Contacts of the helix formed by residues 416 - 445 (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 LEU 416 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414E ASP* 3.2 7.5 - - - +
415E GLN* 1.3 82.1 - - + +
417E ARG* 1.3 63.7 + - - +
418E PHE 3.3 0.7 - - - -
419E PRO* 3.3 7.2 - - + +
420E ARG* 3.0 57.4 + - - +
465F GLU* 3.6 43.5 - - + +
468F TYR* 4.0 18.6 - - + -
469F ALA* 4.4 13.7 - - + +
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Residues in contact with ARG 417 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363E LEU* 3.0 24.3 + - + +
364E GLY* 2.9 29.5 + - - -
365E LEU* 3.7 5.0 - - + +
369E GLU* 2.7 36.7 + - - +
407E THR* 3.1 21.3 - - + +
410E LYS* 3.8 8.3 - - - +
411E ARG* 4.0 42.9 - - - +
414E ASP* 3.4 25.2 + - - +
415E GLN 3.2 1.8 - - - -
416E LEU* 1.3 77.1 - - - +
418E PHE* 1.3 56.8 + - - +
420E ARG* 3.5 16.1 - - - +
421E MET* 3.1 36.7 + - + +
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Residues in contact with PHE 418 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400E VAL* 4.1 13.5 - - + -
403E LEU* 4.2 15.5 - - + -
404E LEU* 3.6 55.4 - - + -
407E THR* 3.7 19.8 - - + +
408E ARG* 4.4 7.6 - - - +
415E GLN 4.0 1.0 + - - -
417E ARG* 1.3 75.8 - - - +
419E PRO* 1.3 77.9 - - + +
421E MET* 3.2 7.4 + - - +
422E LEU* 3.0 58.1 + - + +
486F PHE* 4.5 15.3 - + - -
487F ALA* 3.8 23.6 - - + -
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Residues in contact with PRO 419 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408E ARG* 4.3 3.1 - - - +
415E GLN 3.5 10.5 - - - +
416E LEU* 3.3 23.1 - - + +
418E PHE* 1.3 102.0 - - + +
420E ARG* 1.3 60.5 + - - +
422E LEU* 3.2 2.6 + - + +
423E MET* 2.9 30.0 + - - +
468F TYR* 3.8 30.5 - - + -
472F GLU* 5.6 0.4 - - - +
486F PHE* 4.1 11.4 - - + -
490F LEU* 3.8 27.4 - - + -
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Residues in contact with ARG 420 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363E LEU* 4.2 29.2 - - + +
414E ASP* 2.7 33.9 + - - -
416E LEU* 3.0 48.5 + - - +
417E ARG* 3.5 13.7 - - - +
419E PRO* 1.3 77.4 - - - +
421E MET* 1.3 63.7 + - - +
423E MET* 3.4 10.6 + - - +
424E LYS* 3.5 18.4 + - - +
461F GLU* 5.5 4.7 - - - +
465F GLU* 3.2 34.2 + - + +
468F TYR* 4.4 11.6 - - + +
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Residues in contact with MET 421 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363E LEU* 3.9 17.0 - - + -
365E LEU* 4.0 23.8 - - + -
369E GLU* 3.7 29.8 - - + +
373E LEU* 4.0 19.4 - - + +
403E LEU* 3.5 43.3 - - + -
407E THR* 4.3 13.7 - - - -
417E ARG* 3.1 22.0 + - + +
418E PHE* 3.2 8.3 + - - +
420E ARG* 1.3 73.5 - - - +
422E LEU* 1.3 68.0 + - - +
424E LYS* 2.9 27.3 + - - +
425E LEU 3.9 1.6 + - - -
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Residues in contact with LEU 422 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373E LEU* 4.9 3.4 - - + -
376E ILE* 5.0 7.4 - - + -
400E VAL* 5.0 4.0 - - + -
403E LEU* 4.6 12.8 - - + -
418E PHE* 3.0 53.9 + - + +
419E PRO* 3.2 8.0 + - + +
421E MET* 1.3 75.1 - - - +
423E MET* 1.3 70.3 + - + +
425E LEU* 3.0 40.1 + - + +
426E VAL* 4.0 1.2 + - - +
487F ALA* 4.3 11.2 - - + -
490F LEU* 4.2 22.4 - - + -
491F LEU* 4.4 25.4 - - + -
494F PRO* 5.0 1.2 - - - +
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Residues in contact with MET 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419E PRO* 2.9 17.4 + - + +
420E ARG* 3.7 7.0 - - - +
421E MET 3.1 0.4 - - - -
