Contacts of the helix formed by residues 249 - 269 (chain D) in PDB entry 1OL1
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 LEU 249 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A THR 3.3 12.8 + - - +
27A GLY* 3.5 32.8 - - - +
28A GLU* 5.0 4.5 - - - +
204D PRO* 5.1 7.9 - - + -
205D ASP* 3.6 30.1 - - + +
206D ILE* 4.1 1.6 - - - -
247D SER* 5.5 1.1 - - - +
248D VAL* 1.3 93.7 - - - +
250D ARG* 1.3 59.5 + - + +
251D GLY* 3.3 3.8 - - - +
252D LYS* 3.0 20.4 + - + +
253D LEU* 3.2 2.4 + - - +
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Residues in contact with ARG 250 (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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205D ASP* 3.1 52.4 + - - +
206D ILE* 3.9 9.7 - - - +
210D MET* 3.8 24.4 - - - +
249D LEU* 1.3 73.6 - - + +
251D GLY* 1.3 64.5 + - - +
252D LYS 3.2 1.4 + - - -
253D LEU* 3.3 19.0 + - - +
254D GLN 4.6 0.2 + - - -
504H PFF 3.5 30.6 + - + -
505H NH2 4.2 24.0 + - - -
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Residues in contact with GLY 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D LEU* 3.3 3.2 - - - +
250D ARG* 1.3 86.4 - - - +
252D LYS* 1.3 69.2 + - - +
285D THR* 5.8 0.2 - - - +
286D TYR* 3.2 21.6 + - - -
504H PFF 5.5 1.1 - - - -
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Residues in contact with LYS 252 (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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24A LYS 3.8 18.9 + - - -
25A LEU* 3.1 29.6 - - - +
26A THR* 3.2 28.9 - - - +
27A GLY* 4.3 3.8 - - - +
248D VAL* 4.1 4.0 - - + -
249D LEU* 3.0 9.2 + - + +
251D GLY* 1.3 87.6 - - - +
253D LEU* 1.3 65.9 + - - +
254D GLN 3.2 2.9 - - - -
255D LEU* 3.1 17.3 + - + +
256D VAL* 3.0 23.0 + - - +
286D TYR* 4.3 11.5 - - + -
290D GLN* 4.6 14.5 + - - +
294D MET* 5.0 0.4 - - + -
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Residues in contact with LEU 253 (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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200D MET* 6.5 0.2 - - + -
206D ILE* 4.0 31.0 - - + -
210D MET* 4.3 26.9 - - + +
211D ARG* 4.7 3.4 - - + +
214D LEU* 3.6 23.9 - - + +
239D ILE* 5.0 0.2 - - + -
243D LEU* 4.5 20.2 - - + -
248D VAL* 4.1 9.6 - - + -
249D LEU 3.2 8.9 + - - +
250D ARG* 3.3 17.7 + - - +
252D LYS* 1.3 78.4 - - - +
254D GLN* 1.3 62.1 + - - +
256D VAL* 3.3 10.5 + - + +
257D GLY* 3.1 16.8 + - - -
504H PFF 4.1 13.7 - - + -
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Residues in contact with GLN 254 (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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214D LEU* 4.2 11.7 - - - -
217D TRP* 3.1 45.4 - - + -
250D ARG 4.6 0.2 + - - -
252D LYS 3.2 0.4 - - - -
253D LEU* 1.3 79.4 - - - +
255D LEU* 1.3 53.5 + - - +
257D GLY* 3.3 1.1 + - - -
258D THR* 2.4 41.6 + - - +
282D THR* 4.0 10.8 - - - -
285D THR* 4.7 1.6 + - - +
286D TYR* 3.4 23.7 + - + +
500H CIR 3.5 11.4 + - - -
501H CIR 3.5 9.4 - - - +
502H LEU* 3.0 44.3 + - + +
504H PFF 4.4 6.4 - - + -
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Residues in contact with LEU 255 (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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25A LEU* 4.4 9.9 - - + +
252D LYS* 3.1 17.4 + - - +
254D GLN* 1.3 76.4 - - - +
256D VAL* 1.3 64.8 + - - +
257D GLY 3.1 0.9 - - - -
258D THR* 3.6 3.5 + - - -
259D ALA* 3.1 21.0 + - - +
286D TYR* 3.4 37.1 + - + -
290D GLN* 3.9 23.3 - - + +
291D VAL* 3.9 29.2 - - + +
294D MET* 3.5 37.5 - - + -
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Residues in contact with VAL 256 (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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239D ILE* 4.4 20.6 - - + -
