Contacts of the helix formed by residues 220 - 241 (chain B) in PDB entry 4BOG
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 TYR 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219B PHE* 1.3 91.9 - + + +
221B ILE* 1.3 60.8 + - + +
222B VAL 2.7 11.2 + - - -
223B TYR* 2.8 44.2 + + + -
224B THR* 2.9 24.4 + - - +
273B THR* 6.3 3.6 - - + -
279C PRO* 2.8 40.6 + - + +
282C ALA* 3.8 4.5 - - + +
283C LEU* 3.1 43.4 + - + +
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Residues in contact with ILE 221 (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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135B PHE* 6.0 6.3 - - + -
217B PRO 3.9 6.5 - - - +
218B LEU* 3.0 51.8 - - + -
219B PHE 3.9 2.0 - - - +
220B TYR* 1.3 73.0 - - + +
222B VAL* 1.3 56.0 + - - +
224B THR* 3.2 16.3 - - + +
225B ILE* 2.9 34.6 + - - +
283B TYR* 4.9 26.0 - - + -
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Residues in contact with VAL 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LEU* 3.5 28.5 - - + +
219B PHE* 2.9 25.1 - - - +
220B TYR 2.7 0.8 - - - -
221B ILE* 1.3 78.1 - - - +
223B TYR* 1.3 62.6 + - + +
225B ILE* 3.2 27.9 + - + +
226B VAL* 3.3 10.0 + - + +
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Residues in contact with TYR 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B PHE 4.6 2.9 - - - -
220B TYR* 2.8 69.7 + + + +
222B VAL* 1.3 81.0 - - - +
224B THR* 1.3 58.4 + - - +
226B VAL* 2.6 22.1 - - + +
227B PRO* 2.3 33.4 - - + +
266B LEU* 5.9 2.2 - - + -
269B LYS* 5.2 11.0 + - - +
275C SER* 5.3 8.1 - - - -
276C GLN* 4.1 29.6 + - - -
279C PRO* 4.1 13.8 - - + +
296C MET* 6.0 13.0 - - + -
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Residues in contact with THR 224 (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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220B TYR* 2.9 19.4 + - - +
221B ILE* 3.2 23.1 - - + +
222B VAL 3.0 0.2 - - - -
223B TYR* 1.3 78.3 - - - +
225B ILE* 1.3 55.6 + - + +
227B PRO* 2.5 34.9 - - + +
228B CYS* 3.2 16.9 + - - +
266B LEU* 6.1 0.7 - - + -
269B LYS* 3.8 23.1 + - - +
287B ILE* 6.0 6.7 - - + -
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Residues in contact with ILE 225 (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 2.9 14.8 + - - +
222B VAL* 3.2 17.0 - - + +
224B THR* 1.3 74.4 - - - +
226B VAL* 1.3 73.6 + - + +
228B CYS* 3.1 9.7 + - - +
229B ILE* 2.8 48.1 + - + +
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Residues in contact with VAL 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B VAL* 3.3 13.0 + - + +
223B TYR* 2.6 37.2 - - + +
225B ILE* 1.3 83.3 - - + +
227B PRO* 1.3 58.2 - - + +
229B ILE* 4.6 2.0 - - - -
230B LEU* 2.3 76.6 + - + +
300C THR* 5.5 7.2 - - + +
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Residues in contact with PRO 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B TYR* 2.3 34.3 - - + +
224B THR* 2.5 28.7 - - + +
226B VAL* 1.3 75.3 - - + +
228B CYS* 1.3 63.3 + - - +
230B LEU* 4.5 1.6 - - + -
231B ILE* 2.4 57.6 + - + +
266B LEU* 4.1 30.5 - - + -
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Residues in contact with CYS 228 (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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224B THR* 3.2 17.3 + - - +
225B ILE* 3.1 11.2 + - - +
