Contacts of the helix formed by residues 296 - 319 (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 GLY 296 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294E GLN 4.1 0.4 + - - -
295E LEU* 1.3 77.9 - - - +
297E ARG* 1.3 61.3 + - - -
298E GLU 3.2 2.9 - - - -
299E ASP* 3.3 10.8 + - - +
300E GLN* 3.1 23.7 + - - +
388E GLU* 4.7 10.6 + - - -
391E ARG* 4.6 3.2 - - - +
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Residues in contact with ARG 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293E LEU* 4.6 12.9 - - - +
295E LEU 3.8 1.0 + - - -
296E GLY* 1.3 70.3 - - - -
298E GLU* 1.3 64.9 + - + +
300E GLN* 3.6 29.9 + - - +
301E ILE* 3.2 34.4 + - + +
472E HIS* 3.6 41.5 - - - +
475E LEU* 3.6 38.5 + - + +
476E GLN* 4.4 8.9 + - - +
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Residues in contact with GLU 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296E GLY* 3.2 0.8 - - - -
297E ARG* 1.3 80.7 - - + +
299E ASP* 1.3 58.4 + - - +
301E ILE* 3.5 13.5 + - + +
302E ALA* 3.0 25.6 + - - +
385E ASN 4.9 2.0 - - - +
387E GLN* 3.1 31.8 + - - +
472E HIS* 6.5 0.4 - - + -
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Residues in contact with ASP 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295E LEU* 4.7 16.2 - - + +
296E GLY* 3.3 13.7 + - - +
298E GLU* 1.3 76.9 - - - +
300E GLN* 1.3 60.2 + - - +
301E ILE 3.2 1.6 - - - -
302E ALA* 3.6 4.8 - - - +
303E LEU* 2.8 40.8 + - + +
385E ASN 3.8 5.5 - - - +
386E VAL* 3.8 12.0 - - + +
387E GLN* 3.0 32.6 + - - +
388E GLU* 3.0 37.4 + - - +
392E VAL* 4.9 2.0 - - + +
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Residues in contact with GLN 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292E PHE* 3.1 52.8 + - + +
293E LEU* 3.5 20.3 + - - +
295E LEU* 3.1 25.6 + - + +
296E GLY 3.1 16.0 + - - +
297E ARG* 3.6 37.5 + - - +
299E ASP* 1.3 75.6 - - - +
301E ILE* 1.3 62.3 + - - +
303E LEU* 3.9 1.4 - - - +
304E LEU* 3.1 32.3 + - - +
475E LEU* 3.6 17.7 - - + +
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Residues in contact with ILE 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297E ARG* 3.2 21.9 + - + +
298E GLU* 3.6 15.0 - - + +
299E ASP 3.2 0.6 - - - -
300E GLN* 1.3 77.1 - - - +
302E ALA* 1.3 57.1 + - - +
304E LEU* 3.3 2.1 + - - +
305E LYS* 2.9 45.0 + - + +
469E LYS 5.9 1.8 - - - +
471E LEU* 4.1 25.4 - - + +
472E HIS* 4.0 34.8 - - + +
475E LEU* 3.9 17.0 - - + -
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Residues in contact with ALA 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298E GLU 3.0 18.3 + - - +
299E ASP* 3.1 6.7 + - - +
301E ILE* 1.3 79.9 - - - +
303E LEU* 1.3 63.5 + - - +
305E LYS* 3.6 9.3 + - - +
306E ALA* 3.5 21.1 + - - +
383E ARG* 4.3 4.5 - - - +
384E PRO* 3.6 23.8 - - - +
385E ASN* 3.9 19.5 - - + +
386E VAL* 4.3 5.8 - - + -
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Residues in contact with LEU 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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292E PHE* 4.5 6.1 - - + -
295E LEU* 3.8 28.7 - - + -
299E ASP* 2.8 24.4 + - + +
300E GLN 3.9 3.6 - - - +
302E ALA* 1.3 73.9 - - - +
304E LEU* 1.3 60.1 + - - +
306E ALA* 3.7 2.3 + - - +
307E SER* 3.0 28.3 + - - -
378E ILE* 3.4 33.3 - - + +
379E PHE* 4.4 7.4 - - + -
380E SER 3.4 26.2 - - - +
383E ARG* 4.0 11.2 + - + -
386E VAL* 4.0 14.6 - - + -
392E VAL* 4.3 19.3 - - + -
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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
----------------------------------------------------------
282E ILE* 3.8 30.1 - - + +
283E VAL* 4.4 16.8 - - + -
286E ALA* 4.0 18.8 - - + -
292E PHE* 3.6 22.4 - - + -
300E GLN 3.1 20.3 + - - +
301E ILE* 3.9 3.1 - - - +
303E LEU* 1.3 75.5 - - - +
305E LYS* 1.3 64.9 + - - +
307E SER* 3.8 6.1 - - - +
