Contacts of the helix formed by residues 247 - 273 (chain D) in PDB entry 2F8J
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 HIS 247 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 3.4 34.2 - - + +
40D GLU* 4.7 12.3 - - + -
243D VAL* 3.1 28.4 + - + +
244D ALA 3.1 7.4 + - - -
246D ASP* 1.3 100.6 + - + +
248D ARG* 1.3 62.4 + - - +
249D GLU* 3.3 4.2 + - - -
250D ILE* 3.9 8.1 + - + +
251D PHE* 3.3 15.9 - - - -
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Residues in contact with ARG 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D LYS* 4.0 6.5 + - - +
67D SER* 3.8 14.8 + - - -
68D TYR* 3.6 60.3 + - + +
204D PHE* 4.6 11.4 - - + -
244D ALA 4.0 6.1 - - - +
245D LEU* 3.0 34.1 + - + +
246D ASP 3.9 0.8 - - - -
247D HIS* 1.3 74.1 - - - +
249D GLU* 1.3 65.6 + - - +
250D ILE 3.3 0.2 - - - -
251D PHE* 3.1 12.3 + - - +
252D GLU* 2.9 42.6 + - - +
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Residues in contact with GLU 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D HIS 3.3 2.2 - - - -
248D ARG* 1.3 77.4 - - - +
250D ILE* 1.3 63.0 + - - +
252D GLU* 3.2 15.6 + - - +
253D GLU* 3.0 22.5 + - - +
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Residues in contact with ILE 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D PRO* 4.4 20.6 - - + -
37D LEU* 5.8 1.8 - - + -
247D HIS* 3.9 9.3 + - + +
248D ARG 3.3 0.4 - - - -
249D GLU* 1.3 77.9 - - - +
251D PHE* 1.3 60.6 + - + +
253D GLU* 3.3 8.6 + - + +
254D ARG* 3.1 46.0 + - + +
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Residues in contact with PHE 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D PHE* 3.5 24.2 - + - -
34D PRO* 4.0 5.4 - - + -
37D LEU* 3.8 20.0 - - + -
203D ALA* 3.7 23.6 - - + +
204D PHE* 3.6 42.8 - + + -
244D ALA* 3.5 21.3 - - + -
247D HIS 3.3 27.4 - - - -
248D ARG* 3.1 8.8 + - + +
250D ILE* 1.3 75.8 - - + +
252D GLU* 1.3 59.1 + - + +
254D ARG* 3.4 31.7 + - - +
255D THR* 2.9 34.8 + - - +
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Residues in contact with GLU 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D TYR* 5.6 2.1 - - - -
248D ARG* 2.9 40.8 + - + +
249D GLU* 3.4 14.5 - - - +
251D PHE* 1.3 76.1 - - + +
253D GLU* 1.3 57.6 + - - +
255D THR* 3.5 7.4 + - - -
256D LYS* 3.0 28.4 + - - +
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Residues in contact with GLU 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D GLU 3.0 12.0 + - - +
250D ILE* 3.3 10.3 + - + +
252D GLU* 1.3 73.6 - - - +
254D ARG* 1.3 61.4 + - + +
256D LYS* 3.4 7.5 + - - +
257D PHE* 3.1 27.2 + - - +
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Residues in contact with ARG 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ASN* 4.7 6.7 - - - +
31D PHE* 3.4 46.5 - - + +
32D PRO* 2.8 34.3 + - - +
33D PHE* 4.4 0.2 - - - +
34D PRO* 3.6 34.4 - - - +
203D ALA 5.5 1.8 - - - +
205D SER* 4.0 8.6 + - - -
250D ILE* 3.1 30.5 + - + +
251D PHE* 3.6 23.6 - - - +
253D GLU* 1.3 74.6 - - + +
255D THR* 1.3 64.2 + - - +
257D PHE* 3.3 7.9 + - - +
258D ILE* 3.0 32.7 + - + +
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Residues in contact with THR 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ASN* 5.8 0.5 + - - +
178D GLU* 3.2 31.9 - - + +
179D PHE* 4.2 11.5 - - + -
203D ALA* 4.3 20.4 + - - +
251D PHE 2.9 20.3 + - - -
252D GLU* 3.7 8.2 - - - +
254D ARG* 1.3 75.0 - - - +
256D LYS* 1.3 58.9 + - - +
258D ILE* 3.2 10.4 + - - +