227B PRO* 1.3 82.0 - - - +
229B ILE* 1.3 55.1 + - + +
231B ILE* 4.0 4.2 - - - +
232B SER* 2.5 33.2 + - - -
263B LEU* 6.4 2.5 - - - -
287B ILE* 5.1 18.6 - - - -
290B LEU* 5.2 16.2 - - + -
294B SER* 5.3 2.3 + - - -
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Residues in contact with ILE 229 (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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225B ILE* 2.8 45.4 + - + +
226B VAL* 4.0 2.9 - - - +
227B PRO 2.8 1.2 + - - -
228B CYS* 1.3 72.7 - - + +
230B LEU* 1.3 57.6 + - + +
231B ILE 3.3 1.1 - - - -
232B SER* 2.8 12.8 - - - -
233B ILE* 2.7 34.1 + - + +
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Residues in contact with LEU 230 (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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226B VAL* 2.3 75.9 + - + +
227B PRO* 4.5 1.3 - - + -
229B ILE* 1.3 70.6 - - + +
231B ILE* 1.3 59.5 + - + +
232B SER 2.9 1.3 - - - -
233B ILE* 2.7 56.7 + - + +
234B LEU* 3.1 11.0 + - - +
300C THR* 5.0 19.3 - - + +
303C VAL* 4.2 28.3 - - + -
304C VAL* 5.6 3.4 - - + -
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Residues in contact with ILE 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B PRO* 2.4 63.0 + - + +
228B CYS* 4.0 3.8 - - - +
230B LEU* 1.3 70.1 - - + +
232B SER* 1.3 50.1 + - - +
234B LEU* 3.2 12.6 + - + +
235B ALA* 2.6 32.1 + - + +
259B LEU* 3.2 39.6 - - + +
262B PHE* 4.7 26.7 - - + -
263B LEU* 4.0 12.3 - - + -
266B LEU* 5.3 4.9 - - + -
294B SER* 5.4 4.7 - - - +
272C LEU* 5.6 5.2 - - + -
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Residues in contact with SER 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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228B CYS 2.5 19.6 + - - -
229B ILE* 2.8 19.1 + - - -
231B ILE* 1.3 78.5 - - - +
233B ILE* 1.4 57.7 + - - +
235B ALA* 3.3 11.2 - - - +
236B ILE* 2.4 40.0 + - - +
294B SER* 4.8 7.2 + - - -
446B MET* 4.8 16.0 - - - +
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Residues in contact with ILE 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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229B ILE* 2.7 14.2 + - + +
230B LEU* 2.7 66.3 + - + +
232B SER* 1.4 69.7 - - - +
234B LEU* 1.3 50.8 + - + +
236B ILE* 3.1 11.0 - - + +
237B LEU* 2.6 58.4 + - + +
303C VAL* 5.6 3.6 - - + +
304C VAL* 5.4 15.3 - - + +
307C GLY* 4.4 12.8 - - - -
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Residues in contact with LEU 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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230B LEU 3.1 12.5 + - - +
231B ILE* 3.8 11.2 - - + +
233B ILE* 1.3 80.1 - - + +
235B ALA* 1.3 53.8 - - - +
237B LEU* 2.9 14.6 - - + +
238B VAL* 2.5 44.7 + - + +
255B ALA* 6.0 4.0 - - + +
258B ALA* 6.2 0.2 - - + -
259B LEU* 4.9 12.1 - - + -
262B PHE* 4.9 20.2 - - + -
264C LEU* 3.9 19.7 - - + -
265C LEU* 5.3 8.5 - - + -
268C ALA* 4.9 5.8 - - + -
303C VAL* 5.5 7.6 - - + +
306C CYS* 5.7 0.7 - - + -
307C GLY* 4.5 6.7 - - - +
310C LEU* 3.8 24.7 - - + -
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Residues in contact with ALA 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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231B ILE* 2.6 23.3 + - + +
232B SER* 2.8 14.3 + - - +