242D PHE* 3.8 38.1 - - + -
243D LEU* 5.1 3.8 - - + -
248D VAL* 3.9 16.2 - - + -
252D LYS* 3.0 13.1 + - + +
253D LEU* 3.5 13.7 - - + +
255D LEU* 1.3 74.3 - - - +
257D GLY* 1.3 59.6 + - - +
259D ALA* 4.1 1.4 - - - +
260D ALA* 3.3 21.5 + - - +
294D MET* 3.6 30.1 - - + -
298D VAL* 4.8 5.8 - - + +
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Residues in contact with GLY 257 (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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214D LEU* 4.4 10.5 - - - +
218D LEU* 4.3 7.5 - - - +
239D ILE* 3.9 20.6 - - - -
253D LEU 3.1 12.2 + - - -
254D GLN 3.3 3.8 + - - -
255D LEU 3.1 0.8 - - - -
256D VAL* 1.3 74.9 - - - +
258D THR* 1.3 57.1 + - - +
259D ALA 3.1 0.7 - - - -
260D ALA* 3.0 4.9 + - - +
261D MET* 2.7 35.1 + - - +
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Residues in contact with THR 258 (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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217D TRP* 4.1 13.7 - - - -
254D GLN* 2.4 34.9 + - - +
255D LEU* 3.7 11.7 - - - -
257D GLY* 1.3 69.7 - - - +
259D ALA* 1.3 58.0 + - - +
261D MET* 3.4 8.1 + - - +
262D LEU* 2.8 29.5 + - - +
278D PHE* 3.2 40.3 - - + +
281D ILE* 3.7 11.8 - - + +
282D THR* 4.5 4.7 - - + +
286D TYR* 4.8 1.3 - - + -
291D VAL* 4.3 15.3 - - + -
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Residues in contact with ALA 259 (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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255D LEU* 3.1 18.5 + - + +
256D VAL 4.1 2.9 - - - +
257D GLY 3.1 0.8 - - - -
258D THR* 1.3 75.3 - - - +
260D ALA* 1.3 59.7 + - - +
262D LEU* 3.1 8.5 + - - +
263D LEU* 2.9 33.2 + - - +
291D VAL* 4.5 7.4 - - - +
294D MET* 3.6 23.1 - - + +
295D GLU* 3.6 23.1 - - + +
298D VAL* 4.5 3.8 - - + -
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Residues in contact with ALA 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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235D ALA* 3.7 12.8 - - - +
238D TYR* 3.9 17.8 - - + -
239D ILE* 3.3 33.0 - - + +
256D VAL 3.3 8.3 + - - +
257D GLY 3.0 7.6 + - - +
259D ALA* 1.3 79.1 - - - +
261D MET* 1.3 51.2 + - - +
263D LEU* 3.1 5.8 + - - +
264D ALA* 2.8 37.2 + - - +
298D VAL* 5.1 4.9 - - + +
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Residues in contact with MET 261 (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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217D TRP* 6.4 0.2 - - + -
218D LEU* 3.5 50.0 - - + +
221D VAL* 4.1 9.9 - - + -
222D GLY* 4.4 10.3 - - - +
227D LEU* 4.5 8.7 - - + -
231D THR* 4.4 13.7 - - + +
232D LEU* 4.0 22.7 - - + -
235D ALA* 3.6 18.4 - - - +
257D GLY 2.7 14.9 + - - +
258D THR* 3.6 10.3 - - - +
260D ALA* 1.3 71.6 - - - +
262D LEU* 1.3 57.0 + - - +
264D ALA* 4.0 0.5 - - - +
265D SER* 2.6 36.3 + - - +
278D PHE* 3.7 19.7 - - + -
281D ILE* 6.3 0.7 - - + -
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Residues in contact with LEU 262 (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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258D THR 2.8 18.1 + - - +
259D ALA* 3.4 7.0 - - - +
261D MET* 1.3 75.0 - - - +
263D LEU* 1.3 64.5 + - - +
265D SER* 3.3 4.0 + - - -
266D LYS* 3.0 35.9 + - + +
272D PRO* 5.3 2.9 - - + -
273D PRO 4.1 7.9 - - - +
275D VAL* 3.9 26.9 - - + +
278D PHE* 3.6 34.3 - - + -
291D VAL* 4.3 13.7 - - + -
292D LEU* 5.3 1.1 - - + -
295D GLU* 3.1 39.3 - - + +
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Residues in contact with LEU 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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49C ILE* 3.4 34.4 - - + +
