Contacts of the helix formed by residues 259 - 282 (chain B) in PDB entry 2FGY
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 259 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B CYS 4.5 0.2 + - - -
256B HIS* 3.1 15.9 + - - +
257B GLY 3.1 3.1 - - - +
258B SER* 1.3 75.2 - - - +
260B ASP* 1.3 60.7 + - - +
261B ARG* 3.2 23.5 + - - +
262B ALA* 3.2 21.4 + - + +
263B ALA* 3.0 28.1 + - - +
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Residues in contact with ASP 260 (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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241B TYR* 4.6 5.7 - - + -
242B HIS 4.6 1.4 - - - +
243B PHE* 3.4 40.6 - - + +
244B SER 4.9 1.2 + - - +
248B PRO* 4.2 23.7 - - - +
252B GLY* 4.8 3.5 - - - -
253B CYS 5.3 0.9 + - - -
258B SER 3.8 10.8 + - - +
259B ASN* 1.3 72.1 + - - +
261B ARG* 1.3 61.2 + - - +
263B ALA* 3.3 7.3 + - - +
264B LEU* 3.0 30.5 + - - +
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Residues in contact with ARG 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ASN* 3.2 15.1 + - - +
260B ASP* 1.3 77.1 - - - +
262B ALA* 1.3 59.9 + - - +
264B LEU* 3.6 8.5 + - + +
265B GLU* 3.0 59.4 + - + +
316B TYR* 5.0 11.6 + - - +
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Residues in contact with ALA 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B HIS* 4.0 16.1 + - + +
259B ASN* 3.2 31.8 + - + +
261B ARG* 1.3 78.6 - - - +
263B ALA* 1.3 64.7 + - - +
265B GLU* 4.2 5.8 - - - +
266B ALA* 3.1 26.3 + - - +
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Residues in contact with ALA 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B GLY 5.0 0.9 - - - +
202B SER* 5.7 0.2 + - - -
241B TYR* 4.0 14.8 - - + +
242B HIS 4.6 6.1 - - - +
253B CYS* 4.2 16.2 - - + -
256B HIS* 3.6 28.3 + - + -
259B ASN 3.0 16.0 + - - +
260B ASP* 3.6 8.7 - - - +
261B ARG 3.2 0.2 - - - -
262B ALA* 1.3 75.4 - - - +
264B LEU* 1.3 66.5 + - - +
266B ALA* 3.5 2.1 + - - +
267B ALA* 3.2 23.0 + - - +
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Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B TYR* 3.6 46.8 - - + +
260B ASP 3.0 18.2 + - - +
261B ARG* 3.7 8.3 - - + +
263B ALA* 1.3 77.1 - - - +
265B GLU* 1.3 63.6 + - + +
267B ALA* 3.2 4.0 + - - +
268B LEU* 2.9 29.2 + - + +
292B LEU* 3.7 17.9 - - + +
303B ARG* 6.2 0.9 - - - +
305B HIS* 4.0 10.1 - - + -
315B PRO* 3.8 37.5 - - + +
318B TYR* 6.1 0.2 - - + -
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Residues in contact with GLU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ARG* 3.0 46.2 + - + +
262B ALA* 3.5 5.3 + - - +
263B ALA 3.3 0.2 - - - -
264B LEU* 1.3 85.8 - - + +
266B ALA* 1.3 54.9 + - - +
268B LEU* 3.7 6.4 - - + +
269B THR* 2.8 38.7 + - - +
315B PRO* 4.8 13.6 - - + +
316B TYR* 5.1 5.4 + - - -
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Residues in contact with ALA 266 (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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201B GLY 4.7 0.2 - - - +
203B MET* 4.0 17.5 - - + +
256B HIS* 3.3 31.4 - - + +
262B ALA 3.1 18.7 + - - +
263B ALA 3.8 0.7 - - - +
265B GLU* 1.3 74.5 - - - +
267B ALA* 1.3 65.0 + - - +
269B THR* 3.4 6.4 + - - -
270B GLN* 3.0 24.9 + - - +
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Residues in contact with ALA 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B GLY 4.9 1.2 + - - -
202B SER* 4.2 20.4 - - - -
239B ALA* 3.9 12.8 - - + +
241B TYR* 4.2 11.2 - - + +
263B ALA 3.2 12.1 + - - +
264B LEU 3.6 7.4 - - - +
