Contacts of the helix formed by residues 221 - 245 (chain E) in PDB entry 5I4V
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 221 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511B LYS* 5.8 6.3 - - - +
512B LEU* 6.2 0.7 - - + -
219E GLN* 3.9 2.9 + - - +
220E LEU* 1.3 75.7 - - - +
222E ALA* 1.3 58.0 + - + +
223E ALA* 3.3 25.6 - - + +
224E GLN* 3.0 28.0 + - + +
225E GLU* 2.8 33.9 + - - +
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Residues in contact with ALA 222 (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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508B PHE* 4.8 17.3 - - + -
220E LEU 3.7 1.2 + - - -
221E THR* 1.3 73.5 - - + +
223E ALA* 1.3 64.2 + - - +
225E GLU* 3.0 11.3 + - - +
226E LEU* 2.9 32.9 + - + +
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Residues in contact with ALA 223 (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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508B PHE* 4.0 37.9 - - + +
509B PHE* 4.6 2.3 - - - -
511B LYS* 5.3 6.7 - - + +
512B LEU* 3.9 28.0 - - + +
221E THR* 3.3 15.2 - - + +
222E ALA* 1.3 79.8 - - - +
224E GLN* 1.3 57.5 + - - +
226E LEU* 3.2 3.1 + - - +
227E MET* 3.0 28.6 + - - +
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Residues in contact with GLN 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B LEU* 4.6 16.4 - - + +
219E GLN 3.9 5.7 - - - +
220E LEU* 3.7 15.1 - - + -
221E THR* 3.0 40.2 + - + +
223E ALA* 1.3 75.4 - - - +
225E GLU* 1.3 67.2 + - - +
227E MET* 3.3 7.3 + - - +
228E ILE* 3.1 30.0 + - + +
398E PRO 5.0 0.8 + - - +
401E GLU* 4.0 13.7 + - - +
402E ALA* 3.7 38.8 - - + +
405E SER* 3.9 10.3 + - - -
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Residues in contact with GLU 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A GLU* 3.2 40.7 - - - +
440A PHE* 3.8 38.3 - - + +
220E LEU* 4.2 18.6 - - + +
221E THR 2.8 16.0 + - - +
222E ALA* 3.0 13.1 + - - +
224E GLN* 1.3 73.1 - - - +
226E LEU* 1.3 60.9 + - + +
228E ILE* 3.4 2.3 + - - +
229E GLN* 2.9 37.3 + - - +
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Residues in contact with LEU 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A GLU* 5.5 8.3 - - + +
501B LEU 5.9 0.2 - - - +
504B LEU* 5.9 0.9 - - + -
505B GLU* 4.2 34.1 - - + +
508B PHE* 3.5 35.4 - - + -
509B PHE* 3.8 13.1 - - + -
222E ALA* 2.9 21.9 + - + +
223E ALA* 3.7 4.5 - - - +
225E GLU* 1.3 76.5 - - + +
227E MET* 1.3 61.1 + - - +
229E GLN* 3.5 22.8 - - - +
230E GLN* 2.9 27.9 + - - +
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Residues in contact with MET 227 (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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509B PHE* 3.6 23.3 - - + -
512B LEU* 3.4 36.8 - - + -
513B ILE* 4.3 12.8 - - + -
223E ALA 3.0 15.3 + - - +
224E GLN* 3.7 5.6 - - - +
226E LEU* 1.3 74.7 - - - +
228E ILE* 1.3 68.4 + - + +
230E GLN* 3.1 4.3 + - - +
231E LEU* 3.0 24.8 + - + +
290E PRO* 4.7 8.3 - - + -
372E LEU* 5.9 0.2 - - + -
398E PRO* 5.0 9.6 - - + +
399E TYR* 3.3 53.8 - - + +
402E ALA* 5.3 7.4 - - - -
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Residues in contact with ILE 228 (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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440A PHE* 3.9 16.8 - - + -
220E LEU* 4.5 8.3 - - + -
224E GLN 3.1 17.9 + - - +
225E GLU 3.7 3.4 - - - +
227E MET* 1.3 74.8 - - + +
229E GLN* 1.3 64.2 - - - +
231E LEU* 3.1 10.2 + - + +
232E VAL* 3.0 24.8 + - + +
368E ALA* 3.6 36.8 - - + +
371E ALA* 6.2 0.2 - - + -
372E LEU* 3.9 27.8 - - + -
402E ALA* 4.3 12.1 - - + +
406E TYR* 3.6 30.1 - - + -
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Residues in contact with GLN 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A SER* 3.5 42.8 + - - -
437A GLU* 4.3 2.9 - - - +
440A PHE* 4.4 18.9 - - + +
443A ARG* 5.3 5.8 - - - +
505B GLU* 5.6 2.7 - - - +
225E GLU* 2.9 26.7 + - - +