238D TYR* 4.1 14.8 - - + -
259D ALA 2.9 17.8 + - - +
260D ALA 3.8 3.4 - - - +
262D LEU* 1.3 76.2 - - - +
264D ALA* 1.3 64.8 + - - +
266D LYS* 3.0 16.5 + - + +
267D PHE* 3.0 13.9 + - - +
295D GLU* 3.6 33.9 - - + +
298D VAL* 3.5 33.0 - - + -
299D LEU* 3.7 22.2 - - + -
306D LEU* 4.1 8.1 - - + +
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Residues in contact with ALA 264 (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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231D THR* 3.4 32.2 + - + +
234D LEU* 4.0 5.6 - - + +
235D ALA* 3.6 15.3 - - + +
238D TYR* 3.7 16.8 - - + -
260D ALA 2.8 19.0 + - - +
261D MET 4.0 1.3 - - - +
263D LEU* 1.3 78.9 - - - +
265D SER* 1.3 60.9 + - - +
267D PHE* 3.4 2.1 + - - +
268D GLU* 3.2 26.0 + - - +
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Residues in contact with SER 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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227D LEU* 3.6 14.9 - - - +
231D THR* 3.5 17.2 - - - +
261D MET 2.6 23.2 + - - -
262D LEU* 3.5 6.7 - - - -
264D ALA* 1.3 76.9 - - - +
266D LYS* 1.3 60.1 + - - +
267D PHE 3.0 0.2 + - - -
269D GLU* 2.8 45.5 + - - +
272D PRO* 4.2 5.9 - - - +
273D PRO* 4.1 16.8 - - - -
278D PHE* 3.9 4.7 - - - -
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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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42C GLU* 3.1 24.8 + - - -
44C VAL* 2.6 30.5 + - - +
45C PRO* 5.1 1.1 - - - -
46C SER* 3.3 31.7 - - - +
49C ILE* 4.5 14.6 - - + +
50C ARG* 3.2 22.5 + - - -
262D LEU* 3.0 30.3 + - + +
263D LEU* 3.0 12.7 + - - +
265D SER* 1.3 75.8 - - - +
267D PHE* 1.3 57.3 + - - +
269D GLU 4.5 0.3 - - - +
272D PRO* 4.1 21.0 - - + +
275D VAL* 5.3 0.2 - - - -
295D GLU* 2.5 33.0 + - - +
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Residues in contact with PHE 267 (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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49C ILE* 4.5 8.3 - - + -
50C ARG* 3.2 34.6 + - + +
53C SER* 3.5 31.4 - - - -
54C LEU* 4.0 14.8 - - + -
150C ARG* 3.9 8.1 + - - -
151C ALA* 4.3 14.6 - - + -
234D LEU* 4.3 14.8 - - + -
238D TYR* 4.4 10.5 - - - +
263D LEU 3.0 10.9 + - - +
264D ALA 3.7 7.9 - - - +
265D SER 3.0 0.2 - - - -
266D LYS* 1.3 79.3 - - - +
268D GLU* 1.3 73.3 + - - +
269D GLU 3.9 0.2 - - - -
306D LEU* 4.2 10.1 - - + -
307D ALA* 3.2 38.4 - - + -
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Residues in contact with GLU 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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150C ARG* 3.0 34.1 + - - +
151C ALA* 4.5 7.3 - - - +
154C VAL* 3.2 31.2 - - - +
155C PRO 5.1 1.2 - - - +
228D GLN* 4.8 11.1 - - + +
230D GLU* 3.5 29.8 - - + +
231D THR* 3.6 11.4 - - - +
234D LEU* 4.0 10.6 - - + +
264D ALA 3.2 12.1 + - - +
265D SER 3.1 1.6 + - - -
267D PHE* 1.3 93.6 - - - +
269D GLU* 1.3 62.7 + - - +
270D ILE* 4.1 2.4 + - - +
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Residues in contact with GLU 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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50C ARG* 2.8 22.6 + - - -
150C ARG* 5.0 0.2 - - - -
226D LYS 4.1 3.3 - - - +
227D LEU* 3.3 37.9 - - + +
228D GLN* 2.9 37.5 + - - +
231D THR* 2.8 25.3 + - - +
265D SER* 2.8 28.8 + - - +
266D LYS 4.5 0.3 - - - +
268D GLU* 1.3 73.5 - - - +
270D ILE* 1.3 65.0 + - - +
271D TYR* 4.0 18.8 - - - +
272D PRO* 4.4 2.9 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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