Contacts of the helix formed by residues 253 - 282 (chain E) in PDB entry 5J0Z
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 THR 253 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E PHE* 3.5 36.6 - - + +
117E ARG* 3.8 4.7 - - - +
119E TYR* 4.9 3.1 - - + -
246E LEU* 4.4 22.1 - - + +
249E THR* 3.9 17.6 + - + +
251E TYR* 3.4 4.0 + - + -
252E MET* 1.3 83.8 - - - +
254E TYR* 1.3 60.2 + - - +
255E THR* 4.4 2.5 - - - -
256E GLY* 3.3 21.8 + - - -
257E ALA* 3.0 24.6 + - - +
314E PHE* 3.7 1.8 - - - -
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Residues in contact with TYR 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E PHE 4.5 0.4 + - - -
117E ARG 2.8 22.6 + - - +
118E ARG* 4.4 3.1 - - - -
119E TYR 3.7 14.8 + - - +
120E PRO* 5.3 0.4 - - + -
121E PHE* 4.0 28.7 - + - -
253E THR* 1.3 69.5 - - - +
255E THR* 1.3 69.3 + - - +
256E GLY 3.1 1.3 - - - -
257E ALA* 3.3 4.3 + - - +
258E ILE* 3.1 51.7 + - + +
307E ASN* 5.1 4.3 + - - -
310E LEU* 4.7 4.5 - - + -
311E ALA* 4.3 26.1 - - + +
314E PHE* 3.7 37.5 - + + -
315E PHE* 4.1 22.4 - + - -
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Residues in contact with THR 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E TYR* 2.5 46.6 + - + -
120E PRO* 3.3 10.0 - - + +
201E ILE* 5.4 6.1 - - + -
202E ILE* 6.6 0.2 - - + -
242E VAL* 4.1 29.8 - - + -
246E LEU* 5.7 1.6 - - - -
253E THR* 4.4 2.2 - - - -
254E TYR* 1.3 80.5 - - - +
256E GLY* 1.3 57.6 + - - +
258E ILE* 3.5 9.4 + - + +
259E ILE* 2.9 36.6 + - + +
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Residues in contact with GLY 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D ASN* 5.7 6.3 + - - -
242E VAL* 5.9 2.7 - - - -
252E MET* 3.5 10.6 - - - +
253E THR* 3.3 21.3 + - - -
254E TYR 3.1 0.6 - - - -
255E THR* 1.3 76.1 - - - +
257E ALA* 1.3 56.5 + - - +
259E ILE* 3.8 7.9 - - - +
260E PHE* 2.8 35.2 + - - +
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Residues in contact with ALA 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252E MET* 3.3 11.8 - - + +
253E THR 3.0 13.9 + - - +
254E TYR 3.5 8.3 - - - +
256E GLY* 1.3 72.9 - - - +
258E ILE* 1.3 56.8 + - - +
260E PHE* 2.9 7.7 + - - +
261E MET* 2.7 36.4 + - - +
310E LEU* 3.8 24.0 - - + -
314E PHE* 4.1 14.1 - - + -
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Residues in contact with ILE 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202E ILE* 6.4 1.6 - - + -
205E MET* 5.4 3.1 - - - -
206E LEU* 6.6 0.2 - - + -
254E TYR* 3.1 55.7 + - + +
255E THR* 3.6 12.1 - - + +
257E ALA* 1.3 77.4 - - - +
259E ILE* 1.3 62.9 + - + +
261E MET* 3.3 8.2 + - + +
262E ILE* 3.0 45.2 + - + +
303E PHE* 5.8 1.8 - - + -
307E ASN* 4.0 28.0 - - - +
310E LEU* 4.0 13.6 - - + +
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Residues in contact with ILE 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201E ILE* 5.7 0.2 - - + -
205E MET* 3.8 37.9 - - + -
235E HIS* 3.9 2.2 + - + +
238E PHE 4.2 3.6 - - - +
239E ASN* 3.7 31.6 - - + +
242E VAL* 3.6 37.7 - - + -
255E THR* 2.9 23.5 + - + +
256E GLY* 3.8 7.9 - - - +
258E ILE* 1.3 79.6 - - + +
260E PHE* 1.3 63.7 + - - +
262E ILE* 3.2 17.2 + - - +
263E TYR* 3.2 22.7 + - + -
