Contacts of the helix formed by residues 253 - 281 (chain E) in PDB entry 4LML
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 TYR 253 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E PHE 4.8 0.2 + - - -
116E ARG 3.1 21.3 + - - +
117E ARG* 4.7 0.2 - - - -
118E TYR 4.2 9.4 + - - +
120E PHE* 4.7 14.1 - + - -
252E THR* 1.3 70.2 - - - +
254E THR* 1.3 70.6 + - + +
256E ALA* 3.0 4.7 + - - +
257E ILE* 3.0 57.6 + - + +
306E ASN* 4.7 9.2 + - - -
309E LEU* 4.4 4.0 - - + -
310E ALA* 4.1 33.5 + - + +
313E PHE* 3.6 33.3 - + + -
314E PHE* 3.8 31.9 - + + -
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Residues in contact with THR 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E TYR* 2.4 46.3 + - + +
119E PRO* 3.6 8.3 - - + +
200E ILE* 5.6 7.4 - - + -
201E ILE* 4.9 13.9 - - + -
204E MET* 5.6 3.4 - - + -
241E VAL* 5.2 11.9 - - + -
252E THR* 3.6 2.5 - - - -
253E TYR* 1.3 81.6 - - + +
255E GLY* 1.3 57.3 - - - +
257E ILE* 3.4 21.4 - - + +
258E ILE* 2.9 40.5 + - + +
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Residues in contact with GLY 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B PRO* 4.8 7.5 - - - +
199B ASN* 5.9 2.2 - - - -
251E MET* 5.2 5.1 - - - +
252E THR* 3.5 23.5 + - - -
253E TYR 3.2 0.6 - - - -
254E THR* 1.3 75.9 - - - +
256E ALA* 1.3 63.7 + - - +
258E ILE* 3.5 14.9 - - - +
259E PHE* 3.5 18.4 + - - +
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Residues in contact with ALA 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251E MET* 4.9 12.3 - - + -
252E THR 3.1 15.6 + - - +
253E TYR* 3.0 13.8 + - - +
255E GLY* 1.3 74.2 - - - +
257E ILE* 1.3 68.0 + - - +
258E ILE 3.0 1.1 - - - -
259E PHE* 3.0 6.7 + - - +
260E MET* 2.9 21.7 + - - +
309E LEU* 3.8 24.5 - - + -
313E PHE* 4.3 6.7 - - + -
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Residues in contact with ILE 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201E ILE* 4.9 11.9 - - + -
204E MET* 4.2 22.0 - - + -
205E LEU* 6.5 0.9 - - + -
253E TYR* 3.0 39.4 + - + +
254E THR* 3.4 25.1 - - + +
256E ALA* 1.3 74.6 - - - +
258E ILE* 1.3 61.4 + - - +
260E MET* 3.4 9.1 - - + +
261E ILE* 3.0 37.8 + - + +
302E PHE* 6.3 0.7 - - + -
306E ASN* 4.4 20.6 - - - +
309E LEU* 3.6 22.2 - - + -
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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
----------------------------------------------------------
198B PRO* 5.1 2.7 - - + +
199B ASN* 5.0 5.2 - - - +
200E ILE* 6.1 0.7 - - + -
204E MET* 3.8 28.9 - - + -
234E HIS* 3.2 26.4 - - + +
237E PHE 4.7 2.5 - - - +
238E ASN* 3.4 47.3 - - - +
241E VAL* 5.0 12.6 - - + -
254E THR* 2.9 23.2 + - + +
255E GLY* 3.5 18.4 - - - +
256E ALA 3.0 0.2 - - - -
257E ILE* 1.3 77.8 - - - +
259E PHE* 1.3 64.6 + - + +
261E ILE* 3.5 2.4 + - - -
262E TYR* 3.0 23.2 + - + -
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Residues in contact with PHE 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ILE* 5.8 1.1 - - + -
198B PRO* 4.0 35.4 - - + +
202B LEU* 3.5 37.5 - - + -
203B PRO* 5.0 1.3 - - + -
206B PHE* 3.5 22.4 - + - -
251E MET* 6.5 1.1 - - + -
