Contacts of the helix formed by residues 270 - 296 (chain E) in PDB entry 6NR8
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 SER 270 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ARG* 3.6 9.2 - - - +
266B GLU* 4.9 7.4 + - - -
268E VAL* 3.8 10.6 - - - +
269E THR* 1.3 85.5 + - - +
271E VAL* 1.3 65.7 + - - +
272E GLU* 3.9 16.4 - - - -
273E ASP* 3.0 35.3 + - - +
274E TYR 3.4 4.0 + - - -
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Residues in contact with VAL 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B GLY* 3.4 31.4 - - - +
254B SER* 3.3 27.4 - - - +
255B ARG 5.5 0.2 - - - +
257B ARG* 3.4 14.1 - - - +
266B GLU* 3.4 20.9 + - + +
270E SER* 1.3 72.8 - - - +
272E GLU* 1.3 68.4 + - - +
274E TYR* 3.0 12.1 + - + +
275E LYS* 2.9 40.0 + - + +
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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
----------------------------------------------------------
266B GLU* 5.4 2.8 - - - +
270E SER* 3.9 10.6 - - - -
271E VAL* 1.3 85.4 + - - +
273E ASP* 1.3 61.6 + - - +
275E LYS* 3.3 17.2 + - + +
276E ALA* 3.0 27.2 + - - +
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Residues in contact with ASP 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E VAL* 5.0 4.3 - - + -
269E THR* 3.3 19.6 - - - +
270E SER* 3.0 38.2 + - - +
272E GLU* 1.3 80.1 - - - +
274E TYR* 1.3 55.7 + - - +
276E ALA* 3.5 6.5 + - - +
277E LEU* 2.9 26.1 + - - +
280E TYR* 5.3 2.1 - - - -
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Residues in contact with TYR 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ILE* 4.1 19.4 - - + +
253B GLY 5.4 5.6 - - - -
255B ARG* 3.3 58.2 + - + +
268E VAL* 4.8 10.7 - - + +
270E SER 3.4 5.8 + - - +
271E VAL* 3.0 15.5 + - + +
273E ASP* 1.3 75.5 - - - +
275E LYS* 1.3 72.9 + - + +
277E LEU* 3.2 25.1 + - + +
278E GLN* 3.2 47.7 + - + +
281E GLU* 6.2 0.2 - - - -
309E GLU* 4.4 11.3 + - - -
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Residues in contact with LYS 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ILE* 5.4 10.1 - - - -
252B PHE* 4.2 22.1 + - - +
253B GLY* 5.0 2.2 - - - -
271E VAL* 2.9 34.0 + - + +
272E GLU* 3.3 20.9 + - + +
274E TYR* 1.3 86.0 - - + +
276E ALA* 1.3 60.2 + - - +
278E GLN* 3.8 18.5 + - - +
279E LYS* 3.4 30.1 + - - +
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Residues in contact with ALA 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E GLU 3.0 16.2 + - - +
273E ASP* 3.9 6.3 - - - +
274E TYR 3.3 0.2 - - - -
275E LYS* 1.3 75.8 - - - +
277E LEU* 1.3 54.2 + - - +
278E GLN 3.3 0.2 - - - -
279E LYS* 3.1 12.8 + - + +
280E TYR* 2.7 66.0 + - + +
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Residues in contact with LEU 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ARG* 3.9 12.3 - - - +
268E VAL* 4.8 7.0 - - + -
273E ASP 2.9 17.6 + - - +
274E TYR* 3.2 33.3 + - + +
276E ALA* 1.3 75.6 - - - +
278E GLN* 1.3 59.7 + - - +
280E TYR* 3.6 18.2 - - + +
281E GLU* 2.9 40.6 + - + +
257G VAL* 6.1 3.6 - - + -
258G HIS* 3.4 30.3 - - - +
259G THR* 4.4 9.9 - - - +
260G VAL* 6.0 1.8 - - + -
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Residues in contact with GLN 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ILE* 4.3 12.5 - - - +
274E TYR* 3.2 50.5 + - + +
275E LYS* 4.1 17.1 - - - +
277E LEU* 1.3 77.1 - - - +
279E LYS* 1.3 61.1 + - + +
281E GLU* 3.5 20.6 - - - +
282E LYS* 3.3 25.1 + - - +
309E GLU* 5.6 2.4 + - - -
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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
