Contacts of the helix formed by residues 233 - 259 (chain B) in PDB entry 5V2C
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 ASN 233 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 5.5 2.6 - - - +
135B LEU* 4.1 2.9 - - - +
230B ARG* 2.9 19.3 + - + +
231B MET 3.3 0.4 - - - -
232B GLY* 1.3 76.9 - - - +
234B ILE* 1.3 63.1 + - - +
235B GLU* 2.9 26.3 + - - +
236B THR* 2.9 33.6 + - - +
472B ARG 4.9 0.2 + - - -
473B THR* 4.2 24.5 + - - +
476B ARG* 3.7 48.2 + - - +
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Residues in contact with ILE 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 4.1 38.8 - - + +
19B LEU* 3.4 32.8 - - + -
133B LEU* 4.2 20.0 - - + -
135B LEU* 3.6 28.6 - - + +
138B MET* 6.2 0.4 - - + -
232B GLY 4.0 1.8 + - - -
233B ASN* 1.3 77.0 + - - +
235B GLU* 1.3 65.1 + - + +
236B THR 3.2 0.2 - - - -
237B VAL* 3.1 18.1 + - + +
238B LEU* 3.3 10.3 + - - +
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Residues in contact with GLU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 5.2 6.8 - - + +
233B ASN* 2.9 19.9 + - - +
234B ILE* 1.3 80.6 - - + +
236B THR* 1.4 63.6 + - - +
238B LEU* 3.3 10.8 + - + +
239B SER* 3.0 18.9 + - - -
469B HIS* 2.8 36.3 + - + +
472B ARG* 3.0 59.1 + - - +
473B THR* 3.2 16.0 + - - +
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Residues in contact with THR 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LEU* 2.7 36.5 + - + +
230B ARG 3.6 7.0 - - - +
231B MET* 4.3 11.0 - - + +
233B ASN 2.9 17.8 + - - +
235B GLU* 1.4 75.9 - - - +
237B VAL* 1.3 75.2 + - + +
239B SER* 3.3 6.0 + - - -
240B SER* 3.0 25.6 + - - +
473B THR* 3.4 24.9 + - - +
474B LEU* 6.0 0.2 - - - +
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Residues in contact with VAL 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 3.9 38.6 - - + -
234B ILE* 3.1 14.5 + - + +
236B THR* 1.3 82.8 - - + +
238B LEU* 1.3 58.8 + - - +
240B SER* 3.5 6.7 + - - +
241B SER* 2.8 47.7 + - - +
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ILE 3.3 7.0 + - - +
235B GLU* 3.3 17.7 + - + +
237B VAL* 1.3 79.1 - - - +
239B SER* 1.3 61.8 + - - +
241B SER* 3.9 6.0 - - - -
242B ILE* 2.9 51.1 + - + +
469B HIS* 3.6 37.0 - - + +
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Residues in contact with SER 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B GLU 3.0 13.0 + - - -
236B THR* 3.5 12.1 - - - -
237B VAL 3.2 0.2 - - - -
238B LEU* 1.3 78.5 - - - +
240B SER* 1.3 61.1 + - - +
242B ILE* 3.8 3.7 - - - +
243B ALA 3.1 10.7 + - - -
466B HIS* 3.0 36.3 + - - -
469B HIS* 3.8 8.4 - - - +
470B GLY* 3.1 39.2 + - - +
473B THR* 4.5 0.4 - - - -
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Residues in contact with SER 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B THR* 3.0 16.3 + - - +
237B VAL* 3.5 8.1 + - - +
239B SER* 1.3 77.7 - - - +
241B SER* 1.3 66.4 + - - +
243B ALA* 3.2 8.9 + - - +
244B ALA* 3.0 21.3 + - - +
466B HIS* 4.9 2.7 - - - -
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Residues in contact with SER 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B VAL* 2.8 37.2 + - - +
238B LEU* 3.9 7.2 - - - -
240B SER* 1.3 74.9 + - - +
242B ILE* 1.3 65.3 + - - +
244B ALA* 3.2 7.2 + - - +
245B VAL* 2.9 31.8 + - - +
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Residues in contact with ILE 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B LEU* 2.9 40.9 + - + +
239B SER 3.8 3.1 - - - +
