Contacts of the helix formed by residues 283 - 307 (chain E) in PDB entry 2BG9
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 GLY 283 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E VAL* 6.0 1.4 - - - +
282E ILE* 1.3 74.4 - - - +
284E LYS* 1.3 73.1 + - - +
286E LEU* 2.9 16.2 - - - +
287E ILE* 2.6 38.9 + - - +
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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
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282E ILE* 3.7 14.6 - - + +
283E GLY* 1.3 90.9 - - - +
285E TYR* 1.3 69.1 + - + +
287E ILE* 2.7 29.7 + - + +
288E PHE* 2.9 24.2 - - + -
471E LEU* 4.2 21.8 - - + -
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Residues in contact with TYR 285 (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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134E PHE* 4.1 17.3 - + + -
135E PRO* 4.4 2.9 - - + -
136E PHE* 2.4 55.2 - + - -
282E ILE* 4.2 31.1 + - + -
284E LYS* 1.3 80.2 - - + +
286E LEU* 1.3 62.5 + - - +
287E ILE 3.4 0.3 + - - -
288E PHE* 3.5 19.4 + + - -
289E VAL* 3.4 25.3 + - - +
468E THR* 4.8 16.8 - - + -
471E LEU* 3.2 35.5 - - + +
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Residues in contact with LEU 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D TYR* 5.0 11.2 - - + -
276E SER* 5.7 0.9 - - - +
281E LEU* 3.5 28.5 - - + -
282E ILE 2.8 27.2 + - - +
283E GLY* 2.9 17.0 - - - +
285E TYR* 1.3 79.5 - - - +
287E ILE* 1.3 61.3 + - - +
289E VAL* 3.5 5.2 + - - +
290E MET* 3.4 61.4 + - + +
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Residues in contact with ILE 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283E GLY 2.6 34.1 + - - +
284E LYS* 2.7 30.1 - - + +
286E LEU* 1.3 69.5 - - - +
288E PHE* 1.3 78.2 + - + +
290E MET* 5.2 4.3 - - - -
291E PHE* 2.7 55.9 + - + +
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Residues in contact with PHE 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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284E LYS* 2.9 34.1 + - + -
285E TYR* 3.6 20.2 - + - +
286E LEU 3.5 0.4 - - - -
287E ILE* 1.3 92.9 - - + +
289E VAL* 1.3 56.4 + - + +
291E PHE* 3.8 15.0 - + - -
292E VAL* 2.6 48.4 + - + +
463E LEU* 5.8 2.5 - - + -
464E ALA* 4.6 16.6 - - + -
467E LEU* 3.8 36.3 - - + -
468E THR* 4.9 13.9 - - - +
471E LEU* 4.5 21.3 - - + -
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Residues in contact with VAL 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E ILE* 5.5 15.5 - - + -
268E ILE* 4.8 18.6 - - + -
272E VAL* 6.1 2.2 - - + -
285E TYR 3.4 13.0 + - - +
286E LEU* 3.9 8.1 - - - +
287E ILE 3.3 1.0 - - - -
288E PHE* 1.3 75.4 - - + +
290E MET* 1.3 62.1 + - + +
292E VAL* 3.5 3.2 - - - +
293E SER* 2.5 44.6 + - - -
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Residues in contact with MET 290 (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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216D VAL* 6.5 1.6 - - + -
220D ILE* 5.8 9.0 - - + -
286E LEU* 3.4 45.9 + - + +
287E ILE* 4.6 3.4 - - - +
289E VAL* 1.3 86.5 - - + +
291E PHE* 1.3 52.5 + - + +
293E SER* 2.5 24.3 + - - +
294E LEU* 2.5 29.1 + - + +
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Residues in contact with PHE 291 (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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287E ILE* 2.7 55.1 + - + +
288E PHE* 3.8 15.3 - + - -
290E MET* 1.3 75.3 - - - +
292E VAL* 1.3 69.0 + - + +
293E SER 3.0 1.1 - - - -
294E LEU* 3.8 7.1 - - + +
295E VAL* 2.8 44.9 + - + +
460E LEU* 5.5 4.3 - - + -
463E LEU* 3.6 31.9 - - + -
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Residues in contact with VAL 292 (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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229E CYS* 5.3 12.1 - - - -
