0.7 - - - -
233B GLU 2.9 12.0 + - - +
234B ALA* 3.6 3.8 - - - +
236B SER* 1.3 81.2 + - - +
238B SER* 1.3 62.3 + - - +
240B ALA* 3.1 8.0 + - + +
241B PHE* 3.0 55.2 + - + -
293B PHE* 4.6 7.6 - - + -
294B ASN* 4.0 21.7 - - - +
297B LEU* 4.5 10.5 - - + -
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Residues in contact with SER 238 (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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11A PHE* 3.3 10.5 - - - -
14A LEU* 3.4 25.9 - - - +
15A PHE* 3.9 28.6 - - - -
18A VAL* 3.5 11.7 - - - +
234B ALA 2.5 23.7 + - - -
235B PHE* 3.3 8.9 + - - -
237B LEU* 1.3 76.0 - - - +
239B LEU* 1.3 57.3 + - - +
242B LEU* 2.9 29.3 + - - +
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Residues in contact with LEU 239 (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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15A PHE* 5.6 2.9 - - + -
71B PHE* 5.7 0.2 - - + -
213B LEU* 4.0 29.9 - - + +
214B GLY* 4.8 1.6 - - - +
217B GLY* 4.3 20.2 - - - -
221B ILE* 6.2 0.9 - - + -
235B PHE* 2.9 31.6 + - + +
236B SER* 3.1 10.3 + - - +
238B SER* 1.3 76.0 - - - +
240B ALA* 1.3 59.2 + - - +
242B LEU* 3.2 20.4 + - + +
243B GLY* 2.9 26.0 + - - -
261B THR* 3.8 27.7 + - + +
265B LEU* 4.3 17.9 - - + -
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Residues in contact with ALA 240 (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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67B VAL* 4.9 4.3 - - + -
68B ILE* 5.8 1.8 - - + -
71B PHE* 3.5 43.7 - - + -
236B SER 2.9 12.2 + - - +
237B LEU* 3.1 11.2 + - + +
239B LEU* 1.3 76.5 - - - +
241B PHE* 1.3 63.8 + - + +
243B GLY* 3.2 4.4 + - - -
244B PHE* 2.9 24.9 + - - +
258B ALA* 3.9 13.8 - - + +
261B THR* 5.4 1.8 - - - -
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Residues in contact with PHE 241 (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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11A PHE* 3.8 21.8 - - + -
14A LEU* 5.2 4.5 - - + -
63B VAL 5.5 0.7 - - - -
64B PHE* 3.5 45.3 - + - -
67B VAL* 3.6 34.5 - - + -
68B ILE* 4.7 7.2 - - + -
237B LEU* 3.0 53.2 + - + +
238B SER* 5.0 0.4 - - - -
240B ALA* 1.3 75.6 - - + +
242B LEU* 1.3 60.3 + - - +
244B PHE* 3.6 9.6 - + - +
245B PHE* 2.9 53.9 + + + -
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Residues in contact with LEU 242 (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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11A PHE* 3.4 27.5 - - + -
15A PHE* 4.0 28.7 - - + -
213B LEU* 4.9 11.0 - - + -
238B SER 2.9 20.1 + - - +
239B LEU* 3.3 21.8 - - + +
240B ALA 3.2 0.2 - - - -
241B PHE* 1.3 74.9 - - - +
243B GLY* 1.3 60.0 + - - +
246B ILE* 2.9 68.0 + - + +
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Residues in contact with GLY 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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209B LEU* 4.5 0.2 - - - +
213B LEU* 3.5 24.8 - - - +
239B LEU 2.9 13.7 + - - -
240B ALA 3.6 3.8 - - - -
242B LEU* 1.3 77.4 - - - +
244B PHE* 1.3 56.0 + - - +
246B ILE* 4.2 0.4 - - - +
247B GLY* 2.9 24.8 + - - -
257B VAL* 3.4 25.5 - - - +
258B ALA 5.3 0.7 - - - -
261B THR* 5.3 2.7 - - - -
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Residues in contact with PHE 244 (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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63B VAL* 4.6 15.0 - - + -
67B VAL* 3.5 35.0 - - + -
240B ALA 2.9 12.7 + - - +
241B PHE* 3.6 14.1 - + - +
242B LEU 3.2 0.2 - - - -
243B GLY* 1.3 77.3 - - - +
245B PHE* 1.3 95.0 + + - +
248B GLU* 2.9 50.5 + - + +
254B GLY* 3.4 33.8 + - - +
255B TYR* 3.7 31.6 - + - -
258B ALA* 4.9 0.2 - - + -
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Residues in contact with PHE 245 (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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5A SER* 5.6 0.2 - - - -
7A ALA* 3.4 37.7 - - + -
8A GLU* 3.8 29.2 - - + +
11A PHE* 3.4 42.6 - + + -
241B PHE* 2.9 43.7 + + - +
242B LEU 4.2 1.1 - - - +
244B PHE* 1.3 96.6 - + - +
246B ILE* 1.3 62.1 + - + +
248B GLU* 3.4 5.4 + - + +
249B ARG* 2.9 33.0 + - - +
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Residues in contact with ILE 246 (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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209B LEU* 3.7 24.7 - - + -
213B LEU* 4.7 11.7 - - + -
242B LEU* 2.9 50.4 + - + +
243B GLY* 4.2 2.2 - - - +
245B PHE* 1.3 75.7 - - + +
247B GLY* 1.3 64.2 + - - +
249B ARG* 3.1 20.2 + - + +
250B LEU* 3.3 20.5 - - + +
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Residues in contact with GLY 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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209B LEU* 3.9 15.2 - - - +
243B GLY 2.9 19.0 + - - -
244B PHE 3.8 0.7 - - - -
246B ILE* 1.3 77.7 - - - +
248B GLU* 1.3 52.1 + - - +
249B ARG 3.1 1.1 + - - -
250B LEU* 3.3 9.6 + - - +
252B ALA* 2.7 40.4 + - - +
254B GLY* 4.5 0.7 - - - -
257B VAL* 4.3 10.5 - - - -
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Residues in contact with GLU 248 (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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167B LEU* 4.1 20.3 - - - +
244B PHE* 2.9 39.5 + - + +
245B PHE* 4.0 7.0 - - + +
247B GLY* 1.3 74.4 - - - +
249B ARG* 1.3 61.7 + - - +
250B LEU 3.3 0.2 - - - -
251B ASP* 3.5 10.4 + - - -
252B ALA 3.3 9.0 + - - +
253B SER* 4.1 2.8 - - - -
254B GLY 3.1 23.9 + - - -
255B TYR* 4.5 7.1 - - - -
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Residues in contact with ARG 249 (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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2A ILE* 4.2 13.5 - - - +
3A GLU 4.2 10.9 + - - -
4A LEU* 3.9 20.4 - - - +
8A GLU* 2.3 39.6 + - - -
245B PHE 2.9 18.3 + - - +
246B ILE* 3.1 12.5 + - + +
248B GLU* 1.3 79.8 - - - +
250B LEU* 1.3 58.2 + - + +
251B ASP 3.3 2.1 + - - -
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Residues in contact with LEU 250 (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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181B ILE* 4.5 1.6 - - - +
201B TYR* 3.1 23.4 + - - +
205B VAL* 3.7 23.3 - - + -
209B LEU* 4.7 8.1 - - + -
246B ILE* 3.3 24.9 - - + +
247B GLY* 3.3 19.9 + - - +
248B GLU 3.3 0.2 - - - -
249B ARG* 1.3 75.6 - - + +
251B ASP* 1.3 67.8 + - - +
252B ALA* 3.4 17.3 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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