Contacts of the helix formed by residues 249 - 276 (chain D) in PDB entry 1ZQ1
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 ASP 249 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D LYS* 2.7 37.5 + - - +
247D GLU* 3.1 9.0 - - + +
248D LEU* 1.3 79.5 - - - +
250D MET* 1.3 59.7 + - + +
251D ILE 3.4 0.4 - - - -
252D PRO* 3.3 16.5 - - - +
253D ILE* 4.4 4.3 - - - +
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Residues in contact with MET 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D VAL* 4.5 2.0 - - + -
246D GLN* 3.1 41.5 - - + +
247D GLU* 2.9 23.5 + - + +
249D ASP* 1.3 78.2 - - + +
251D ILE* 1.3 64.4 + - - +
252D PRO 3.4 0.4 - - - -
253D ILE* 2.8 38.3 - - - +
254D ILE* 2.9 21.3 + - + +
415D LEU 3.7 7.0 - - - +
416D PRO* 3.0 30.5 - - + +
417D ASP 4.5 0.4 - - - -
418D GLY* 4.1 11.0 - - - +
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Residues in contact with ILE 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 4.9 8.1 - - + -
202D ALA* 3.6 29.8 - - + -
203D LYS* 3.8 7.0 - - - +
206D ALA* 3.2 33.4 - - + -
228D GLN* 4.1 11.9 - - + +
230D LEU* 4.3 11.0 - - + -
245D VAL* 4.3 17.4 - - + +
247D GLU 4.4 1.8 - - - +
248D LEU* 3.6 21.8 - - + +
250D MET* 1.3 78.1 - - - +
252D PRO* 1.3 71.7 - - + +
254D ILE* 3.2 4.4 + - - +
255D ILE* 3.0 35.5 + - + +
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Residues in contact with PRO 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D PRO* 3.5 32.6 - - + +
200D GLU* 3.3 24.0 - - - +
203D LYS* 3.5 33.9 - - + +
248D LEU 3.6 7.0 - - - +
249D ASP 3.3 17.0 - - - +
251D ILE* 1.3 95.9 - - + +
253D ILE* 1.3 61.2 + - - +
256D GLU* 3.4 15.4 + - - +
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Residues in contact with ILE 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D ASP 4.4 3.4 - - - +
250D MET* 2.8 48.5 - - - +
252D PRO* 1.3 74.4 - - - +
254D ILE* 1.3 62.7 + - + +
256D GLU* 2.8 25.6 + - + +
257D ARG* 2.8 37.1 + - + +
417D ASP 3.5 24.7 - - - +
418D GLY* 4.0 4.5 - - - -
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Residues in contact with ILE 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D LEU* 4.2 9.9 - - + -
242D ILE* 3.8 32.3 - - + +
245D VAL* 3.7 21.5 - - + -
246D GLN* 4.0 13.2 - - - +
250D MET* 2.9 24.4 + - + +
251D ILE* 3.8 3.6 - - - +
253D ILE* 1.3 78.1 - - + +
255D ILE* 1.3 63.3 + - - +
256D GLU 3.2 0.7 + - - -
257D ARG* 3.4 2.1 + - - +
258D GLU* 3.3 21.5 + - - +
414D ALA* 3.4 28.3 - - + -
415D LEU 4.6 0.9 - - - +
418D GLY* 3.5 30.4 - - - +
420D THR* 5.1 3.8 - - + +
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Residues in contact with ILE 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D LEU* 4.3 4.5 - - + -
17D VAL* 3.6 37.0 - - + -
199D PRO* 4.0 23.8 - - + -
202D ALA* 3.3 33.9 - - + -
230D LEU* 3.6 19.3 - - + -
232D VAL* 4.2 13.0 - - + +
251D ILE* 3.0 27.6 + - + +
252D PRO 3.9 4.9 - - - +
254D ILE* 1.3 77.2 - - - +
256D GLU* 1.3 57.1 + - - +
258D GLU* 3.8 5.8 - - - +
259D VAL* 3.1 23.6 + - - +
