Contacts of the helix formed by residues 259 - 282 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A CYS* 4.5 0.4 + - - +
256A HIS* 3.1 16.6 + - - +
257A GLY* 3.2 3.1 - - - +
258A SER* 1.3 74.6 - - - +
260A ASP* 1.3 61.0 + - - +
261A ARG* 3.1 24.0 + - - +
262A ALA* 3.2 21.8 + - + +
263A ALA* 2.9 28.7 + - - +
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Residues in contact with ASP 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A TYR* 4.6 5.8 - - + -
242A HIS 4.5 2.6 - - - +
243A PHE* 3.3 40.1 - - + +
244A SER 5.0 0.5 - - - +
248A PRO* 4.3 22.8 - - - +
252A GLY* 4.7 3.5 - - - -
253A CYS 5.2 0.5 + - - -
258A SER 3.7 12.2 + - - +
259A ASN* 1.3 70.5 + - - +
261A ARG* 1.3 59.6 + - - +
263A ALA* 3.4 6.8 + - - +
264A LEU* 2.9 31.5 + - - +
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Residues in contact with ARG 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ASN* 3.1 15.1 + - - +
260A ASP* 1.3 77.5 - - - +
262A ALA* 1.3 60.3 + - - +
264A LEU* 3.5 8.0 + - - +
265A GLU* 3.0 53.8 + - + +
316A TYR* 4.9 11.7 + - - +
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Residues in contact with ALA 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A HIS* 4.1 15.1 + - + +
259A ASN* 3.2 31.7 + - + +
261A ARG* 1.3 79.3 - - - +
263A ALA* 1.3 58.9 + - - +
265A GLU* 4.1 5.9 - - - +
266A ALA* 3.0 31.7 + - - +
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Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLY 5.1 0.9 - - - +
241A TYR* 3.9 14.7 - - + +
242A HIS 4.6 4.9 - - - +
253A CYS* 4.1 17.5 - - + -
256A HIS* 3.5 29.8 + - + +
259A ASN 2.9 16.5 + - - +
260A ASP* 3.4 8.7 + - - +
262A ALA* 1.3 74.4 - - - +
264A LEU* 1.3 66.2 + - - +
266A ALA* 3.6 1.7 + - - +
267A ALA* 3.3 22.9 + - - +
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A TYR* 3.6 47.2 - - + +
260A ASP 2.9 17.4 + - - +
261A ARG* 3.8 8.3 - - - +
263A ALA* 1.3 76.7 - - - +
265A GLU* 1.3 65.5 + - + +
267A ALA* 3.3 4.0 + - - +
268A LEU* 3.0 29.3 + - + +
292A LEU* 3.7 17.3 - - + +
303A ARG* 6.2 0.4 - - - +
305A HIS* 3.9 11.2 - - + -
315A PRO* 3.8 36.8 - - + +
318A TYR* 6.0 0.7 - - + -
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Residues in contact with GLU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A ARG* 3.0 45.0 + - + +
262A ALA* 4.1 5.0 - - - +
264A LEU* 1.3 85.4 - - + +
266A ALA* 1.3 58.4 + - - +
268A LEU* 3.8 6.1 - - + +
269A THR* 2.7 39.3 + - - +
315A PRO* 4.9 14.4 - - + +
316A TYR* 5.1 5.7 + - - -
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Residues in contact with ALA 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A GLY 4.8 0.2 - - - +
203A MET* 4.0 16.6 - - + +
256A HIS* 3.4 31.4 - - + +
262A ALA 3.0 19.3 + - - +
263A ALA 3.9 0.4 - - - +
265A GLU* 1.3 75.2 - - - +
267A ALA* 1.3 59.3 + - - +
269A THR* 3.5 6.2 + - - -
270A GLN* 3.1 28.9 + - - +
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Residues in contact with ALA 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A GLY 5.0 0.4 + - - -
202A SER* 4.2 21.5 - - - +
239A ALA* 3.8 13.8 - - + +
241A TYR* 4.3 10.5 - - + +