255E GLY 3.7 13.5 - - - +
256E ALA* 3.0 5.4 + - - +
258E ILE* 1.3 79.3 - - + +
260E MET* 1.3 68.1 + - - +
262E TYR* 3.0 18.1 + + + +
263E LEU* 2.9 45.6 + - + +
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Residues in contact with MET 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256E ALA 2.9 12.5 + - - +
257E ILE* 3.4 12.3 - - + +
259E PHE* 1.3 78.2 - - - +
261E ILE* 1.3 61.5 + - - +
263E LEU* 2.9 25.0 + - + +
264E PHE* 3.0 43.0 + - + -
302E PHE* 4.1 7.4 - - + -
305E ALA* 3.6 31.2 - - + -
306E ASN* 3.4 30.1 - - - +
309E LEU* 3.9 26.0 - - + -
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Residues in contact with ILE 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E MET* 3.6 36.1 - - + +
205E LEU* 5.6 2.5 - - + -
208E LEU* 3.6 23.1 - - + -
234E HIS* 3.3 26.0 - - + +
257E ILE* 3.0 26.5 + - + +
258E ILE 3.6 0.4 - - - +
259E PHE 3.3 0.2 - - - -
260E MET* 1.3 74.3 - - + +
262E TYR* 1.3 63.7 + - - +
264E PHE* 3.2 8.6 + - - +
265E TYR* 3.0 50.7 + - + -
302E PHE* 4.1 24.5 - - + -
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Residues in contact with TYR 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B PRO 4.5 2.5 - - - -
203B PRO* 3.6 38.5 - - + +
206B PHE* 4.6 15.6 - + + +
207B ILE* 5.4 3.6 - - + -
237B PHE* 3.7 14.4 - + - -
231E LEU* 4.3 23.1 - - + -
234E HIS* 3.6 19.0 - + - -
235E ILE* 3.6 28.6 - - + +
238E ASN* 3.7 29.2 + - - -
258E ILE 3.0 23.4 + - - -
259E PHE* 3.0 30.4 + + + +
261E ILE* 1.3 74.8 - - - +
263E LEU* 1.3 61.3 + - - +
265E TYR* 3.2 9.2 + - - +
266E PHE* 3.0 20.6 + - - +
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Residues in contact with LEU 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B PHE* 3.4 35.9 - - + -
259E PHE* 2.9 37.0 + - + +
260E MET* 2.9 16.2 + - + +
262E TYR* 1.3 76.0 - - - +
264E PHE* 1.3 65.9 + - + +
266E PHE* 3.1 7.3 + - + +
267E VAL* 3.0 36.9 + - + +
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Residues in contact with PHE 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E LEU* 4.8 6.7 - - + -
212E TRP* 3.9 23.0 - + + -
260E MET* 3.0 36.0 + - + +
261E ILE* 3.2 10.7 + - - +
263E LEU* 1.3 78.8 - - + +
265E TYR* 1.3 61.5 + - - +
267E VAL* 3.3 15.2 - - + +
268E ALA* 3.0 30.0 + - - +
298E PHE* 3.9 8.1 - + + -
301E VAL* 3.3 33.7 - - + -
302E PHE* 3.3 48.2 - + + -
305E ALA* 4.9 1.3 - - + -
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Residues in contact with TYR 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ILE* 5.0 1.3 - - + -
207E ILE* 3.2 33.8 + - - +
208E LEU* 3.5 13.0 + - + -
211E SER* 3.5 14.8 - - - -
227E VAL* 3.6 17.5 - - + +
230E THR* 3.1 34.9 + - - -
231E LEU* 3.2 40.8 - - + -
234E HIS* 4.3 7.6 - + + -
261E ILE* 3.0 49.0 + - + -
262E TYR 3.4 8.1 - - - +
264E PHE* 1.3 78.7 - - - +
266E PHE* 1.3 62.4 + - - +
268E ALA* 3.3 6.8 + - - +
269E VAL* 3.0 28.0 + - - +
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Residues in contact with PHE 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B PHE* 3.9 29.4 - + + -
209B PHE* 3.6 40.4 - + + -
210B ILE* 3.4 34.7 - - + +
213B THR* 6.4 0.7 - - - -
262E TYR 3.0 12.2 + - - +