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Residues in contact with GLU 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D LYS* 3.1 42.5 + - - +
8D PHE* 3.7 12.1 - - + -
10D TYR* 2.9 26.0 + - + +
199D PRO* 4.9 3.2 - - + +
252D PRO 3.4 10.8 + - - +
253D ILE* 2.8 12.5 + - + +
255D ILE* 1.3 77.9 - - - +
257D ARG* 1.3 60.1 + - + +
258D GLU 2.9 5.6 - - - -
259D VAL* 3.1 4.8 + - - +
260D GLU* 2.8 31.8 + - - +
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Residues in contact with ARG 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D ILE* 2.8 29.4 + - + +
254D ILE 3.4 1.3 + - - +
256D GLU* 1.3 77.6 + - + +
258D GLU* 1.3 56.7 + - - +
260D GLU* 3.6 19.2 + - - +
261D ARG* 3.1 14.9 + - - +
328D GLN* 2.8 26.1 + - - +
329D PRO* 3.6 31.8 - - - +
417D ASP* 3.1 25.8 + - - +
418D GLY 3.2 26.7 - - - +
419D ASN* 3.0 34.3 + - - +
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Residues in contact with GLU 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D VAL* 3.9 27.8 - - + -
240D ILE* 3.1 20.5 - - + +
242D ILE* 4.2 9.4 - - + -
254D ILE 3.3 16.0 + - - +
255D ILE 3.8 6.1 - - - +
256D GLU 2.9 0.2 - - - -
257D ARG* 1.3 77.9 - - - +
259D VAL* 1.3 66.0 + - - +
260D GLU 2.9 1.7 + - - -
261D ARG* 3.0 33.0 + - - +
262D GLN* 2.8 41.7 + - - +
328D GLN* 4.2 1.4 + - - -
412D ARG* 4.6 0.3 - - - -
420D THR* 3.1 31.0 + - - +
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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
----------------------------------------------------------
8D PHE* 3.9 14.6 - - + -
10D TYR* 4.0 17.0 - - + -
13D LEU* 3.4 33.2 - - + -
15D LEU* 3.6 30.1 - - + -
232D VAL* 4.5 4.3 - - + -
234D ILE* 3.3 19.8 - - + +
255D ILE* 3.1 17.7 + - + +
256D GLU 3.1 6.7 + - - +
258D GLU* 1.3 77.1 - - - +
260D GLU* 1.3 56.5 + - - +
263D LEU* 3.0 27.5 + - - +
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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
----------------------------------------------------------
7D LYS* 4.4 18.1 + - - -
8D PHE* 3.6 24.3 - - + -
256D GLU* 2.8 18.9 + - - +
257D ARG* 3.6 26.0 + - - +
259D VAL* 1.3 76.4 - - - +
261D ARG* 1.3 65.9 + - - +
263D LEU* 3.1 4.8 + - - +
264D ASN* 3.0 32.6 + - - +
326D GLU* 5.6 0.7 - - - +
327D ILE 3.6 12.7 - - - +
328D GLN* 4.2 0.8 - - - -
329D PRO* 3.3 28.8 - - - +
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Residues in contact with ARG 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D ILE* 2.9 36.6 - - - +
257D ARG 3.1 8.7 + - - +
258D GLU* 3.0 15.7 + - - +
260D GLU* 1.3 79.5 - - - +
262D GLN* 1.3 56.8 + - - +
264D ASN* 3.4 1.9 + - - +
265D LEU* 2.9 48.4 + - + +
327D ILE* 3.5 33.2 + - + +
328D GLN* 3.4 34.3 - - + +
336D GLU* 2.6 34.9 + - - -
407D VAL* 4.9 0.8 - - - +
410D GLU* 4.0 7.9 + - - -
412D ARG* 2.5 43.7 - - - +
420D THR* 4.3 0.7 - - - -
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Residues in contact with GLN 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D VAL* 3.5 12.7 + - - +
234D ILE* 3.4 44.9 + - + +
237D GLY* 3.6 4.8 - - - -
238D ALA 3.1 27.8 + - - -