263A ALA 3.3 12.1 + - - +
264A LEU 3.6 8.3 - - - +
266A ALA* 1.3 74.5 - - - +
268A LEU* 1.3 64.2 + - - +
270A GLN* 3.5 6.6 + - - +
271A LEU* 3.2 26.5 + - - +
292A LEU* 3.7 19.1 - - + -
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Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A LEU* 3.0 23.4 + - + +
265A GLU* 3.8 8.1 - - + +
267A ALA* 1.3 74.8 - - - +
269A THR* 1.3 65.6 + - - +
271A LEU* 3.3 8.9 + - + +
272A MET* 3.1 47.6 + - + +
290A ILE* 4.9 0.4 - - + -
292A LEU* 4.0 14.2 - - + +
313A LEU* 3.8 44.4 - - + +
314A ASN 5.0 0.4 - - - -
315A PRO* 4.1 33.0 - - + -
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Residues in contact with THR 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A GLU* 2.7 27.5 + - - +
266A ALA* 3.9 5.6 - - - -
267A ALA 3.4 0.2 - - - -
268A LEU* 1.3 74.8 - - - +
270A GLN* 1.3 60.5 + - - +
272A MET* 3.3 13.1 + - + +
273A LYS* 2.9 55.5 + - + +
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Residues in contact with GLN 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A SER 4.6 2.5 - - - +
203A MET* 3.5 30.8 + - - +
204A PHE* 2.7 70.4 + - + +
206A ILE* 3.7 19.6 - - + +
266A ALA 3.1 16.0 + - - +
267A ALA* 3.7 7.6 - - - +
269A THR* 1.3 78.9 - - - +
271A LEU* 1.3 56.2 + - - +
273A LYS* 3.5 14.3 + - - +
274A PHE* 3.0 22.5 + - - +
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Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A PHE* 4.0 5.2 - - + -
237A LYS* 3.5 45.3 - - + +
239A ALA* 3.7 25.6 - - + +
267A ALA 3.2 16.4 + - - +
268A LEU* 3.5 9.0 - - - +
270A GLN* 1.3 76.5 - - - +
272A MET* 1.3 57.9 - - - +
274A PHE* 3.3 3.5 + - - +
275A ARG* 3.0 27.5 + - - +
290A ILE* 3.9 21.2 - - + +
291A LEU 3.4 27.4 - - - +
292A LEU* 4.0 9.6 - - + -
313A LEU* 4.0 14.8 - - + -
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Residues in contact with MET 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A LEU* 3.1 38.2 + - + +
269A THR* 3.6 13.9 - - + +
271A LEU* 1.3 73.7 - - - +
273A LYS* 1.3 59.5 - - + +
275A ARG* 3.3 10.2 + - - +
276A GLU* 2.9 38.8 + - - +
290A ILE* 4.6 10.8 - - + -
312A PHE* 6.2 4.0 - - + -
313A LEU 6.2 0.2 - - - +
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Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A MET* 6.1 1.8 - - - +
206A ILE* 3.5 23.3 - - + +
269A THR* 2.9 41.3 + - + +
270A GLN* 3.8 16.4 + - - +
271A LEU 3.4 0.2 - - - -
272A MET* 1.3 75.2 - - + +
274A PHE* 1.3 58.3 - - - +
276A GLU* 3.5 17.2 + - - +
277A ALA* 3.1 25.6 + - - +
463B PRO 4.9 6.5 - - - +
464B GLY* 6.1 6.3 - - - -
468B ARG* 5.0 7.2 + - - +
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Residues in contact with PHE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A PHE* 3.7 14.4 - + + -
206A ILE* 4.0 19.9 - - + +
209A ASP* 3.5 26.7 - - + -
210A LEU* 3.5 24.0 - - - -
213A TRP* 4.6 2.0 - - + -
235A TYR* 4.3 17.0 - + - -
237A LYS* 3.8 36.8 - - + -
270A GLN 3.0 17.2 + - - +
271A LEU 3.3 4.0 + - - +
273A LYS* 1.3 73.4 - - - +
275A ARG* 1.3 65.8 + - - +
277A ALA* 3.2 4.0 + - + +
278A VAL* 3.1 43.7 + - + +
288A ILE* 3.4 26.7 - - + -