----------------------------------------------------------
275E LYS* 3.4 25.1 + - - +
276E ALA* 3.1 13.7 + - + +
278E GLN* 1.3 78.1 + - + +
280E TYR* 1.3 69.4 + - + +
282E LYS* 3.8 6.9 + - - +
283E GLU* 3.7 17.0 + - - +
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Residues in contact with TYR 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273E ASP 5.3 2.0 - - - -
276E ALA* 2.7 44.6 + - + +
277E LEU* 3.2 21.1 + - + +
279E LYS* 1.3 82.1 - - + +
281E GLU* 1.3 63.2 - - - +
283E GLU* 3.3 13.4 + - - +
284E LYS* 3.2 26.1 + - + +
259G THR* 6.0 2.5 - - - +
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Residues in contact with GLU 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E TYR* 6.2 0.2 - - - -
277E LEU* 2.9 28.6 + - + +
278E GLN* 3.5 23.6 - - - +
280E TYR* 1.3 74.7 - - - +
282E LYS* 1.3 57.0 + - - +
284E LYS* 3.1 11.4 + - - +
285E PHE* 2.7 62.7 + - + -
309E GLU* 5.7 0.7 - - - +
313E LEU* 4.8 7.8 - - - +
260G VAL* 3.7 30.3 - - + +
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Residues in contact with LYS 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278E GLN 3.3 19.0 + - - +
279E LYS* 4.0 8.5 - - - +
280E TYR 3.2 0.6 - - - -
281E GLU* 1.3 75.3 - - - +
283E GLU* 1.3 64.6 + - - +
285E PHE* 3.4 9.3 + - - +
286E GLU* 3.2 26.5 + - + +
313E LEU* 3.4 40.7 + - - +
316E GLN* 4.8 5.1 + - - -
317E ASN* 3.1 40.2 + - - +
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Residues in contact with GLU 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E LYS 3.7 9.1 + - - +
280E TYR* 3.3 13.5 + - - +
281E GLU 3.3 0.2 - - - -
282E LYS* 1.3 77.9 - - - +
284E LYS* 1.3 64.0 + - - +
286E GLU* 3.2 9.9 + - + +
287E GLU* 3.0 43.6 + - + +
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Residues in contact with LYS 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280E TYR* 3.2 18.3 + - + +
281E GLU* 3.1 10.4 + - - +
283E GLU* 1.3 82.9 - - - +
285E PHE* 1.3 66.6 + - + +
287E GLU* 2.9 42.1 + - - +
288E MET* 3.3 29.5 + - + +
259G THR* 4.7 6.7 - - - +
260G VAL* 3.7 26.5 - - + -
261G GLU* 3.7 29.6 + - + +
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Residues in contact with PHE 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257E PRO* 4.3 24.5 - - + -
281E GLU* 2.7 51.9 + - + +
282E LYS* 3.5 27.4 - - - +
283E GLU 3.2 0.4 - - - -
284E LYS* 1.3 76.4 - - + +
286E GLU* 1.3 62.8 + - - +
288E MET* 3.4 12.9 + - - +
289E ILE* 3.2 26.8 + - - +
310E ALA* 3.6 21.3 - - + -
313E LEU* 3.8 26.0 - - + -
314E LEU* 3.6 27.9 - - + +
317E ASN* 3.9 13.7 - - - +
260G VAL* 5.0 5.8 - - + -
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Residues in contact with GLU 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282E LYS* 3.2 16.9 + - + +
283E GLU* 3.2 11.0 + - + +
285E PHE* 1.3 74.7 - - - +
287E GLU* 1.3 60.6 + - + +
289E ILE* 3.2 20.3 + - - +
290E GLN* 2.8 42.4 + - + +
317E ASN* 3.0 37.6 - - - +
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Residues in contact with GLU 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283E GLU* 3.0 29.2 + - + +
284E LYS* 2.9 47.8 + - - +
285E PHE 3.3 0.2 - - - -
286E GLU* 1.3 76.1 - - + +
288E MET* 1.3 65.1 + - + +
290E GLN* 4.0 5.0 - - - +
291E GLN* 3.1 32.1 + - + +
345E PHE* 4.6 6.1 - - + -
261G GLU* 4.4 5.4 - - - +
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Residues in contact with MET 288 (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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254E PRO* 3.8 7.6 - - + +
255E PHE* 3.2 53.7 - - + +