240D ILE* 3.0 26.5 - - + +
258D GLU* 2.8 28.8 + - - +
261D ARG* 1.3 72.9 - - - +
263D LEU* 1.3 65.5 + - - +
265D LEU* 3.9 6.9 - - - +
266D LEU* 3.3 30.4 + - + +
407D VAL* 3.8 21.8 - - + +
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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
----------------------------------------------------------
8D PHE* 3.8 33.2 - - + -
13D LEU* 3.5 38.8 - - + -
234D ILE* 4.2 6.3 - - + +
259D VAL 3.0 17.7 + - - +
260D GLU* 3.1 6.0 + - - +
262D GLN* 1.3 77.3 - - - +
264D ASN* 1.3 61.0 + - - +
266D LEU* 3.9 10.0 - - + +
267D LYS* 3.1 55.0 + - + +
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Residues in contact with ASN 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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260D GLU* 3.0 26.0 + - - +
261D ARG 3.9 0.7 - - - +
263D LEU* 1.3 75.6 - - - +
265D LEU* 1.3 66.9 + - - +
266D LEU 3.1 1.6 - - - -
267D LYS* 3.0 32.2 + - - +
268D ILE* 3.0 20.5 + - + +
325D ARG* 5.8 3.6 - - - -
326D GLU 3.9 7.5 + - - +
327D ILE* 2.7 47.3 + - + +
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Residues in contact with LEU 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D ARG* 2.9 45.8 + - + +
262D GLN* 3.9 5.2 - - - +
263D LEU 3.5 0.2 - - - -
264D ASN* 1.3 75.7 - - - +
266D LEU* 1.3 58.2 + - - +
268D ILE* 3.1 13.2 + - + +
269D ARG* 3.0 23.4 + - - +
327D ILE* 3.8 23.1 - - + -
333D LEU* 3.9 19.1 - - + -
336D GLU* 4.7 0.9 - - - +
399D ARG* 3.3 32.8 - - - +
403D ALA* 5.0 2.4 - - + +
406D GLY 5.2 4.8 - - - +
407D VAL* 4.5 25.6 - - + -
408D PRO* 4.7 1.8 - - + -
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Residues in contact with LEU 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D ILE* 5.8 4.3 - - + -
235D LYS 4.3 7.4 - - - +
236D GLY* 3.1 35.2 - - - +
237D GLY* 4.4 4.7 - - - +
262D GLN* 3.3 18.6 + - + +
263D LEU* 3.9 11.9 - - + +
264D ASN 3.1 0.4 - - - -
265D LEU* 1.3 75.3 - - - +
267D LYS* 1.3 53.2 + - + +
268D ILE 2.6 15.1 + - - -
269D ARG* 2.7 46.3 + - - +
270D ASP* 2.7 25.9 + - - +
406D GLY* 4.3 7.0 - - - -
407D VAL* 4.2 15.0 - - + -
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Residues in contact with LYS 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D PHE* 6.2 0.2 - - - -
263D LEU* 3.1 40.2 + - + +
264D ASN* 3.0 26.7 + - - +
266D LEU* 1.3 76.7 - - + +
268D ILE* 1.3 57.4 + - - +
270D ASP* 4.2 9.9 - - - +
271D GLU* 3.8 15.8 + - - +
325D ARG* 3.9 16.1 + - - +
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Residues in contact with ILE 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D ASN 3.0 15.9 - - - +
265D LEU* 3.1 14.6 - - + +
266D LEU 2.6 1.4 + - - -
267D LYS* 1.3 79.5 - - - +
269D ARG* 1.3 57.1 + - - +
270D ASP 3.2 1.1 - - - -
271D GLU* 3.1 8.5 + - - +
272D LEU* 2.9 35.3 + - + +
322D LEU* 4.2 23.1 - - + +
325D ARG* 3.8 31.6 - - + +
327D ILE* 3.9 24.7 - - + -
333D LEU* 4.1 34.8 - - + -
403D ALA* 5.6 2.0 - - + +
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Residues in contact with ARG 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D GLY* 4.3 8.7 + - - -