259D VAL* 3.0 35.8 + - + +
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Residues in contact with LYS 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D GLU 3.0 18.0 + - - +
253D GLU* 3.6 8.7 - - - +
254D ARG 3.3 0.2 - - - -
255D THR* 1.3 77.0 - - - +
257D PHE* 1.3 61.6 + - - +
259D VAL* 3.1 12.0 - - + +
260D GLU* 3.1 50.4 + - + +
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Residues in contact with PHE 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D PHE* 3.5 36.8 - + + -
253D GLU 3.1 13.8 + - - +
254D ARG* 3.5 9.0 - - - +
255D THR 3.3 0.2 - - - -
256D LYS* 1.3 77.1 - - - +
258D ILE* 1.3 63.2 + - + +
260D GLU* 3.4 12.1 + - + +
261D GLU* 2.9 59.0 + - + +
319D GLY 3.9 17.7 - - - -
320D LYS* 4.5 2.7 - - + -
321D ARG* 3.9 27.1 - - + -
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Residues in contact with ILE 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ASN* 3.4 30.5 - - - +
30D PRO* 3.7 24.0 - - + -
31D PHE* 4.5 2.2 - - + -
179D PHE* 4.0 19.3 - - + -
254D ARG 3.0 23.7 + - - +
255D THR* 3.2 4.5 + - - +
257D PHE* 1.3 86.9 - - + +
259D VAL* 1.3 58.6 + - + +
261D GLU* 3.4 2.3 + - - +
262D ARG* 2.9 28.1 + - + +
281D GLY 5.2 0.4 - - - +
282D ASN* 3.7 31.6 - - + -
318D ILE* 4.0 21.2 - - + +
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Residues in contact with VAL 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D PHE* 3.6 41.3 - - + +
255D THR* 3.0 26.2 + - + +
256D LYS* 3.1 23.3 - - + +
258D ILE* 1.3 77.5 - - + +
260D GLU* 1.3 59.2 + - + +
262D ARG* 3.3 23.3 + - - +
263D GLU* 3.0 34.0 + - + +
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Residues in contact with GLU 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D LYS* 3.1 40.4 + - + +
257D PHE* 3.7 11.9 - - + +
259D VAL* 1.3 76.1 - - + +
261D GLU* 1.3 63.4 + - + +
263D GLU* 3.4 5.3 + - - +
264D ARG* 2.9 30.1 + - - +
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Residues in contact with GLU 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D PHE* 2.9 49.0 + - + +
258D ILE 3.7 3.8 - - - +
260D GLU* 1.3 77.2 - - + +
262D ARG* 1.3 57.0 + - - +
264D ARG* 2.8 39.0 + - - +
265D MET* 3.0 33.6 + - - +
318D ILE* 4.0 8.3 - - + -
321D ARG* 3.8 14.6 - - - +
324D ASN* 2.8 37.1 + - - +
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Residues in contact with ARG 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D PHE 3.0 26.5 + - - -
258D ILE 2.9 17.9 + - - +
259D VAL* 3.4 22.5 + - - +
260D GLU 3.2 0.2 - - - -
261D GLU* 1.3 77.2 - - - +
263D GLU* 1.3 84.6 + - - +
265D MET* 3.3 3.6 + - - +
266D LYS* 2.9 40.2 + - + +
279D SER 3.3 22.1 + - - +
280D ARG* 3.3 21.2 - - - +
281D GLY 3.1 28.8 + - - +
283D PHE 3.9 20.9 - - - +
284D VAL* 5.4 1.1 - - + -
318D ILE* 3.9 17.7 - - + +
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Residues in contact with GLU 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D VAL* 3.0 20.9 + - + +
260D GLU* 4.0 5.4 - - - +
262D ARG* 1.3 96.3 + - - +
264D ARG* 1.3 60.0 + - - +
266D LYS* 2.8 39.4 + - - +
267D SER* 3.0 32.7 + - - -
280D ARG* 4.6 2.9 + - - -
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Residues in contact with ARG 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D GLU 2.9 17.4 + - - +
261D GLU* 2.8 48.4 + - - +
263D GLU* 1.3 76.7 - - - +
265D MET* 1.3 68.6 + - - +
267D SER* 3.5 5.9 + - - -
268D ALA* 3.1 19.4 + - - -
321D ARG* 5.1 2.2 - - - +