288E PHE* 2.6 35.6 + - + +
289E VAL* 3.8 2.9 - - - +
291E PHE* 1.3 85.2 - - + +
293E SER* 1.3 51.0 + - - +
295E VAL* 3.4 7.4 + - - +
296E ILE* 2.4 42.3 + - + +
460E LEU* 4.4 27.6 - - + +
461E GLY* 6.1 0.9 - - - -
463E LEU* 5.3 2.2 - - + -
464E ALA* 4.0 25.1 - - + -
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Residues in contact with SER 293 (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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265E LEU* 4.6 9.4 - - - +
268E ILE* 6.6 0.2 - - - -
289E VAL* 2.5 27.6 + - - -
290E MET* 2.5 25.0 + - - +
292E VAL* 1.3 73.2 - - - +
294E LEU* 1.3 52.7 + - - +
295E VAL 3.2 0.2 - - - -
296E ILE* 2.8 25.8 - - - +
297E VAL* 2.6 29.0 + - - +
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Residues in contact with LEU 294 (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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220D ILE* 3.5 43.5 - - + -
224D LEU* 5.0 13.9 - - + -
290E MET* 2.5 30.3 + - + +
291E PHE* 3.3 9.1 + - + +
293E SER* 1.3 75.0 + - - +
295E VAL* 1.3 53.0 + - + +
297E VAL* 3.2 13.6 + - + +
298E THR* 2.6 50.4 + - - +
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Residues in contact with VAL 295 (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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291E PHE* 2.8 33.3 + - + +
292E VAL 3.8 4.7 - - - +
293E SER 3.2 0.2 - - - -
294E LEU* 1.3 77.4 - - + +
296E ILE* 1.3 59.1 + - - +
298E THR* 3.8 12.1 - - + +
299E ASN* 2.9 34.1 + - + +
456E LEU* 4.5 9.8 - - + +
460E LEU* 3.4 40.2 - - + -
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Residues in contact with ILE 296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229E CYS* 5.5 8.7 - - - -
232E ILE* 4.4 17.9 - - + -
236E VAL* 5.0 10.1 - - + +
240E TYR* 3.7 6.4 + - - -
261E GLN* 2.7 38.4 - - - +
265E LEU* 3.0 17.0 - - + -
292E VAL* 2.4 40.7 + - + +
293E SER* 2.8 18.6 - - - +
295E VAL* 1.3 74.8 - - - +
297E VAL* 1.3 64.2 + - + +
299E ASN* 5.4 0.9 - - - -
300E CYS* 2.9 28.9 + - - +
460E LEU* 4.8 6.2 - - + +
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Residues in contact with VAL 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D LEU* 3.4 37.7 - - + -
258E LEU* 5.5 4.7 - - + -
261E GLN* 5.2 0.2 - - - +
262E THR* 4.0 5.6 - - - +
265E LEU* 3.9 24.5 - - + -
293E SER* 2.6 28.5 - - - +
294E LEU* 3.2 21.3 - - + +
296E ILE* 1.3 87.7 - - + +
298E THR* 1.3 53.1 - - - +
300E CYS* 3.0 7.2 + - + +
301E VAL* 2.7 43.6 + - + +
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Residues in contact with THR 298 (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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224D LEU* 5.8 2.4 - - - +
227D PHE* 5.3 1.2 - - + -
294E LEU* 2.6 38.7 + - - +
295E VAL* 3.4 14.0 - - + +
297E VAL* 1.3 74.3 - - - +
299E ASN* 1.3 53.3 + - + +
301E VAL* 3.2 8.0 - - - +
302E ILE* 2.7 55.9 + - + +
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Residues in contact with ASN 299 (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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240E TYR* 3.0 14.0 + - + +
295E VAL* 2.9 19.5 + - + +
296E ILE* 4.6 0.7 - - - +
298E THR* 1.3 74.1 - - + +
300E CYS* 1.3 52.2 + - - +
302E ILE* 3.4 26.3 - - + +
303E VAL* 2.7 32.6 + - - +
306E VAL* 5.7 0.2 - - - +
449E ALA* 6.0 0.7 - - - +
452E TRP* 5.1 4.0 - - - +
453E ILE* 3.1 34.5 - - + +
456E LEU* 3.8 26.3 - - + +
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Residues in contact with CYS 300 (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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236E VAL* 4.4 13.2 - - + -
239E VAL* 5.5 7.9 - - - -
240E TYR* 3.0 14.9 + - - +