234B LEU* 1.3 67.8 - - - +
236B ILE* 1.3 51.9 + - - +
237B LEU 2.7 3.1 - - - -
238B VAL* 2.6 22.7 + - - -
239B PHE* 2.6 50.0 - - + -
259B LEU* 4.3 11.8 - - + +
294B SER* 4.8 10.5 - - - +
446B MET* 5.9 0.4 - - - -
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Residues in contact with ILE 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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232B SER* 2.4 43.0 + - - +
233B ILE* 3.1 16.8 - - + +
235B ALA* 1.3 68.5 - - - +
237B LEU* 1.3 51.8 + - + +
239B PHE* 3.1 15.1 + - + +
240B TYR* 2.5 62.8 + - + +
439B PHE* 4.8 14.8 - - + -
442B ILE* 5.7 0.9 - - + -
446B MET* 3.7 29.1 - - + -
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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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233B ILE* 2.6 48.0 + - + +
234B LEU* 2.9 17.5 - - + +
235B ALA 2.7 0.4 + - - -
236B ILE* 1.3 78.5 - - + +
238B VAL* 1.3 49.5 + - + -
239B PHE 3.1 4.3 - - - -
240B TYR* 3.8 7.2 - - + -
241B LEU* 2.3 42.6 + - - +
307C GLY* 3.9 8.5 - - - +
310C LEU* 3.2 45.1 - - + -
311C ASN* 3.7 25.1 - - + +
314C PHE* 4.3 2.9 - - + -
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Residues in contact with VAL 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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234B LEU* 2.5 29.6 + - + +
235B ALA* 2.6 9.1 + - - +
237B LEU* 1.3 71.5 - - + +
239B PHE* 1.3 68.0 + - + +
241B LEU* 4.0 5.2 - - + -
242B PRO* 2.8 22.3 - - - +
248B LYS* 2.7 31.1 + - - +
252B SER* 4.6 6.7 - - - +
255B ALA* 3.2 32.8 - - + -
256B LEU* 4.8 13.5 - - + -
259B LEU* 5.4 2.7 - - + -
301B VAL* 5.2 1.8 - - + -
305B HIS* 4.1 15.0 + - + +
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Residues in contact with PHE 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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235B ALA* 2.6 52.7 + - + -
236B ILE* 3.1 12.1 - - - +
238B VAL* 1.3 96.4 - - + +
240B TYR* 1.3 58.5 + - - +
242B PRO* 2.9 23.1 - - - +
243B PRO* 3.8 1.6 - - - +
256B LEU* 5.1 0.7 - - + -
259B LEU* 5.1 1.6 - - + -
294B SER* 5.5 4.5 - - - -
297B LEU* 4.9 9.2 - - + -
298B SER* 4.4 18.2 - - - -
301B VAL* 4.3 28.0 - - + -
305B HIS* 6.0 0.2 - - - -
439B PHE* 3.6 22.6 - - + +
442B ILE* 3.9 37.0 - - + -
446B MET* 4.4 11.2 - - + -
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Residues in contact with TYR 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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236B ILE* 2.5 41.7 + - + +
237B LEU* 3.5 9.0 - - + +
239B PHE* 1.3 75.1 - - - +
241B LEU* 1.3 55.6 + - - +
242B PRO* 3.2 3.0 - - - -
243B PRO* 3.4 9.6 - - + +
244B ASP* 2.8 51.2 + - - +
439B PHE* 4.6 25.6 - + + -
311C ASN* 4.3 18.1 + - - +
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Residues in contact with LEU 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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237B LEU 2.3 31.8 + - - +
238B VAL* 4.8 4.5 - - + -
240B TYR* 1.3 67.4 - - - +
242B PRO* 1.4 56.5 - - - +
244B ASP* 3.4 5.8 - - - -
245B ALA* 2.4 46.5 + - + -
248B LYS* 3.2 35.0 - - + +
251B LEU* 3.2 41.1 - - + -
310C LEU* 5.0 6.5 - - + -
314C PHE* 2.9 56.5 - - + -
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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