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Residues in contact with ARG 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A LEU 3.0 14.2 + - - +
272A MET* 3.6 12.3 - - - +
274A PHE* 1.3 77.0 - - - +
276A GLU* 1.3 58.2 + - + +
278A VAL* 3.4 2.1 + - - +
279A GLU* 3.0 61.4 + - + +
288A ILE* 3.0 48.8 + - + +
289A ASP* 3.9 7.5 + - - +
290A ILE* 3.5 30.3 - - + +
310A LYS 4.6 3.9 + - - -
311A GLY* 3.1 41.3 + - - -
312A PHE* 3.9 23.3 - - - +
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Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A MET* 2.9 20.4 + - - +
273A LYS* 3.7 23.9 - - - +
275A ARG* 1.3 79.5 - - + +
277A ALA* 1.3 60.5 + - - +
279A GLU* 4.5 5.8 - - - +
280A ASN* 2.7 41.9 + - - +
463B PRO* 3.8 34.4 - - + +
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Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ILE* 4.0 20.4 - - + -
210A LEU* 4.3 17.5 - - + -
273A LYS 3.1 14.9 + - - +
274A PHE* 3.2 9.1 + - + +
276A GLU* 1.3 72.6 - - - +
278A VAL* 1.3 60.2 + - - +
281A ALA* 2.8 37.6 + - - +
462B VAL* 3.8 21.5 - - + +
463B PRO 5.2 0.4 + - - -
468B ARG* 4.4 4.3 - - - +
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Residues in contact with VAL 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A LEU* 4.1 18.6 - - + -
213A TRP* 3.8 40.6 - - + -
274A PHE* 3.1 42.4 + - + +
275A ARG 4.0 3.6 - - - +
277A ALA* 1.3 76.3 - - - +
279A GLU* 1.3 63.6 + - - +
282A HIS* 3.5 19.8 + - - -
286A ALA* 3.6 11.8 - - + +
287A SER* 4.2 7.6 - - - +
288A ILE* 4.0 20.6 - - + -
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Residues in contact with GLU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ARG* 3.0 48.8 + - + +
276A GLU* 4.2 7.6 - - - +
278A VAL* 1.3 76.5 - - - +
280A ASN* 1.3 67.7 + - - +
282A HIS 3.1 16.1 - - - +
286A ALA* 3.3 25.4 + - - +
287A SER* 4.1 16.5 - - - -
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Residues in contact with ASN 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A GLU* 2.7 37.6 + - - +
279A GLU* 1.3 83.6 + - - +
281A ALA* 1.3 63.0 + - - +
282A HIS 3.3 4.5 + - - +
459B ASP* 4.5 1.9 - - - +
461B ASN* 3.3 35.9 + - + +
462B VAL* 3.9 10.0 - - - +
463B PRO* 3.6 17.6 - - + +
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Residues in contact with ALA 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A LEU* 4.2 15.3 - - + -
214A GLU* 5.3 0.4 - - - +
277A ALA 2.8 20.4 + - - +
280A ASN* 1.3 77.7 - - - +
282A HIS* 1.3 80.9 + - + +
459B ASP* 4.5 5.1 - - - +
462B VAL* 3.8 17.0 - - + +
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Residues in contact with HIS 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LEU* 3.4 15.4 - - + +
213A TRP* 3.7 20.8 - + - -
214A GLU* 2.8 43.3 + - + +
278A VAL 3.5 19.8 + - - +
279A GLU 3.1 19.6 - - - +
280A ASN 3.3 2.5 - - - -
281A ALA* 1.3 94.1 + - + +
283A CYS* 1.3 62.9 + - - +
285A GLY 5.2 0.3 + - - -
286A ALA* 3.7 9.6 + - + +
215B LYS* 5.4 7.2 - - + -
218B LEU* 4.5 7.9 - - + +
222B ARG* 3.5 18.4 + - - +
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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