Contacts of the helix formed by residues 233 - 258 (chain O) in PDB entry 6CNB
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 SER 233 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231O PRO 3.7 0.2 + - - -
232O LEU* 1.3 97.5 + - - +
234O ASP* 1.3 58.9 + - - +
235O LEU* 2.8 16.5 + - - +
236O LYS* 3.0 29.4 + - - +
237O LYS* 4.3 0.2 - - - +
65X C 3.2 23.1 + - - -
66X A 4.6 15.5 - - - -
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Residues in contact with ASP 234 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223O TYR* 3.8 14.7 + - - -
231O PRO 4.6 2.1 + - - +
232O LEU 3.7 1.0 - - - -
233O SER* 1.3 72.7 - - - +
235O LEU* 1.3 50.5 + - - +
236O LYS 3.3 0.2 - - - -
237O LYS* 2.9 33.2 + - + +
238O ARG* 2.7 49.4 + - - +
65X C 3.2 20.8 + - - +
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Residues in contact with LEU 235 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233O SER* 2.8 8.6 + - - +
234O ASP* 1.3 77.2 - - - +
236O LYS* 1.3 58.1 + - - +
238O ARG* 2.9 48.5 + - - +
239O SER* 3.2 26.4 + - - +
240O GLN 4.3 0.3 + - - -
65X C 4.6 13.7 + - - +
66X A 3.3 28.5 - - - +
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Residues in contact with LYS 236 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226O ILE* 6.5 0.2 - - - -
229O ASN* 3.0 39.4 + - - +
230O SER* 5.4 3.5 - - - +
232O LEU* 3.9 18.5 - - + +
233O SER* 3.0 38.5 + - - +
235O LEU* 1.3 78.4 - - - +
237O LYS* 1.3 64.6 + - + +
240O GLN* 3.1 45.5 - - - +
241O ALA 4.5 0.2 + - - -
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Residues in contact with LYS 237 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223O TYR* 3.1 19.9 - - + -
226O ILE* 4.1 30.1 - - + +
230O SER 2.7 29.5 + - - -
231O PRO* 2.9 28.9 + - - +
232O LEU 3.0 12.3 + - - -
233O SER 4.3 1.9 + - - +
234O ASP* 2.9 33.0 + - + +
236O LYS* 1.3 81.9 - - + +
238O ARG* 1.3 56.9 + - - +
241O ALA* 3.1 22.5 - - - +
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Residues in contact with ARG 238 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223O TYR* 3.1 18.6 - - - +
234O ASP* 2.7 27.5 + - - +
235O LEU* 2.9 34.9 + - - +
236O LYS 3.2 0.4 - - - -
237O LYS* 1.3 74.0 - - - +
239O SER* 1.3 65.9 + - - +
240O GLN 3.2 0.7 - - - -
241O ALA* 2.9 4.7 + - - +
242O LYS* 2.4 80.2 + - + +
338O ASP* 5.1 11.2 + - - +
341O GLU* 5.3 1.6 - - - +
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Residues in contact with SER 239 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235O LEU* 3.2 17.0 + - - +
238O ARG* 1.3 101.2 + - - +
240O GLN* 1.3 54.9 + - - +
242O LYS* 3.9 10.4 + - - +
243O MET* 2.3 55.3 + - - +
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Residues in contact with GLN 240 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235O LEU 4.3 1.0 + - - -
236O LYS* 3.1 36.1 + - - +
238O ARG 3.2 0.2 - - - -
239O SER* 1.3 77.1 - - - +
241O ALA* 1.3 54.4 + - - +
243O MET* 3.6 5.6 - - - +
244O ASN* 2.7 53.5 + - - +
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Residues in contact with ALA 241 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219O TYR* 6.2 0.4 - - + -
222O HIS* 3.5 33.3 - - + +
223O TYR* 3.6 18.4 - - + -
237O LYS 3.1 23.7 + - - +
238O ARG 2.9 5.8 + - - +
240O GLN* 1.3 75.8 - - - +
242O LYS* 1.3 53.4 + - - +