422E LEU* 1.3 78.6 - - + +
424E LYS* 1.3 61.9 + - + +
425E LEU 3.2 0.2 - - - -
426E VAL* 3.0 41.1 + - + +
427E SER* 3.4 7.4 + - - -
444F ILE* 4.3 11.0 - - - -
464F ARG* 4.5 13.0 + - - +
468F TYR* 2.9 34.1 - - + +
490F LEU* 3.9 27.1 - - + +
493F LEU* 3.6 33.4 - - + -
494F PRO* 5.3 0.4 - - + -
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Residues in contact with LYS 424 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314E LEU* 5.7 0.4 - - + -
356E PHE* 4.5 9.1 - - + -
359E ALA* 3.6 28.2 + - - +
360E MET* 3.5 41.0 - - + +
362E ARG* 5.7 0.4 - - - +
363E LEU* 4.0 23.4 - - + +
373E LEU* 4.9 9.0 - - + -
420E ARG* 3.6 10.5 - - - +
421E MET* 2.9 21.2 + - - +
423E MET* 1.3 76.1 - - + +
425E LEU* 1.3 59.6 + - - +
426E VAL 3.1 0.7 - - - -
427E SER* 3.3 13.2 + - - +
428E LEU* 3.0 36.4 + - + +
461F GLU* 6.0 0.2 + - - -
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Residues in contact with LEU 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310E GLU* 4.9 1.0 - - - +
314E LEU* 5.6 0.2 - - + -
373E LEU* 3.8 28.7 - - + +
376E ILE* 3.9 24.9 - - + -
377E ASN* 3.6 34.3 - - + +
396E GLN* 5.4 1.1 - - - +
422E LEU* 3.0 25.0 + - + +
424E LYS* 1.3 77.9 - - - +
426E VAL* 1.3 60.0 + - - +
428E LEU* 3.6 11.6 + - + +
429E ARG* 3.4 26.7 + - - +
491F LEU* 4.1 19.7 - - + -
494F PRO* 4.0 16.2 - - + +
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Residues in contact with VAL 426 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422E LEU 4.5 0.2 - - - +
423E MET* 3.0 32.3 + - + +
425E LEU* 1.3 74.7 - - - +
427E SER* 1.3 66.5 + - - +
428E LEU 3.1 1.1 - - - -
429E ARG* 3.0 15.3 + - - +
430E THR 3.3 7.4 + - - -
378F GLU* 5.3 0.4 - - - +
464F ARG* 6.3 0.4 - - - +
493F LEU* 3.8 18.2 - - + +
494F PRO* 3.7 27.4 - - + -
497F ARG* 3.5 48.9 + - + +
----------------------------------------------------------
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Residues in contact with SER 427 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356E PHE* 4.2 21.3 - - - -
423E MET 3.4 7.4 + - - -
424E LYS* 3.3 21.6 + - - +
426E VAL* 1.3 76.4 - - - +
428E LEU* 1.3 57.2 + - - +
430E THR* 3.1 10.7 + - - +
431E LEU* 2.9 32.2 + - - +
450F ASP* 4.5 13.0 + - - -
497F ARG* 4.9 3.4 - - - +
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Residues in contact with LEU 428 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310E GLU* 3.8 42.8 - - + +
313E LEU* 4.0 11.8 - - + +
314E LEU* 4.0 26.9 - - + -
356E PHE* 3.5 30.1 - - + -
373E LEU* 6.1 0.2 - - + -
377E ASN* 3.7 20.6 - - - +
424E LYS* 3.0 24.1 + - + +
425E LEU* 3.8 11.9 - - + +
426E VAL 3.1 0.4 - - - -
427E SER* 1.3 72.9 - - - +
429E ARG* 1.3 59.9 + - - +
431E LEU* 3.8 7.6 - - + +
432E SER* 2.9 29.6 + - - -
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Residues in contact with ARG 429 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310E GLU* 3.4 19.5 + - - -
380E SER* 3.9 12.1 + - - -
382E ASP* 2.7 44.0 + - - -
383E ARG* 3.3 24.7 - - - +
425E LEU* 3.4 15.3 + - - +
426E VAL 3.0 9.8 + - - +
428E LEU* 1.3 77.4 - - - +
430E THR* 1.3 63.4 + - - +
432E SER* 3.5 5.0 + - - -
433E SER* 3.3 19.1 + - - -
494F PRO* 3.3 38.1 + - + +
495F ALA 4.5 0.2 - - - +
497F ARG* 3.7 12.3 - - + -
498F SER* 2.7 41.7 + - - +
501F LEU* 4.1 5.6 - - - +
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Residues in contact with THR 430 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426E VAL 3.3 1.2 + - - -