324D ASN* 4.1 9.5 - - - +
325D ASP* 2.5 34.9 + - - +
328D LEU* 3.8 23.0 - - + +
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Residues in contact with MET 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D GLU 3.0 17.1 + - - +
262D ARG* 3.7 4.5 - - - +
264D ARG* 1.3 85.9 - - - +
266D LYS* 1.3 65.6 + - - +
268D ALA* 3.3 1.4 + - - -
269D LEU* 2.9 22.2 + - - -
284D VAL* 5.3 11.9 - - + -
316D ILE* 5.0 12.1 - - + +
317D THR 5.7 2.2 - - - +
318D ILE* 3.5 29.8 - - + -
324D ASN* 3.8 24.5 - - + +
327D ILE* 4.0 31.2 - - + -
328D LEU* 4.1 29.5 - - + +
331D LEU* 6.2 0.2 - - + -
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Residues in contact with LYS 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262D ARG* 2.9 23.4 + - + +
263D GLU* 2.8 45.3 + - - +
264D ARG 3.4 0.2 - - - -
265D MET* 1.3 75.5 - - - +
267D SER* 1.3 57.6 + - - +
269D LEU 3.5 0.2 + - - -
270D ARG* 3.0 36.2 + - - +
276D ILE* 3.4 20.0 - - + +
277D THR 3.8 20.4 - - - +
278D ASP* 2.7 29.8 + - - -
279D SER* 3.0 26.9 + - - +
280D ARG* 4.1 1.6 - - - +
284D VAL* 4.8 11.9 - - + -
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Residues in contact with SER 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D GLU* 3.0 18.1 + - - -
264D ARG* 3.7 6.7 - - - -
265D MET 3.3 0.2 - - - -
266D LYS* 1.3 74.1 - - - +
268D ALA* 1.3 59.1 - - - +
270D ARG* 3.3 10.2 + - - +
271D GLU* 3.0 28.9 + - - +
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Residues in contact with ALA 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264D ARG 3.1 11.9 + - - -
265D MET 3.3 2.9 + - - -
267D SER* 1.3 78.5 - - - +
269D LEU* 1.3 55.9 - - - +
271D GLU* 3.4 8.2 + - - +
272D MET* 3.0 42.0 + - - +
328D LEU* 5.0 7.9 - - - -
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Residues in contact with LEU 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D MET 2.9 15.8 + - - -
266D LYS* 3.9 1.6 - - - +
268D ALA* 1.3 73.9 - - - +
270D ARG* 1.3 64.1 + - - +
272D MET* 3.2 19.5 + - - +
273D GLY 3.2 0.2 + - - -
274D TYR* 3.1 36.3 + - - +
276D ILE* 5.2 6.5 - - - -
328D LEU* 4.8 3.0 - - - +
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Residues in contact with ARG 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D LYS* 3.0 24.3 + - - +
267D SER* 3.3 9.2 + - - +
269D LEU* 1.3 74.8 - - - +
271D GLU* 1.3 57.2 + - - +
273D GLY* 2.8 22.5 + - - -
274D TYR 4.2 8.7 - - - +
276D ILE* 3.8 21.7 - - + +
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Residues in contact with GLU 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267D SER 3.0 13.8 + - - +
268D ALA* 3.6 11.7 - - - +
270D ARG* 1.3 75.6 - - - +
272D MET* 1.3 60.9 + - + +
273D GLY 3.5 0.7 + - - -
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Residues in contact with MET 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D ALA* 3.0 21.9 + - - +
269D LEU* 3.5 10.5 - - - +
270D ARG 3.1 0.6 - - - -
271D GLU* 1.3 76.5 - - + +
273D GLY* 1.3 57.6 + - - +
274D TYR* 3.6 25.6 - - + -
328D LEU* 3.5 43.7 - - + +
331D LEU* 4.0 3.4 - - + +
332D GLU* 3.6 41.5 - - + +
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Residues in contact with GLY 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D ARG 2.8 14.1 + - - -
271D GLU 3.3 1.2 + - - -
272D MET* 1.3 78.5 - - - +
274D TYR* 1.3 64.5 + - - +
275D ARG 3.7 1.4 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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