265D LEU 3.0 11.0 + - - +
266D LEU* 2.7 38.3 + - - +
268D ILE* 1.3 69.6 - - - +
270D ASP* 1.3 87.6 + - - +
272D LEU* 3.3 4.6 + - - +
273D ARG* 2.9 63.3 + - - +
403D ALA 3.6 15.9 - - - +
404D ILE 2.9 24.2 - - - +
405D GLU 2.9 28.2 + - - +
406D GLY* 3.8 6.5 - - - -
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Residues in contact with ASP 270 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D LEU* 2.7 27.1 + - - +
267D LYS* 4.5 8.5 - - - +
269D ARG* 1.3 105.1 + - - +
271D GLU* 1.3 59.0 + - - +
273D ARG* 3.7 9.3 + - - +
274D LYS* 3.0 28.9 + - - +
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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 LYS 3.8 14.2 + - - +
268D ILE* 3.1 13.4 + - - +
270D ASP* 1.3 77.9 - - - +
272D LEU* 1.3 64.5 + - - +
274D LYS* 3.3 21.4 - - - +
275D ARG* 2.9 57.7 + - - +
322D LEU* 3.6 21.7 - - + +
325D ARG* 4.7 9.4 - - - +
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Residues in contact with LEU 272 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D ILE* 2.9 24.7 + - + +
269D ARG* 3.7 5.4 - - - +
270D ASP 3.3 0.2 - - - -
271D GLU* 1.3 74.1 - - - +
273D ARG* 1.3 55.0 + - - +
275D ARG* 2.9 7.5 + - - +
276D GLY 2.7 31.0 + - - -
277D VAL* 3.5 10.3 + - + +
318D LYS 3.6 6.7 - - - +
319D PHE* 3.3 52.0 - - + -
322D LEU* 3.4 26.2 - - + -
403D ALA* 3.7 10.3 - - + +
404D ILE* 3.4 35.2 - - + +
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Residues in contact with ARG 273 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D ARG* 2.9 63.7 + - - +
270D ASP* 3.7 10.0 + - - +
272D LEU* 1.3 74.6 - - - +
274D LYS* 1.3 60.6 + - - +
276D GLY* 2.9 20.7 + - - +
277D VAL 4.9 4.5 - - - +
404D ILE* 4.4 13.4 + - + +
405D GLU* 4.6 5.9 + - - +
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Residues in contact with LYS 274 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D ASP 3.0 15.4 + - - +
271D GLU* 3.3 24.5 - - - +
273D ARG* 1.3 74.2 - - - +
275D ARG* 1.3 61.1 + - + +
276D GLY* 2.8 10.6 + - - -
----------------------------------------------------------
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Residues in contact with ARG 275 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D GLU* 2.9 36.5 + - - +
272D LEU* 2.9 10.1 + - - +
274D LYS* 1.3 79.9 - - + +
276D GLY* 1.3 58.1 + - - +
277D VAL* 4.3 0.4 - - + -
318D LYS* 2.6 91.3 + - + +
319D PHE 3.8 1.0 - - - -
320D ARG* 2.7 34.1 + - - +
321D GLY* 4.9 1.0 - - - -
322D LEU* 3.9 10.8 - - - +
376D GLU* 3.6 33.7 + - - +
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Residues in contact with GLY 276 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D LEU 2.7 6.5 + - - -
273D ARG* 3.2 12.3 - - - -
274D LYS 2.8 6.3 - - - -
275D ARG* 1.3 77.2 - - - +
277D VAL* 1.3 57.4 + - - -
278D LYS* 5.0 7.0 - - - +
318D LYS* 2.7 25.3 + - - -
----------------------------------------------------------
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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