263E LEU* 3.1 11.2 + - + +
265E TYR* 1.3 77.5 - - - +
267E VAL* 1.3 64.1 + - + +
269E VAL* 3.3 5.3 + - + +
270E ILE* 2.9 52.2 + - + +
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Residues in contact with VAL 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263E LEU* 3.0 18.5 + - + +
264E PHE* 3.3 25.8 - - + +
266E PHE* 1.3 79.5 - - + +
268E ALA* 1.3 62.0 + - - +
270E ILE* 3.5 12.5 - - + +
271E GLU* 2.9 26.9 + - - +
298E PHE* 3.6 21.9 - - + -
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Residues in contact with ALA 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211E SER* 5.0 5.6 - - - +
212E TRP* 5.4 5.8 - - + -
215E PHE* 5.2 5.9 - - + -
227E VAL* 4.2 17.5 - - + -
264E PHE 3.0 20.6 + - - +
265E TYR* 3.4 7.6 - - - +
267E VAL* 1.3 75.3 - - - +
269E VAL* 1.3 64.5 + - - +
271E GLU* 3.0 13.0 + - - +
272E VAL* 3.0 19.8 + - - +
298E PHE* 3.5 20.6 - - + -
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Residues in contact with VAL 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ILE* 3.9 37.7 - - + -
213B THR* 3.8 34.1 - - + +
226B LEU* 5.4 1.6 - - + -
227E VAL* 3.7 26.4 - - + +
228E VAL* 5.1 7.2 - - + -
231E LEU* 5.9 0.9 - - + -
265E TYR 3.0 11.3 + - - +
266E PHE* 3.5 9.0 - - + +
268E ALA* 1.3 74.3 - - - +
270E ILE* 1.3 66.5 + - + +
272E VAL* 3.2 10.1 - - + +
273E THR* 3.0 28.8 + - - +
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Residues in contact with ILE 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B THR* 4.3 14.8 - - - +
266E PHE* 2.9 46.1 + - + +
267E VAL* 3.5 14.8 - - + +
269E VAL* 1.3 78.2 - - + +
271E GLU* 1.3 59.9 + - - +
273E THR* 3.6 5.2 - - + +
274E VAL* 2.9 37.5 + - + +
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Residues in contact with GLU 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E PHE* 3.3 21.3 - - + -
267E VAL 2.9 15.4 + - - +
268E ALA* 3.0 11.2 + - - +
270E ILE* 1.3 77.5 - - - +
272E VAL* 1.3 92.6 + - - +
274E VAL* 3.0 10.2 + - - +
275E GLN* 2.9 26.0 + - - +
290E ILE* 4.3 13.4 - - + +
291E THR* 3.1 31.0 + - - +
294E SER* 3.0 28.5 + - - +
298E PHE* 4.4 6.7 - - + -
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Residues in contact with VAL 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214E ALA* 4.6 10.3 - - + +
215E PHE* 5.2 4.5 - - + -
220E TYR* 3.3 19.1 - - + -
223E ASN* 3.5 44.0 - - + +
224E VAL* 5.3 4.0 - - + -
227E VAL* 4.6 11.9 - - + -
268E ALA 3.0 17.1 + - - +
269E VAL* 3.2 20.9 - - + +
271E GLU* 1.3 89.0 + - - +
273E THR* 1.3 63.2 + - - +
275E GLN* 3.2 10.8 + - - +
276E HIS 3.0 18.0 + - - -
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Residues in contact with THR 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B THR* 3.2 42.5 + - - +
216B TRP* 3.7 24.6 - - + +
220E TYR* 2.8 25.6 + - - +
269E VAL* 3.0 20.6 + - - +
270E ILE* 3.6 6.3 - - + +
272E VAL* 1.3 76.5 - - - +
274E VAL* 1.3 65.7 - - + +
276E HIS* 3.1 4.5 + - - +
277E TYR* 3.0 22.5 + - - +
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Residues in contact with VAL 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B TRP* 6.3 3.6 - - + -