226E LEU* 3.5 30.3 - - + +
228E ILE* 1.3 77.1 - - - +
230E GLN* 1.3 54.9 + - - +
232E VAL* 3.5 6.1 + - - +
233E ALA* 3.0 30.6 + - + +
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Residues in contact with GLN 230 (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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502B LYS* 3.5 24.2 + - - -
505B GLU* 3.7 6.0 + - - +
506B HIS* 6.4 1.6 - - - -
509B PHE* 3.8 27.0 - - + -
226E LEU 2.9 15.2 + - - +
227E MET 3.1 9.6 + - - +
229E GLN* 1.3 77.0 - - - +
231E LEU* 1.3 57.4 + - - +
233E ALA* 3.3 7.9 + - - +
234E ALA* 2.9 26.4 + - - +
288E GLN* 3.5 45.5 + - - +
290E PRO* 4.3 8.5 - - + -
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Residues in contact with LEU 231 (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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227E MET* 3.0 18.5 + - + +
228E ILE* 3.1 8.5 + - - +
230E GLN* 1.3 73.3 - - - +
232E VAL* 1.3 68.6 + - - +
234E ALA* 3.1 7.7 + - + +
235E GLN* 3.1 20.4 + - - +
285E PHE* 3.6 13.0 - - + -
288E GLN 5.0 1.3 - - - +
289E VAL* 4.1 25.6 - - + -
290E PRO* 4.1 26.2 - - + -
371E ALA* 3.9 26.9 - - + +
372E LEU* 3.9 31.4 - - + +
375E ALA* 4.2 2.9 - - + -
399E TYR* 4.0 15.9 - - + -
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Residues in contact with VAL 232 (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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443A ARG* 3.9 33.9 - - - +
458A ASP 5.3 1.3 - - - +
459A VAL 4.7 0.7 - - - +
228E ILE* 3.0 20.7 + - + +
229E GLN 3.8 3.6 - - - +
231E LEU* 1.3 76.9 - - - +
233E ALA* 1.3 65.1 + - - +
235E GLN* 3.3 13.2 + - - +
236E LEU* 3.3 27.5 + - + +
367E ASP* 4.1 14.4 - - + +
368E ALA* 3.6 38.1 - - + +
371E ALA* 4.4 6.3 - - + -
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Residues in contact with ALA 233 (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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458A ASP* 6.2 2.5 - - + -
229E GLN* 3.0 18.8 + - + +
230E GLN* 3.6 10.3 - - - +
232E VAL* 1.3 76.9 - - - +
234E ALA* 1.3 63.3 + - - +
236E LEU* 3.2 11.2 + - - +
237E GLN* 3.1 25.7 + - - +
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Residues in contact with ALA 234 (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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230E GLN* 2.9 19.6 + - - +
231E LEU* 3.5 7.4 - - - +
233E ALA* 1.3 76.6 - - - +
235E GLN* 1.3 57.3 + - - +
237E GLN* 3.5 4.9 + - - +
238E CYS* 3.0 33.6 + - - -
285E PHE* 3.9 17.7 - - + -
288E GLN* 3.9 39.5 - - + +
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Residues in contact with GLN 235 (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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231E LEU 3.1 10.0 + - - +
232E VAL* 3.7 9.0 - - - +
233E ALA 3.3 0.2 - - - -
234E ALA* 1.3 75.7 - - - +
236E LEU* 1.3 60.7 + - + +
238E CYS* 3.3 5.6 + - - +
239E ASN* 2.8 39.9 + - - +
281E GLU* 5.7 1.2 + - - -
285E PHE* 3.5 29.6 - - + -
315E GLU* 3.3 18.4 + - - -
318E ARG* 3.0 42.1 + - - +
367E ASP 4.1 0.2 - - - +
371E ALA* 3.5 23.6 - - + +
374E ILE* 3.6 13.6 - - - +
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Residues in contact with LEU 236 (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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458A ASP* 3.4 42.6 - - + +
459A VAL 4.4 4.9 - - - +
460A HIS 3.6 17.3 - - - +
461A GLU* 3.9 15.5 - - + -
464A GLY 4.5 2.0 - - - +
465A SER* 3.3 38.6 - - - +
232E VAL* 3.3 25.5 + - + +
233E ALA* 3.2 9.7 + - - +
235E GLN* 1.3 74.3 - - + +
237E GLN* 1.3 65.9 + - - +
239E ASN* 3.3 7.8 + - - +
240E LYS* 3.0 21.5 + - - +
367E ASP* 5.7 1.1 - - - +
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Residues in contact with GLN 237 (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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233E ALA* 3.1 18.3 + - - +
234E ALA* 3.6 6.2 - - - +