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Residues in contact with PHE 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D PRO* 3.6 39.3 - - + +
203D LEU* 3.6 44.2 - - + -
204D PRO* 4.9 4.7 - - + -
207D PHE* 4.0 19.3 - + - -
252E MET* 5.6 1.8 - - + -
256E GLY 2.8 21.4 + - - +
257E ALA* 3.6 6.3 - - - +
259E ILE* 1.3 73.2 - - - +
261E MET* 1.3 72.6 + - + +
263E TYR* 3.3 21.8 + - + +
264E LEU* 3.9 17.6 + - + +
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Residues in contact with MET 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257E ALA 2.7 21.0 + - - +
258E ILE* 3.6 8.5 - - + +
260E PHE* 1.3 77.3 - - + +
262E ILE* 1.3 67.4 + - - +
264E LEU* 3.0 31.1 + - + +
265E PHE* 3.5 23.5 - - + -
303E PHE* 3.3 29.6 - - + -
306E ALA* 4.0 30.3 - - + +
307E ASN* 3.2 26.7 - - - +
310E LEU* 4.4 12.8 - - + -
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Residues in contact with ILE 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E MET* 4.1 18.4 - - + +
206E LEU* 5.3 4.5 - - + -
209E LEU* 4.5 12.6 - - + -
235E HIS* 3.1 37.9 - - + +
258E ILE* 3.0 37.7 + - + +
259E ILE* 3.2 8.3 + - - +
261E MET* 1.3 75.9 - - - +
263E TYR* 1.3 57.5 + - - +
264E LEU 2.8 6.6 + - - -
265E PHE* 2.9 18.7 + - - +
266E TYR* 3.2 32.5 + - + -
303E PHE* 4.2 26.2 - - + -
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Residues in contact with TYR 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D PRO* 3.6 36.6 - - + -
207D PHE* 3.8 23.9 - + + +
208D ILE* 5.1 5.2 - - + -
238D PHE* 3.5 10.8 - + - -
232E LEU* 4.6 11.9 - - + -
235E HIS* 3.4 25.8 - + - -
236E ILE* 3.5 26.2 - - + +
239E ASN* 2.7 46.2 + - - +
259E ILE* 3.2 25.8 + - + -
260E PHE* 3.3 14.9 + - + +
261E MET 3.2 1.2 - - - -
262E ILE* 1.3 75.0 - - - +
264E LEU* 1.3 59.2 + - - +
266E TYR* 4.2 7.3 - - - +
267E PHE* 3.4 20.6 + - - +
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Residues in contact with LEU 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D PHE* 3.3 41.7 - - + -
260E PHE* 4.0 22.7 - - + +
261E MET* 3.3 22.2 - - + +
262E ILE 3.0 0.8 - - - -
263E TYR* 1.3 74.8 - - - +
265E PHE* 1.3 63.7 + - + +
266E TYR 3.0 4.0 - - - -
267E PHE* 2.6 12.8 + - + -
268E VAL* 2.5 43.8 + - + +
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Residues in contact with PHE 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209E LEU* 4.3 14.0 - - + +
212E SER* 4.2 8.3 + - - -
213E TRP* 4.0 23.1 + + - +
261E MET* 3.5 34.3 - - + +
262E ILE* 2.9 10.6 + - - +
264E LEU* 1.3 81.9 - - + +
266E TYR* 1.3 58.7 + - - +
268E VAL* 4.7 6.3 - - + -
269E ALA* 3.3 21.1 + - - +
299E PHE* 4.0 17.4 - + - -
302E VAL* 3.9 26.7 - - + -
303E PHE* 3.3 50.3 - + + -
306E ALA* 5.0 1.8 - - + -
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Residues in contact with TYR 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D ILE* 4.9 1.3 - - + -
208E ILE* 3.2 39.2 + - - +
209E LEU* 3.3 19.9 - - + +
212E SER* 4.0 10.3 - - - -
228E VAL* 3.8 11.2 - - + +
231E THR* 3.4 14.9 + - - -
232E LEU* 3.4 59.0 - - + -
235E HIS* 4.0 9.4 - + + -
262E ILE* 3.2 41.7 + - + +
263E TYR* 4.4 5.2 - - - +
264E LEU 3.0 0.4 - - - -
265E PHE* 1.3 79.7 - - - +
267E PHE* 1.3 66.4 + - - +
268E VAL 3.3 0.2 - - - -
269E ALA* 3.3 4.2 + - - +
270E VAL* 3.0 28.4 + - - +