266B ALA* 1.3 78.0 - - - +
268B LEU* 1.3 61.9 + - - +
270B GLN* 3.5 7.1 + - - +
271B LEU* 3.2 26.5 + - - +
292B LEU* 3.6 20.2 - - + -
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Residues in contact with LEU 268 (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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264B LEU* 2.9 22.6 + - + +
265B GLU* 3.7 7.6 - - + +
267B ALA* 1.3 77.2 - - - +
269B THR* 1.3 60.0 + - - +
271B LEU* 3.3 6.8 + - + +
272B MET* 3.2 41.3 + - + +
290B ILE* 5.0 1.1 - - + -
292B LEU* 4.1 16.1 - - + +
313B LEU* 3.8 43.7 - - + +
314B ASN 4.9 0.2 - - - -
315B PRO* 4.0 34.1 - - + -
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Residues in contact with THR 269 (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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265B GLU* 2.8 25.7 + - - +
266B ALA* 3.8 6.7 - - - -
268B LEU* 1.3 73.1 - - - +
270B GLN* 1.3 60.5 + - - +
272B MET* 3.4 13.0 + - + +
273B LYS* 2.9 57.1 + - + +
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Residues in contact with GLN 270 (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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202B SER 4.3 4.0 - - - +
203B MET* 3.5 36.3 + - - +
204B PHE* 2.7 67.7 + - + +
206B ILE* 3.7 19.9 - - + +
266B ALA 3.0 16.5 + - - +
267B ALA 3.7 4.5 - - - +
268B LEU 3.3 0.2 - - - -
269B THR* 1.3 75.8 - - - +
271B LEU* 1.3 59.7 + - - +
273B LYS* 3.5 15.4 + - - +
274B PHE* 3.0 22.7 + - - +
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Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B PHE* 3.9 6.5 - - + -
237B LYS* 3.5 42.4 - - + +
239B ALA* 3.7 23.8 - - + +
267B ALA 3.2 16.6 + - - +
268B LEU* 3.5 9.4 - - - +
270B GLN* 1.3 77.7 - - - +
272B MET* 1.3 57.2 + - - +
274B PHE* 3.3 3.7 + - - +
275B ARG* 2.9 27.9 + - - +
290B ILE* 3.9 20.6 - - + +
291B LEU 3.4 28.9 - - - +
292B LEU* 4.0 10.1 - - + -
313B LEU* 3.9 15.3 - - + -
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Residues in contact with MET 272 (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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268B LEU* 3.2 40.2 + - + +
269B THR* 3.7 12.8 - - + +
270B GLN 3.4 0.2 - - - -
271B LEU* 1.3 72.1 - - - +
273B LYS* 1.3 61.6 + - + +
275B ARG* 3.4 9.5 + - - +
276B GLU* 2.9 38.7 + - - +
290B ILE* 4.6 10.3 - - + -
312B PHE* 6.2 5.6 - - + -
313B LEU 6.0 0.9 - - - +
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Residues in contact with LYS 273 (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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463A PRO 4.9 6.6 - - - +
464A GLY* 6.1 5.8 - - - -
468A ARG* 5.0 9.4 + - - +
203B MET* 6.0 2.4 - - - +
206B ILE* 3.6 23.4 - - + +
269B THR* 2.9 39.7 + - + +
270B GLN* 3.8 16.6 + - - +
272B MET* 1.3 77.0 - - + +
274B PHE* 1.3 56.2 + - - +
276B GLU* 3.5 16.2 + - - +
277B ALA* 3.1 26.5 + - - +
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Residues in contact with PHE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B PHE* 3.8 13.5 - + + -
206B ILE* 4.1 20.4 - - + +
209B ASP* 3.5 44.9 - - + -
210B LEU* 3.6 4.3 - - - -
213B TRP* 4.6 2.0 - - + -
235B TYR* 4.2 18.6 - + - -
237B LYS* 3.7 37.5 - - + -
270B GLN 3.0 17.3 + - - +
271B LEU 3.6 3.8 - - - +
272B MET 3.3 0.2 - - - -
273B LYS* 1.3 72.4 - - - +
275B ARG* 1.3 66.8 + - - +
277B ALA* 3.2 3.3 + - + +
278B VAL* 3.1 42.8 + - + +
288B ILE* 3.4 26.7 - - + -
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Residues in contact with ARG 275 (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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271B LEU 2.9 14.1 + - - +