308E THR* 2.8 34.1 + - - +
378E ILE* 5.3 6.3 - - + -
456E ILE* 4.7 1.3 - - + -
471E LEU* 4.3 13.0 - - + -
475E LEU* 4.2 22.2 - - + -
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Residues in contact with LYS 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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301E ILE* 2.9 37.3 + - + +
302E ALA* 3.8 8.7 - - - +
304E LEU* 1.3 77.0 - - - +
306E ALA* 1.3 62.7 + - + +
308E THR* 4.0 4.9 + - - -
309E ILE* 4.9 1.4 + - - +
385E ASN* 5.6 7.9 - - - +
455E GLU* 3.4 15.3 + - + +
456E ILE* 3.8 43.6 - - + +
457E TRP* 4.6 7.1 + - - -
458E ASP* 3.0 31.4 + - - -
471E LEU* 4.5 5.8 - - + +
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Residues in contact with ALA 306 (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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302E ALA 3.5 9.2 + - - +
303E LEU 4.1 0.4 - - - +
304E LEU 3.2 0.2 - - - -
305E LYS* 1.3 80.5 - - + +
307E SER* 1.3 61.1 + - - +
308E THR 3.8 0.3 + - - -
309E ILE* 4.0 13.7 - - - +
310E GLU* 3.9 13.2 - - - +
383E ARG* 3.4 44.5 + - + +
384E PRO* 4.6 9.2 - - + -
432E SER* 4.6 3.5 + - - -
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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
----------------------------------------------------------
303E LEU 3.0 18.4 + - - -
304E LEU* 3.7 7.8 + - - +
306E ALA* 1.3 77.3 - - - +
308E THR* 1.3 68.0 + - - +
309E ILE 3.3 2.7 - - - -
310E GLU* 3.0 4.9 + - - +
311E ILE* 2.8 41.1 + - - +
377E ASN* 3.4 24.7 - - - -
378E ILE* 4.1 8.9 - - - +
383E ARG* 3.8 12.8 - - - +
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Residues in contact with THR 308 (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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279E VAL* 4.1 15.4 - - + +
282E ILE* 3.6 26.2 - - + +
304E LEU* 2.8 24.9 + - - +
305E LYS 4.2 2.7 - - - -
306E ALA 3.5 0.8 - - - -
307E SER* 1.3 78.5 + - - +
309E ILE* 1.3 59.3 + - - +
311E ILE* 3.3 1.1 + - - -
312E MET* 2.8 50.2 + - - +
456E ILE* 3.1 29.5 - - + +
457E TRP* 4.4 7.6 - - + -
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Residues in contact with ILE 309 (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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305E LYS 4.9 1.3 + - - +
306E ALA 4.0 11.9 - - - +
308E THR* 1.3 81.5 - - - +
310E GLU* 1.3 61.4 + - + +
312E MET* 3.3 27.5 + - + +
313E LEU* 2.9 42.5 + - + +
349E PHE* 4.6 8.5 - - + -
432E SER* 3.7 31.4 - - - +
435E HIS* 3.7 47.6 - - + +
457E TRP* 4.1 15.1 - - + +
501E 67S 5.0 2.5 - - + +
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Residues in contact with GLU 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306E ALA 3.9 7.1 - - - +
307E SER 3.0 6.8 + - - +
309E ILE* 1.3 88.1 - - + +
311E ILE* 1.3 57.0 + - - +
313E LEU* 3.1 7.0 + - - +
314E LEU* 3.0 31.1 + - - +
377E ASN* 2.7 38.4 + - - +
383E ARG* 2.8 36.8 + - - -
425E LEU 4.9 0.7 - - - +
428E LEU* 3.8 42.7 - - + +
429E ARG* 3.4 16.6 + - - -
432E SER* 4.1 7.4 + - - -
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Residues in contact with ILE 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282E ILE* 3.8 37.5 - - + -
285E PHE* 6.3 0.2 - - + -
307E SER* 2.8 41.7 + - - +
308E THR 3.8 2.7 - - - +
310E GLU* 1.3 68.5 - - - +
312E MET* 1.3 60.9 + - - +
314E LEU* 3.0 8.9 + - + +
315E GLU* 2.8 41.9 + - + +
374E ILE* 4.1 30.5 - - + +
377E ASN* 4.1 10.5 - - + +
378E ILE* 3.7 25.6 - - + -
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Residues in contact with MET 312 (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 ALA* 4.7 4.0 - - + +
278E SER* 3.1 31.4 - - - +
279E VAL* 4.7 6.5 - - - -
282E ILE* 4.2 3.6 - - + +
308E THR* 2.8 42.3 + - - +
309E ILE* 3.3 15.9 - - + +
311E ILE* 1.3 74.0 - - - +
313E LEU* 1.3 54.4 + - + +
315E GLU* 3.5 4.7 + - - +