236E LEU* 1.3 78.4 - - - +
238E CYS* 1.3 60.2 + - - +
240E LYS* 3.5 10.7 + - + +
241E ARG* 3.4 46.2 + - - +
288E GLN* 3.3 34.9 + - - +
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Residues in contact with CYS 238 (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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234E ALA 3.0 25.6 + - - +
235E GLN* 3.6 7.2 - - - +
236E LEU 3.2 0.2 - - - -
237E GLN* 1.3 75.6 - - - +
239E ASN* 1.3 65.6 + - - +
241E ARG* 3.3 12.9 + - - +
242E SER* 3.1 23.2 + - - -
281E GLU* 3.9 20.9 - - + +
284E ASP* 3.6 16.8 - - + +
285E PHE* 3.5 38.4 - - + -
288E GLN* 4.1 9.4 - - - -
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Residues in contact with ASN 239 (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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461A GLU* 3.7 25.3 - - - +
465A SER* 3.8 13.6 + - - +
235E GLN* 2.8 29.6 + - - +
236E LEU* 3.6 11.8 - - - +
238E CYS* 1.3 75.7 - - - +
240E LYS* 1.3 62.9 + - - +
242E SER* 3.1 8.2 + - - -
243E PHE* 2.9 36.3 + - + -
281E GLU* 3.0 25.1 + - - -
315E GLU* 4.4 3.1 + - - +
318E ARG* 6.1 0.2 - - - -
319E ARG* 3.3 20.7 - - - +
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Residues in contact with LYS 240 (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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385A ASN* 5.1 9.5 + - - -
465A SER* 3.5 30.2 - - - +
466A GLY* 5.8 4.5 - - - -
469A LYS* 6.3 3.1 - - - +
236E LEU 3.0 10.2 + - - +
237E GLN* 3.6 13.7 - - + +
238E CYS 3.3 0.2 - - - -
239E ASN* 1.3 75.9 - - - +
241E ARG* 1.3 65.6 + - + +
243E PHE* 3.2 11.6 + - - +
244E SER* 3.1 23.9 + - - +
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Residues in contact with ARG 241 (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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237E GLN* 3.4 47.4 + - - +
238E CYS* 3.3 11.8 + - - +
239E ASN 3.2 0.6 - - - -
240E LYS* 1.3 81.7 - - + +
242E SER* 1.3 63.5 + - - +
244E SER* 3.2 25.3 - - - +
245E ASP* 3.5 11.3 - - - +
284E ASP* 2.9 48.0 + - - +
288E GLN* 4.5 7.0 + - - -
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Residues in contact with SER 242 (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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238E CYS 3.1 10.6 + - - -
239E ASN* 3.1 9.9 + - - -
241E ARG* 1.3 77.6 - - - +
243E PHE* 1.3 63.9 + - - +
245E ASP* 3.0 20.3 + - - +
246E GLN 3.8 0.9 + - - -
277E ILE* 3.8 20.8 - - - +
281E GLU* 2.6 39.9 + - - +
330E LEU* 3.6 21.1 - - - +
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Residues in contact with PHE 243 (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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461A GLU* 4.5 13.5 - - - -
462A GLY* 4.2 4.9 - - - -
465A SER* 3.3 26.5 - - - -
467A SER* 3.2 35.0 - - - -
239E ASN* 2.9 32.8 + - + -
240E LYS* 3.2 10.5 + - - +
242E SER* 1.3 77.5 - - - +
244E SER* 1.3 62.3 + - - +
246E GLN* 3.1 23.0 + - - +
247E PRO* 4.2 1.4 - - - +
319E ARG* 5.4 5.6 - - - -
330E LEU* 3.4 47.1 - - + -
331E LYS* 3.8 10.1 - - + -
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Residues in contact with SER 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E LYS* 3.1 18.3 + - - +
241E ARG* 3.2 15.7 + - - +
242E SER 3.2 0.2 - - - -
243E PHE* 1.3 76.0 - - - +
245E ASP* 1.3 61.8 - - - +
247E PRO* 3.2 18.7 - - - +
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Residues in contact with ASP 245 (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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241E ARG 3.5 12.1 + - - +
242E SER* 3.0 14.9 + - - +
244E SER* 1.3 78.1 - - - +
246E GLN* 1.3 64.3 + - - +
247E PRO* 3.4 2.7 - - - -
248E LYS* 3.1 43.1 + - + +
249E VAL* 3.6 10.0 - - - +
277E ILE* 3.8 22.4 - - + +
280E GLN* 4.4 12.6 - - - +
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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