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Residues in contact with PHE 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D PHE* 4.0 27.1 - + + -
210D PHE* 3.5 42.2 - + + -
211D ILE* 3.6 30.7 - - + +
214D THR* 5.8 1.1 - - + -
263E TYR 3.4 15.2 + - - +
264E LEU* 2.6 18.5 + - + +
266E TYR* 1.3 75.9 - - - +
268E VAL* 1.3 64.1 + - + +
270E VAL* 3.3 5.5 + - - +
271E ILE* 3.1 50.2 + - + +
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Residues in contact with VAL 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264E LEU* 2.5 28.1 + - + +
265E PHE* 4.7 3.6 - - + -
267E PHE* 1.3 81.6 - - + +
269E ALA* 1.3 65.1 + - - +
271E ILE* 3.0 12.9 + - + +
272E GLU* 2.9 21.8 + - - +
299E PHE* 3.4 27.6 - - + -
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Residues in contact with ALA 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212E SER* 4.5 6.7 - - - +
216E PHE* 4.5 9.0 - - + -
228E VAL* 4.3 18.4 - - + -
265E PHE 3.3 21.6 + - - +
266E TYR* 3.3 8.5 + - - +
268E VAL* 1.3 79.2 - - - +
270E VAL* 1.3 63.4 + - - +
272E GLU* 3.2 5.3 + - - +
273E VAL* 2.9 27.3 + - + +
299E PHE* 3.7 20.2 - - + -
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Residues in contact with VAL 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D ILE* 4.0 36.3 - - + -
214D THR* 3.5 33.7 - - + +
227D LEU* 5.0 2.2 - - + -
228E VAL* 3.3 28.0 - - + +
229E VAL* 4.8 6.1 - - + -
232E LEU* 6.1 0.7 - - + -
266E TYR 3.0 13.5 + - - +
267E PHE 3.4 9.0 - - - +
269E ALA* 1.3 73.7 - - - +
271E ILE* 1.3 54.1 + - + +
273E VAL* 3.2 7.1 + - + +
274E THR* 2.7 44.2 + - - +
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Residues in contact with ILE 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D THR* 4.9 12.8 - - + -
267E PHE* 3.1 45.6 + - + +
268E VAL* 3.0 17.9 + - + +
270E VAL* 1.3 77.2 - - + +
272E GLU* 1.3 54.0 + - - +
274E THR* 3.1 5.3 + - + -
275E VAL* 2.8 46.5 + - + +
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Residues in contact with GLU 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E ALA 4.4 0.5 - - - +
216E PHE* 3.2 26.3 - - + -
268E VAL 2.9 12.2 + - - +
269E ALA* 3.5 6.5 - - - +
271E ILE* 1.3 75.9 - - - +
273E VAL* 1.3 88.7 + - - +
275E VAL* 3.3 8.7 + - - +
276E GLN* 2.9 29.6 + - - +
291E ILE* 4.0 13.6 - - + +
292E THR* 2.6 39.8 + - - +
295E SER* 3.5 20.9 - - - +
299E PHE* 4.5 6.5 - - + -
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Residues in contact with VAL 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E ALA* 4.1 13.5 - - + -
216E PHE* 5.1 1.6 - - + -
221E TYR* 3.6 24.7 - - + -
224E ASN* 3.7 38.6 - - + +
225E VAL* 4.6 6.5 - - + +
228E VAL* 4.6 8.5 - - + -
269E ALA* 2.9 19.4 + - + +
270E VAL* 3.6 5.8 - - + +
272E GLU* 1.3 94.9 + - - +
274E THR* 1.3 65.9 + - - +
276E GLN* 3.7 6.1 - - - +
277E HIS* 3.0 24.4 + - - +
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Residues in contact with THR 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D THR* 3.2 49.4 + - + +
217D TRP* 4.1 21.2 - - + +
221E TYR* 3.3 19.6 + - - +
225E VAL* 5.8 0.3 - - - +
270E VAL* 2.7 26.4 + - - +
271E ILE* 3.6 5.8 - - + +
273E VAL* 1.3 73.8 - - - +
275E VAL* 1.3 57.4 + - + +
277E HIS* 3.8 5.5 - - - +
278E TYR* 2.9 24.8 + - - +
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Residues in contact with VAL 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271E ILE* 2.8 27.7 + - + +