316E THR* 2.6 38.1 + - - -
457E TRP* 3.7 30.3 - - + -
501E 67S 3.3 47.7 - - + +
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Residues in contact with LEU 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309E ILE* 2.9 29.3 + - + +
310E GLU* 3.4 8.3 - - - +
311E ILE 3.1 0.4 - - - -
312E MET* 1.3 75.4 - - - +
314E LEU* 1.3 60.4 + - - +
316E THR* 3.4 5.6 - - - -
317E ALA* 2.9 28.9 + - - +
349E PHE* 4.9 7.0 - - + -
353E ILE* 3.8 39.3 - - + -
356E PHE* 3.8 11.6 - - + -
357E SER* 5.4 0.2 + - - -
428E LEU* 4.0 12.1 - - + -
431E LEU* 3.4 46.0 - - + +
432E SER 4.9 0.7 - - - +
501E 67S 4.8 11.0 - - + -
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Residues in contact with LEU 314 (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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310E GLU 3.0 14.9 + - - +
311E ILE* 3.0 10.7 + - - +
313E LEU* 1.3 75.5 - - - +
315E GLU* 1.3 63.7 + - - +
316E THR 3.2 0.2 + - - -
317E ALA* 3.2 3.9 + - - +
318E ARG* 3.0 23.4 + - - +
356E PHE* 4.1 21.5 - - + -
360E MET* 4.3 15.3 - - - -
370E TYR* 3.8 20.9 - - + +
373E LEU* 4.5 24.9 - - + +
374E ILE* 4.0 34.3 - - + -
377E ASN* 5.0 4.9 - - + +
424E LYS* 5.7 0.9 - - + -
425E LEU* 5.6 0.2 - - + -
428E LEU* 4.0 22.2 - - + -
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Residues in contact with GLU 315 (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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235E GLN* 3.3 16.4 + - - -
239E ASN* 4.4 2.1 + - - +
278E SER* 6.0 0.4 - - - +
281E GLU* 3.9 10.9 - - - +
282E ILE* 5.9 2.0 - - + -
311E ILE* 2.8 34.9 + - + +
312E MET* 3.8 4.5 - - - +
314E LEU* 1.3 73.4 - - - +
316E THR* 1.3 62.9 + - - +
318E ARG* 2.8 39.6 + - - +
319E ARG* 2.7 55.7 + - - +
370E TYR* 5.1 0.2 - - - -
374E ILE* 3.5 8.1 - - + +
501E 67S 4.1 19.1 - - + +
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Residues in contact with THR 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312E MET 2.6 25.8 + - - -
313E LEU* 3.4 9.4 - - - -
314E LEU 3.1 0.2 - - - -
315E GLU* 1.3 75.1 - - - +
317E ALA* 1.3 66.6 + - - +
319E ARG* 2.9 19.2 + - - +
320E TYR* 3.4 7.6 + - - +
327E ILE* 3.6 36.2 - - + +
329E PHE* 4.2 8.3 - - + -
353E ILE* 4.0 19.1 - - + -
357E SER* 4.6 1.8 - - - +
501E 67S 3.5 30.2 - - + +
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Residues in contact with ALA 317 (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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313E LEU 2.9 12.7 + - - +
314E LEU 3.6 7.9 - - - +
316E THR* 1.3 76.1 - - - +
318E ARG* 1.3 62.9 + - - +
320E TYR* 3.0 21.1 + - - +
356E PHE* 4.1 8.5 - - + -
357E SER* 3.5 37.2 + - - +
360E MET* 3.9 23.3 - - + +
361E ARG* 4.9 3.6 + - - +
370E TYR* 4.2 3.7 + - - -
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Residues in contact with ARG 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A GLU* 4.2 28.0 - - - +
235E GLN* 3.0 33.4 + - - +
314E LEU 3.0 12.1 + - - +
315E GLU* 2.8 44.7 + - - +
317E ALA* 1.3 78.2 - - - +
319E ARG* 1.3 69.7 + - - +
320E TYR 3.3 4.1 + - - +
361E ARG* 4.9 4.4 + - - +
367E ASP* 3.3 46.0 + - - +
370E TYR* 3.6 47.0 + - + +
374E ILE* 4.2 0.6 - - - +
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Residues in contact with ARG 319 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A GLU* 3.6 28.8 + - - +
239E ASN* 3.3 29.3 + - - +
243E PHE* 5.4 5.9 - - - -
281E GLU* 4.2 3.8 + - - -
315E GLU* 2.7 50.1 + - - +
316E THR 2.9 10.9 + - - +
318E ARG* 1.3 84.1 - - - +
320E TYR* 1.3 60.3 + - - +
321E ASN* 3.8 1.6 + - - +
326E CYS 3.8 0.3 - - - +
327E ILE* 3.4 5.4 - - + -
328E THR* 3.0 52.3 + - - +
329E PHE* 4.5 9.0 - - - -
330E LEU* 4.9 6.9 + - - +
501E 67S 3.9 25.0 + - - -
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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