244O ASN* 3.5 4.6 - - - +
245O ALA* 2.4 38.2 + - - +
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Residues in contact with LYS 242 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215O TRP* 5.4 11.2 - - + -
219O TYR* 6.0 3.6 - - + -
223O TYR* 5.3 4.5 - - + +
238O ARG* 2.4 76.7 + - + +
239O SER* 3.4 7.9 + - - +
241O ALA* 1.3 65.6 - - + +
243O MET* 1.3 58.2 - - + +
245O ALA* 2.9 8.7 + - - +
246O LYS* 2.3 59.4 + - + +
335O LEU* 6.4 3.4 - - - -
338O ASP* 5.7 1.6 - - - +
341O GLU* 3.4 31.8 + - - +
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Residues in contact with MET 243 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239O SER* 2.3 49.4 + - - +
240O GLN* 3.6 6.1 - - - +
242O LYS* 1.3 73.9 - - + +
244O ASN* 1.3 56.5 + - - +
246O LYS* 2.9 40.7 + - + +
247O THR* 2.5 41.2 + - + +
341O GLU* 5.6 2.9 - - + +
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Residues in contact with ASN 244 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222O HIS* 3.2 30.8 + - + +
240O GLN* 2.7 45.2 + - - +
241O ALA* 3.5 2.9 + - - +
243O MET* 1.3 72.0 - - - +
245O ALA* 1.3 63.4 + - - +
247O THR* 3.7 11.9 - - - +
248O ASP* 2.9 33.1 + - - +
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Residues in contact with ALA 245 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215O TRP* 3.7 24.5 - - + +
218O LEU* 3.3 16.0 - - + +
219O TYR* 5.4 8.1 - - + -
222O HIS* 3.9 14.7 + - + -
241O ALA 2.4 29.4 + - - +
242O LYS* 3.1 13.5 - - + +
244O ASN* 1.3 69.2 - - - +
246O LYS* 1.3 56.6 + - - +
249O PHE* 2.9 31.4 + - - +
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Residues in contact with LYS 246 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215O TRP* 4.1 14.5 - - + -
242O LYS* 2.3 42.2 + - - +
243O MET* 2.9 37.4 + - + +
245O ALA* 1.3 66.9 - - - +
247O THR* 1.3 59.4 + - - +
249O PHE* 2.9 24.1 + - - +
250O ALA* 3.0 12.5 + - - +
331O THR* 5.4 2.4 + - - -
335O LEU* 4.6 18.4 - - - +
341O GLU* 3.2 27.3 + - - -
345O PHE* 5.0 12.1 - - - -
348O GLU* 5.1 12.1 + - - +
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Residues in contact with THR 247 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243O MET* 2.5 24.5 + - - +
244O ASN* 3.6 18.4 - - - +
246O LYS* 1.3 73.9 - - - +
248O ASP* 1.3 72.2 + - - +
250O ALA* 3.5 19.6 + - - +
251O LYS* 4.1 5.2 + - - +
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Residues in contact with ASP 248 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218O LEU* 3.9 19.1 - - + +
222O HIS* 3.1 30.7 + - - -
244O ASN* 2.9 21.3 + - - +
247O THR* 1.3 81.4 - - - +
249O PHE* 1.3 65.5 + - - +
251O LYS* 3.3 21.9 - - + +
252O ILE* 3.1 18.8 - - + +
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Residues in contact with PHE 249 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211O ILE* 4.5 10.8 - - + -
214O LEU* 3.5 32.5 - - + -
215O TRP* 3.9 22.9 - + + -
218O LEU* 3.4 12.3 - - + +
245O ALA 2.9 19.7 + - - +
246O LYS* 2.9 8.3 + - - +
248O ASP* 1.3 77.0 - - - +
250O ALA* 1.3 65.1 + - - +
252O ILE* 2.9 22.9 + - + +
253O ILE* 3.3 22.8 + - + -
330O LEU* 3.4 38.4 - - + -
331O THR* 3.4 26.5 - - + -
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Residues in contact with ALA 250 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246O LYS 3.0 10.6 + - - +