256E GLU* 4.4 4.0 - - - -
257E PRO* 4.8 10.8 - - + -
284E LYS* 3.3 17.3 + - + +
285E PHE* 3.7 13.0 - - + +
286E GLU 3.3 0.2 - - - -
287E GLU* 1.3 75.9 - - + +
289E ILE* 1.3 62.2 + - - +
291E GLN* 4.4 0.3 - - - +
292E ILE* 3.3 18.5 + - - +
345E PHE* 3.8 26.0 - - + -
260G VAL* 4.6 23.6 - - + +
261G GLU* 4.7 7.0 - - - +
264G GLN* 3.4 28.0 - - + +
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Residues in contact with ILE 289 (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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255E PHE* 3.6 24.7 - - + -
285E PHE 3.2 17.8 + - - +
286E GLU* 3.3 21.1 - - - +
287E GLU 3.2 0.2 - - - -
288E MET* 1.3 77.4 - - - +
290E GLN* 1.3 76.2 + - - +
292E ILE* 3.2 2.3 + - - +
293E LYS* 2.8 43.5 + - - +
314E LEU* 3.8 7.0 - - + -
317E ASN* 3.3 43.1 - - + +
318E ASN 5.5 0.4 - - - +
319E LEU* 3.7 19.7 - - + +
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Residues in contact with GLN 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286E GLU* 2.8 32.0 + - + +
287E GLU* 3.5 4.9 + - - +
289E ILE* 1.3 80.6 - - + +
291E GLN* 1.3 62.3 + - - +
293E LYS* 3.2 37.7 + - - +
294E GLU* 3.2 31.9 + - - +
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Residues in contact with GLN 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287E GLU* 3.1 19.8 + - + +
288E MET 4.4 2.7 - - - +
290E GLN* 1.3 79.6 - - - +
292E ILE* 1.3 66.6 + - + +
294E GLU* 3.3 23.0 + - - +
295E THR* 3.1 18.4 + - - -
345E PHE* 4.1 28.1 + - + +
348E LEU* 3.3 31.6 - - + +
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Residues in contact with ILE 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249E ALA* 4.2 13.2 - - + -
251E LEU* 4.2 27.8 - - + -
253E CYS* 5.0 6.7 - - - -
255E PHE* 4.0 18.2 - - + -
288E MET* 3.3 20.1 + - - +
289E ILE 3.2 2.3 + - - +
291E GLN* 1.3 79.7 - - + +
293E LYS* 1.3 60.3 + - - +
295E THR* 3.0 18.5 + - - -
296E GLY 2.8 20.7 + - - +
297E ALA* 4.0 20.0 - - + +
298E ASN* 5.6 1.1 - - - -
300E ALA* 5.1 4.3 - - + -
319E LEU* 5.1 5.8 - - + -
345E PHE* 5.5 8.5 - - + -
348E LEU* 3.8 22.2 - - + -
353E LEU* 5.5 4.0 - - + -
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Residues in contact with LYS 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289E ILE* 2.8 26.8 + - + +
290E GLN* 3.2 31.7 + - - +
292E ILE* 1.3 78.4 - - - +
294E GLU* 1.3 59.6 + - - +
296E GLY* 3.3 12.7 + - - -
298E ASN* 3.3 28.7 - - - +
318E ASN 5.6 1.9 + - - +
319E LEU* 4.3 15.3 - - + -
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Residues in contact with GLU 294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290E GLN* 3.2 24.4 + - - +
291E GLN* 3.3 35.4 + - - +
293E LYS* 1.3 78.7 - - - +
295E THR* 1.3 63.2 + - - +
348E LEU* 4.6 2.8 - - - +
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Residues in contact with THR 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247E LYS* 5.2 2.1 - - - +
291E GLN 3.1 15.0 + - - -
292E ILE 3.0 8.4 + - - -
294E GLU* 1.3 82.8 - - - +
296E GLY* 1.3 56.9 + - - +
348E LEU* 3.5 19.5 + - + +
349E THR* 3.7 14.8 - - - +
350E ALA* 3.7 39.2 - - + +
353E LEU* 3.7 14.8 - - + +
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Residues in contact with GLY 296 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247E LYS* 4.5 6.5 - - - -
292E ILE* 2.8 19.4 + - - +
293E LYS* 3.3 13.4 + - - -
295E THR* 1.3 79.8 - - - +
297E ALA* 1.3 72.9 + - - +
298E ASN* 3.7 5.6 - - - -
353E LEU* 4.2 2.1 - - - +
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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