258E LEU* 3.2 38.2 - - - +
261E GLN* 4.1 19.5 - - - +
296E ILE 2.9 19.3 + - - +
297E VAL* 3.0 9.8 + - - +
298E THR 3.0 0.8 - - - -
299E ASN* 1.3 74.4 - - - +
301E VAL* 1.3 60.8 + - - +
303E VAL* 3.0 29.1 + - - +
304E LEU* 3.4 1.6 + - - +
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Residues in contact with VAL 301 (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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224D LEU* 4.7 9.9 - - + -
227D PHE* 3.9 29.2 - - + -
228D LEU* 3.6 32.1 - - + -
231D LEU* 4.1 13.6 - - + +
258E LEU* 3.9 19.3 - - + -
297E VAL* 2.7 24.7 + - + +
298E THR* 3.2 13.9 - - - +
300E CYS* 1.3 70.2 - - - +
302E ILE* 1.3 65.0 + - - +
304E LEU* 3.1 8.0 + - + +
305E ASN* 2.8 21.5 + - - +
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Residues in contact with ILE 302 (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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227D PHE* 4.5 8.2 - - + -
298E THR* 2.7 43.4 + - + +
299E ASN* 3.2 29.8 - - - +
301E VAL* 1.3 78.9 - - + +
303E VAL* 1.3 50.6 + - - +
305E ASN* 2.8 16.6 + - - +
306E VAL* 2.4 55.1 + - + +
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Residues in contact with VAL 303 (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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239E VAL* 3.9 28.9 - - + +
240E TYR* 3.1 39.5 - - + -
254E SER* 4.1 7.2 - - - +
255E ILE* 6.1 0.7 - - + -
299E ASN* 2.7 16.1 + - - +
300E CYS* 3.0 13.0 - - - +
302E ILE* 1.3 74.2 - - - +
304E LEU* 1.3 56.6 + - + +
306E VAL* 2.6 17.8 + - + +
307E SER* 2.3 41.9 + - - +
449E ALA* 5.6 6.3 - - + -
453E ILE* 5.5 0.7 - - + -
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Residues in contact with LEU 304 (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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231D LEU* 4.2 17.5 - - + -
235D LEU* 3.9 20.0 - - + -
242D LYS* 3.0 34.1 - - + +
245D LEU* 4.5 4.5 - - + -
249D VAL* 5.9 2.0 - - + -
251E CYS* 4.7 3.1 - - + +
255E ILE* 3.2 40.6 - - + -
258E LEU* 6.1 5.6 - - + -
300E CYS 3.4 1.9 + - - +
301E VAL* 3.1 10.4 + - + +
303E VAL* 1.3 79.1 - - + +
305E ASN* 1.3 51.7 + - - +
306E VAL 2.7 4.3 - - - -
307E SER* 2.8 23.0 - - - +
308E LEU* 2.5 41.8 + - + +
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Residues in contact with ASN 305 (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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227D PHE* 4.3 15.9 - - + -
231D LEU* 4.4 1.6 - - + +
238D ASP* 5.6 1.0 - - - +
301E VAL 2.8 11.9 + - - +
302E ILE* 2.8 19.6 + - - +
304E LEU* 1.3 77.7 - - - +
306E VAL* 1.3 59.0 + - - +
308E LEU* 3.0 41.0 - - + +
309E ARG* 3.2 15.2 + - - +
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Residues in contact with VAL 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299E ASN* 5.7 0.2 - - - +
302E ILE* 2.4 44.1 + - + +
303E VAL* 2.6 19.2 + - + +
305E ASN* 1.3 77.4 - - - +
307E SER* 1.2 49.4 + - - +
308E LEU 2.9 4.3 - - - -
309E ARG* 2.4 47.4 + - - +
445E VAL* 4.4 18.4 - - + -
446E ILE* 4.4 13.7 - - + -
449E ALA* 4.2 25.6 - - + -
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Residues in contact with SER 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D LYS* 3.0 13.2 + - - +
243E PRO* 6.5 0.4 - - - -
251E CYS* 4.7 16.7 + - - +
254E SER* 5.0 4.5 - - - -
303E VAL* 2.3 32.6 + - - +
304E LEU* 2.8 26.4 - - - +
306E VAL* 1.2 67.9 - - - +
308E LEU* 1.4 52.7 + - - +
309E ARG* 3.6 6.7 - - - +
314E HIS* 2.3 26.1 - - - +
446E ILE* 5.1 10.5 - - - -
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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) + - + + + + + -
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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