247O THR* 3.5 15.5 - - - +
248O ASP 3.2 0.8 - - - -
249O PHE* 1.3 81.9 - - - +
251O LYS* 1.3 63.7 + - - +
252O ILE 3.0 1.4 + - - -
253O ILE* 3.1 10.6 - - - +
254O ASN* 3.0 29.3 + - - +
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Residues in contact with LYS 251 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247O THR 4.1 3.5 + - - +
248O ASP* 3.3 24.0 - - + +
250O ALA* 1.3 77.7 - - - +
252O ILE* 1.3 62.0 + - + +
253O ILE 3.3 0.2 - - - -
254O ASN* 3.6 11.6 - - - +
255O LYS* 2.6 36.5 + - - +
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Residues in contact with ILE 252 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206O LEU* 4.5 31.3 - - + +
214O LEU* 4.7 22.0 - - + -
218O LEU* 4.6 12.1 - - + -
248O ASP* 3.1 20.4 - - + +
249O PHE* 2.9 20.7 + - + +
251O LYS* 1.3 86.9 - - + +
253O ILE* 1.3 60.0 + - + +
255O LYS* 3.7 5.2 + - + +
256O PRO* 3.0 21.5 - - - +
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Residues in contact with ILE 253 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211O ILE* 6.1 3.8 - - + -
214O LEU* 6.2 1.1 - - + -
249O PHE* 3.3 34.1 + - + +
250O ALA* 3.1 15.0 + - - +
252O ILE* 1.3 79.7 - - + +
254O ASN* 1.3 87.2 + - - +
255O LYS 3.3 0.2 - - - -
256O PRO* 3.1 17.6 - - - +
257O ASN* 3.4 10.8 + - - +
327O ARG* 3.7 26.7 - - + +
330O LEU* 4.2 24.5 - - + -
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Residues in contact with ASN 254 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250O ALA* 3.0 28.8 + - - +
251O LYS* 3.9 9.0 - - + +
253O ILE* 1.3 94.8 - - - +
255O LYS* 1.3 65.7 + - - +
257O ASN* 3.1 37.9 + - + +
258O GLU 3.8 8.5 + - - +
327O ARG* 4.4 3.3 + - - -
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Residues in contact with LYS 255 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202O GLN* 4.0 17.2 + - - +
206O LEU* 5.1 12.1 - - + -
251O LYS* 2.6 24.7 + - - +
252O ILE* 3.7 5.8 - - + +
254O ASN* 1.3 74.0 - - - +
256O PRO* 1.3 71.3 - - + +
258O GLU 4.1 1.2 - - - +
259O LEU* 3.6 46.8 - - + +
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Residues in contact with PRO 256 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201O ILE* 3.1 41.6 - - + +
202O GLN* 4.9 6.3 - - + +
206O LEU* 4.6 14.1 - - + -
207O HIS* 4.9 20.4 - - + +
252O ILE 3.0 27.6 - - - +
253O ILE* 3.1 15.7 - - - +
255O LYS* 1.3 81.4 - - + +
257O ASN* 1.3 66.9 + - - +
258O GLU* 3.3 2.4 + - - -
259O LEU* 4.9 0.5 + - - +
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Residues in contact with ASN 257 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201O ILE* 3.8 16.0 - - - +
253O ILE* 3.4 6.9 + - + +
254O ASN* 3.1 42.0 + - + +
256O PRO* 1.3 78.7 - - - +
258O GLU* 1.3 65.6 + - - +
286O ARG* 4.3 18.8 + - - +
321O GLN* 5.9 0.5 + - - -
322O LYS* 6.1 2.8 - - - +
327O ARG* 4.9 12.4 - - - +
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Residues in contact with GLU 258 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254O ASN 3.8 8.5 + - - +
255O LYS* 4.1 4.1 - - - +
256O PRO 3.9 1.8 - - - -
257O ASN* 1.3 86.7 - - - +
259O LEU* 1.3 86.7 + - - +
260O SER* 3.1 20.5 + - - -
263O LEU* 3.2 40.8 - - + +
272O ARG* 5.5 0.7 + - - -
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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