241B SER* 1.3 76.1 - - - +
243B ALA* 1.4 59.7 + - - +
245B VAL* 3.3 7.8 + - - +
246B PHE* 2.9 27.2 + - - +
462B PHE* 3.1 50.6 - - + +
465B GLY* 4.0 9.0 - - - +
466B HIS* 3.5 10.1 - - - +
469B HIS* 3.7 29.8 - - + +
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Residues in contact with ALA 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B SER 3.1 7.2 + - - +
240B SER* 3.4 11.4 - - - +
241B SER 3.2 0.4 - - - -
242B ILE* 1.4 76.7 - - - +
244B ALA* 1.3 62.9 + - - +
246B PHE* 3.4 23.8 + - + -
247B PHE* 3.1 22.0 + - - +
466B HIS* 3.6 31.1 - - + +
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Residues in contact with ALA 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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240B SER 3.0 13.0 + - - +
241B SER* 3.2 11.2 + - - +
243B ALA* 1.3 75.6 - - - +
245B VAL* 1.3 59.2 + - + +
247B PHE* 3.3 12.4 + - + +
248B ALA* 3.0 27.9 + - - +
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Residues in contact with VAL 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B SER* 2.9 23.2 + - - +
242B ILE* 3.6 7.2 - - - +
244B ALA* 1.3 75.9 - - + +
246B PHE* 1.3 59.8 + - - +
248B ALA* 3.3 7.2 + - + +
249B ALA* 2.9 30.2 + - + +
462B PHE* 4.1 25.1 - - + -
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Residues in contact with PHE 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ILE 2.9 22.8 + - - -
243B ALA* 3.5 23.1 - - + -
245B VAL* 1.3 72.1 - - - +
247B PHE* 1.3 71.4 + - + +
249B ALA* 3.3 7.1 + - - +
250B PHE* 3.0 49.4 + + - -
459B ALA* 3.4 21.9 - - - +
462B PHE* 3.7 15.7 - - + -
463B PHE* 3.7 36.3 - + + -
466B HIS* 3.7 24.0 - + + -
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Residues in contact with PHE 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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243B ALA 3.1 13.4 + - - +
244B ALA* 3.4 14.1 - - - +
245B VAL 3.2 0.2 - - - -
246B PHE* 1.3 83.4 - - + +
248B ALA* 1.3 65.0 + - - +
250B PHE* 3.2 7.8 + - + +
251B VAL* 3.0 42.3 + - + +
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Residues in contact with ALA 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ALA 3.0 16.5 + - - +
245B VAL* 3.3 7.4 + - - +
247B PHE* 1.3 79.1 - - + +
249B ALA* 1.4 57.6 + - - +
251B VAL* 3.2 9.2 + - - +
252B VAL* 2.9 34.9 + - + +
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Residues in contact with ALA 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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245B VAL* 2.9 21.6 + - + +
246B PHE* 3.7 4.5 - - - +
247B PHE 3.2 0.4 - - - -
248B ALA* 1.4 73.3 - - - +
250B PHE* 1.3 63.4 + - - +
252B VAL* 3.4 12.3 - - + +
253B ALA* 3.0 24.3 + - - +
455B HIS* 4.0 18.8 - - + +
458B PHE* 5.3 1.8 - - + -
459B ALA* 3.8 22.4 - - + +
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Residues in contact with PHE 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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246B PHE* 3.0 46.7 + + - +
247B PHE* 3.2 6.5 + - + +
249B ALA* 1.3 76.3 - - - +
251B VAL* 1.3 59.5 + - + +
253B ALA* 3.3 6.1 + - + +
254B GLY* 2.9 25.3 + - - -
456B ALA* 4.0 20.2 - - + -
459B ALA* 3.5 26.2 - - + -
460B LEU* 3.7 27.4 - - + -
463B PHE* 5.6 2.5 - - + -
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Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B PHE* 3.0 44.8 + - + +
248B ALA* 3.2 10.5 + - - +
250B PHE* 1.3 77.9 - - + +
252B VAL* 1.3 62.7 + - + +