272E GLU* 3.4 10.3 - - - +
273E VAL 3.1 0.2 - - - -
274E THR* 1.3 74.2 - - + +
276E GLN* 1.3 62.4 + - - +
277E HIS 3.2 1.3 - - - -
278E TYR* 2.7 26.9 + - + +
279E LEU* 2.8 25.7 + - + +
291E ILE* 3.8 31.9 - - + -
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Residues in contact with GLN 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E ALA 4.2 0.9 - - - +
218E SER 3.0 22.7 + - - +
219E THR* 3.7 22.3 - - + +
224E ASN* 3.5 20.3 + - - -
272E GLU* 2.9 24.5 + - - +
273E VAL* 3.7 10.0 - - - +
275E VAL* 1.3 75.5 - - - +
277E HIS* 1.3 62.6 + - - +
279E LEU 3.6 0.2 + - - -
280E LYS* 3.2 27.4 + - + +
288E ALA* 3.7 24.6 - - + +
289E ALA* 5.3 2.7 - - + +
291E ILE* 5.7 0.9 - - + -
292E THR* 3.0 39.5 + - - +
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Residues in contact with HIS 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D TRP 3.9 16.1 + - - -
218D SER* 4.1 16.7 + - - -
219D THR* 4.5 5.9 + - - -
220D SER* 4.9 8.7 - - - -
221E TYR* 3.4 59.3 - + + +
222E GLU* 5.1 6.8 + - - -
273E VAL 3.0 10.3 + - - +
274E THR 3.8 3.8 - - - +
276E GLN* 1.3 77.5 + - - +
278E TYR* 1.3 71.1 + + - +
280E LYS* 3.3 9.6 + - - +
281E VAL* 3.2 37.7 + - + +
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Residues in contact with TYR 278 (chain E).
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* 3.9 37.0 - + + +
293D ARG* 5.7 1.0 - - - -
296D ARG* 3.8 33.3 + - - -
274E THR 2.9 16.7 + - - +
275E VAL* 2.7 20.3 + - + +
277E HIS* 1.3 74.9 - + - +
279E LEU* 1.3 66.3 - - + +
281E VAL* 2.9 28.4 + - + +
282E GLU* 3.0 50.0 + - + +
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Residues in contact with LEU 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E VAL* 2.8 27.6 + - + +
278E TYR* 1.3 87.0 - - + +
280E LYS* 1.3 51.8 + - - +
282E GLU* 3.0 12.5 + - + -
283E SER 2.7 31.0 + - - -
284E GLN* 3.2 22.0 + - + +
287E ARG* 3.9 24.2 - - + +
288E ALA* 3.5 40.8 - - + +
291E ILE* 3.9 15.0 - - + -
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Residues in contact with LYS 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E THR* 4.2 38.1 + - + +
276E GLN* 3.2 20.6 + - + +
277E HIS* 3.8 7.4 - - - +
278E TYR 3.2 0.2 - - - -
279E LEU* 1.3 80.2 - - - +
281E VAL* 1.3 58.4 + - - +
283E SER* 3.7 9.9 + - - +
285E PRO* 4.7 26.1 - - + +
288E ALA* 4.4 7.5 - - + +
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Residues in contact with VAL 281 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D THR* 4.9 14.4 - - + +
277E HIS* 3.2 36.4 + - + +
278E TYR* 2.9 15.0 + - + +
280E LYS* 1.3 75.9 - - - +
282E GLU* 1.3 71.2 + - - +
283E SER* 3.2 7.7 + - - -
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Residues in contact with GLU 282 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278E TYR* 3.0 58.7 + - + +
279E LEU* 3.0 15.6 + - + +
281E VAL* 1.3 93.7 - - - +
283E SER* 1.3 68.6 + - - +
284E GLN* 3.6 4.9 - - + +
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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
------------------------------------------------------------
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).
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