270E ILE* 2.9 21.9 + - + +
271E GLU* 3.0 12.5 + - - +
273E THR* 1.3 76.5 - - + +
275E GLN* 1.3 65.1 + - - +
277E TYR* 4.2 4.8 - - - +
278E LEU* 3.0 30.8 + - + +
290E ILE* 3.5 39.0 - - + -
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Residues in contact with GLN 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217E SER 3.7 21.2 + - - +
218E THR* 3.7 24.1 + - - +
219E SER 5.1 2.2 - - - -
220E TYR* 5.2 3.4 - - - +
223E ASN* 4.0 12.1 + - - +
271E GLU* 2.9 14.2 + - - +
272E VAL* 3.2 15.4 + - - +
274E VAL* 1.3 81.2 - - + +
276E HIS* 1.3 57.7 + - - +
278E LEU* 3.8 3.9 - - - +
279E LYS* 2.9 38.7 + - + +
287E ALA* 4.2 19.4 - - + +
290E ILE* 5.8 1.6 - - + -
291E THR* 2.6 39.6 + - - +
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Residues in contact with HIS 276 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B TRP 3.6 6.1 - - - -
217B SER* 3.1 42.6 + - - -
218B THR* 3.5 13.2 + - - -
219B SER* 4.3 10.3 - - - -
220E TYR* 3.4 44.4 - + + +
272E VAL 3.0 5.9 + - - -
273E THR* 3.1 7.4 + - + +
275E GLN* 1.3 76.4 - - - +
277E TYR* 1.3 65.6 + - - +
279E LYS* 3.0 15.7 + - - +
280E VAL* 2.9 47.2 + - + +
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Residues in contact with TYR 277 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B TRP* 3.5 46.0 - + + +
295B ARG* 3.6 33.9 + - - -
273E THR 3.0 13.7 + - - +
274E VAL* 4.2 4.3 - - - +
276E HIS* 1.3 76.8 - - - +
278E LEU* 1.3 68.0 + - + +
280E VAL* 3.3 13.4 - - + +
281E GLU* 3.1 62.7 + - + +
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Residues in contact with LEU 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E VAL* 3.0 20.0 + - + +
275E GLN 3.8 2.7 - - - +
277E TYR* 1.3 84.4 - - + +
279E LYS* 1.3 57.8 + - - +
281E GLU* 3.3 14.4 + - + +
283E GLN* 3.1 50.0 + - + +
286E ARG* 3.5 20.9 - - + +
287E ALA* 3.4 33.7 - - + +
290E ILE* 3.8 18.8 - - + -
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Residues in contact with LYS 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218E THR* 3.6 41.9 + - + -
220E TYR* 5.8 2.0 - - - +
275E GLN* 2.9 29.2 + - + +
276E HIS* 3.0 15.1 + - - +
278E LEU* 1.3 77.6 - - - +
280E VAL* 1.3 65.2 + - - +
281E GLU 3.3 0.2 - - - -
282E SER* 3.4 13.6 + - - +
283E GLN 4.7 2.5 - - - +
284E PRO* 4.4 24.3 - - + +
287E ALA* 4.6 8.5 - - + -
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Residues in contact with VAL 280 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B TRP 5.2 0.4 - - - +
218B THR* 4.7 15.0 - - - +
276E HIS* 2.9 46.5 + - + +
277E TYR* 3.3 28.7 - - + +
279E LYS* 1.3 80.6 - - + +
281E GLU* 1.3 64.5 + - + +
282E SER* 3.0 10.8 + - - -
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Residues in contact with GLU 281 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277E TYR* 3.1 62.7 + - + +
278E LEU* 3.5 13.5 - - + +
279E LYS 3.3 0.6 - - - -
280E VAL* 1.3 81.3 - - - +
282E SER* 1.3 70.2 + - - +
283E GLN* 3.4 9.3 + - + +
----------------------------------------------------------
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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