272B MET* 3.5 11.4 - - - +
274B PHE* 1.3 78.2 - - - +
276B GLU* 1.3 59.6 + - + +
278B VAL* 3.4 1.6 + - - +
279B GLU* 3.0 59.6 + - + +
287B SER* 5.8 0.2 - - - -
288B ILE* 2.9 47.7 + - + +
289B ASP* 3.9 12.9 + - - +
290B ILE* 3.4 24.4 - - + +
310B LYS 4.5 4.7 + - - -
311B GLY* 2.9 41.1 + - - -
312B PHE* 3.9 23.6 - - - -
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Residues in contact with GLU 276 (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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463A PRO* 3.8 34.0 - - + +
272B MET* 2.9 25.0 + - + +
273B LYS* 3.7 19.6 - - - +
275B ARG* 1.3 77.2 - - + +
277B ALA* 1.3 57.1 + - - +
279B GLU* 4.5 6.7 - - - +
280B ASN* 2.8 46.6 + - - +
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Residues in contact with ALA 277 (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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462A VAL* 3.8 20.3 - - + +
463A PRO 5.2 0.4 + - - +
468A ARG* 4.4 4.5 - - - +
206B ILE* 3.9 21.1 - - + -
210B LEU* 4.4 17.0 - - + -
273B LYS 3.1 15.3 + - - +
274B PHE* 3.2 9.8 + - + +
276B GLU* 1.3 72.9 - - - +
278B VAL* 1.3 61.4 + - - +
281B ALA* 2.9 35.7 + - - +
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Residues in contact with VAL 278 (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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210B LEU* 4.2 9.6 - - + -
213B TRP* 3.7 44.2 - - + +
274B PHE* 3.1 44.4 + - + +
275B ARG* 4.0 3.4 - - - +
277B ALA* 1.3 75.8 - - - +
279B GLU* 1.3 62.1 + - + +
280B ASN 3.4 0.2 + - - -
282B HIS* 3.5 25.2 + - - -
286B ALA* 3.6 12.7 - - + +
287B SER* 4.2 7.0 - - - +
288B ILE* 4.1 18.8 - - + -
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Residues in contact with GLU 279 (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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275B ARG* 3.0 46.0 + - + +
276B GLU* 4.1 9.6 - - - +
278B VAL* 1.3 77.3 - - + +
280B ASN* 1.3 65.1 + - - +
282B HIS 3.1 17.2 - - - +
286B ALA 3.4 23.4 + - - +
287B SER* 4.2 16.5 - - - -
288B ILE 5.4 0.2 - - - +
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Residues in contact with ASN 280 (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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459A ASP* 4.5 2.1 - - - +
461A ASN* 3.3 35.1 - - - +
462A VAL* 3.8 9.9 - - + +
463A PRO* 3.7 18.2 - - + +
276B GLU* 2.8 36.0 + - - +
279B GLU* 1.3 83.5 + - - +
281B ALA* 1.3 62.3 + - - +
282B HIS 3.3 3.9 + - - +
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Residues in contact with ALA 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A ASP* 4.6 5.4 - - - +
462A VAL* 3.7 17.4 - - + +
210B LEU* 4.0 18.8 - - + -
214B GLU* 5.3 0.2 - - - +
277B ALA 2.9 20.3 + - - +
280B ASN* 1.3 78.4 - - - +
282B HIS* 1.3 76.2 + - + +
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Residues in contact with HIS 282 (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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215A LYS* 5.4 6.5 - - + -
218A LEU* 4.4 9.1 - - + +
222A ARG* 3.6 17.6 + - - +
210B LEU* 3.3 15.7 - - + +
213B TRP* 3.7 20.9 - + - -
214B GLU* 2.7 43.9 + - + +
278B VAL 3.5 19.0 + - - +
279B GLU 3.1 19.9 - - - +
280B ASN 3.3 2.6 - - - +
281B ALA* 1.3 94.1 + - + +
283B CYS* 1.3 62.9 + - - +
286B ALA* 3.7 10.2 + - + +
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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