254B GLY* 3.2 2.8 + - - +
255B THR* 2.9 40.7 + - + +
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ALA* 2.9 21.1 + - + +
249B ALA* 3.4 18.6 - - - +
251B VAL* 1.3 76.5 - - + +
253B ALA* 1.3 64.3 + - - +
255B THR* 3.6 9.6 + - - +
256B MET* 3.1 26.0 + - - +
263B THR* 5.5 0.2 - - - +
451B PHE* 3.5 29.5 - - + -
455B HIS* 4.2 9.6 - - + -
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Residues in contact with ALA 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ALA 3.0 18.7 + - - +
250B PHE* 3.5 7.9 - - + +
251B VAL 3.2 0.2 - - - -
252B VAL* 1.3 79.9 - - - +
254B GLY* 1.3 58.0 + - - +
256B MET* 3.7 1.0 - - - +
257B TRP* 3.0 29.3 + - - +
451B PHE* 4.6 7.2 - - - -
452B THR* 3.6 21.0 - - + +
455B HIS* 4.3 1.1 - - + -
456B ALA* 4.0 30.5 - - + +
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Residues in contact with GLY 254 (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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250B PHE 2.9 15.5 + - - -
251B VAL* 3.2 2.6 + - - -
253B ALA* 1.3 77.3 - - - +
255B THR* 1.3 57.7 + - - +
257B TRP* 3.1 3.4 + - - -
258B TYR* 2.9 52.2 + - - -
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Residues in contact with THR 255 (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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192B PRO* 5.8 4.7 - - + -
251B VAL* 2.9 34.4 + - + +
252B VAL* 3.6 11.3 + - - +
254B GLY* 1.3 73.8 - - - +
256B MET* 1.3 62.4 + - - +
258B TYR* 5.1 1.1 - - - -
259B GLY* 2.9 21.9 + - - +
260B SER* 4.0 21.0 + - - +
262B THR* 4.6 4.2 + - - +
263B THR* 2.9 25.8 + - - +
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Residues in contact with MET 256 (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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65B PHE* 4.5 3.8 - - + -
68B ARG* 5.8 0.7 - - - +
252B VAL 3.1 20.3 + - - +
253B ALA 3.7 1.1 - - - +
255B THR* 1.3 79.7 + - - +
257B TRP* 1.4 59.6 + - - +
263B THR* 3.8 21.5 - - + +
268B PHE* 3.7 44.9 - - + -
448B ARG* 2.7 63.1 + - + +
451B PHE* 3.7 34.1 - - + -
452B THR* 3.3 18.6 - - - +
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Residues in contact with TRP 257 (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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253B ALA 3.0 18.2 + - - +
254B GLY* 3.1 5.6 + - - +
256B MET* 1.4 79.8 - - - +
258B TYR* 1.4 67.4 + + + +
259B GLY 3.8 0.2 + - - -
271B THR* 3.8 13.9 - - - -
272B ARG* 3.6 29.2 + - + +
273B TYR* 3.3 43.0 + + - -
319B PRO* 3.8 47.8 - - + -
320B ALA* 4.1 8.1 - - + -
448B ARG* 4.4 6.5 - - + -
449B GLY* 3.9 16.6 - - - -
452B THR* 3.7 28.0 - - + -
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Residues in contact with TYR 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B TYR* 2.8 20.9 + - - +
254B GLY* 2.9 36.6 + - - +
255B THR* 5.1 0.7 - - - -
257B TRP* 1.4 83.5 - + + +
259B GLY* 1.3 63.2 + - - +
271B THR* 4.0 11.1 + - - +
273B TYR* 3.4 44.8 + + - +
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Residues in contact with GLY 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B PRO* 4.8 3.1 - - - +
193B TYR* 3.1 25.3 + - - -
255B THR* 2.9 17.0 + - - +
256B MET 3.8 1.4 + - - -
257B TRP 3.4 2.4 - - - -
258B TYR* 1.3 82.7 - - - +
260B SER* 1.3 65.8 + - - -
263B THR* 3.3 8.1 - - - -
271B THR* 4.4 5.6 - - - -
448B ARG* 4.0 8.9 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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