427E SER* 3.1 11.5 + - - +
429E ARG* 1.3 79.4 - - - +
431E LEU* 1.3 60.7 + - + +
433E SER* 2.9 12.8 + - - -
434E VAL* 2.9 37.5 + - + +
497F ARG* 2.8 38.4 + - - +
501F LEU* 4.5 7.3 - - + +
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Residues in contact with LEU 431 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313E LEU* 3.4 30.0 - - + +
349E PHE* 4.7 4.5 - - + -
352E PRO* 3.5 40.4 - - + +
353E ILE* 4.4 5.4 - - + +
356E PHE* 3.6 40.6 - - + -
427E SER* 2.9 22.1 + - - +
428E LEU* 3.9 6.5 - - + +
429E ARG 3.3 0.2 - - - -
430E THR* 1.3 79.6 - - + +
432E SER* 1.3 62.7 + - - +
434E VAL* 3.2 11.5 + - + +
435E HIS* 2.9 24.6 + - - +
----------------------------------------------------------
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Residues in contact with SER 432 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306E ALA 4.6 3.3 + - - -
309E ILE* 3.7 31.1 - - - +
310E GLU* 4.1 12.1 + - - -
313E LEU* 4.9 0.8 - - - +
428E LEU 2.9 18.1 + - - -
429E ARG* 3.6 7.6 - - - -
431E LEU* 1.3 74.3 - - - +
433E SER* 1.3 60.9 + - - +
435E HIS* 3.3 8.4 + - - +
436E SER* 3.2 21.9 + - - -
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Residues in contact with SER 433 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429E ARG 3.3 9.0 + - - -
430E THR* 2.9 12.9 + - - -
432E SER* 1.3 76.4 - - - +
434E VAL* 1.3 61.5 + - - +
435E HIS 3.1 1.6 - - - -
436E SER* 3.0 19.4 + - - +
437E GLU* 3.2 26.5 + - - +
501F LEU* 3.9 30.8 - - - +
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Residues in contact with VAL 434 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348E GLU* 3.4 26.5 - - + +
349E PHE* 3.8 18.5 - - + +
352E PRO* 4.2 14.1 - - + -
430E THR* 2.9 34.4 + - + +
431E LEU* 3.6 13.5 - - + +
433E SER* 1.3 72.7 - - - +
435E HIS* 1.3 62.0 + - - +
437E GLU* 3.4 19.5 + - + +
438E GLN* 3.1 18.5 + - - +
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Residues in contact with HIS 435 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309E ILE* 3.7 33.6 - - + +
349E PHE* 3.8 27.8 - + + -
431E LEU 2.9 12.9 + - - +
432E SER 3.4 11.2 + - - +
433E SER 3.1 0.2 - - - -
434E VAL* 1.3 75.7 - - - +
436E SER* 1.3 67.2 + - - +
438E GLN* 3.0 6.1 + - + +
439E VAL* 3.0 32.0 + - + +
457E TRP* 3.5 46.9 - + - -
501E 67S 2.9 28.3 + + - -
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Residues in contact with SER 436 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432E SER 3.2 11.9 + - - -
433E SER* 3.0 14.9 + - - -
435E HIS* 1.3 78.4 + - - +
437E GLU* 1.3 60.9 + - - +
439E VAL* 3.1 11.5 + - - +
440E PHE* 3.0 22.2 + - - +
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Residues in contact with GLU 437 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346E GLN* 4.0 6.0 + - - +
348E GLU* 6.5 0.4 - - + -
433E SER* 3.2 26.9 + - - +
434E VAL* 3.5 21.7 - - + +
436E SER* 1.3 78.8 - - - +
438E GLN* 1.3 60.3 + - - +
440E PHE* 3.5 11.9 - - + +
441E ALA* 3.3 18.7 + - - +
----------------------------------------------------------
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Residues in contact with GLN 438 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344E GLY 4.2 1.2 + - - -
345E LEU* 3.6 12.5 - - + +
346E GLN* 2.9 47.9 + - - +
349E PHE* 3.3 43.5 - - + +
434E VAL 3.1 10.6 + - - +
435E HIS* 3.0 11.5 + - - +
437E GLU* 1.3 74.8 - - - +
439E VAL* 1.3 65.2 + - - +
441E ALA* 3.1 14.4 + - - +
442E LEU* 3.1 30.3 + - + +
445E GLN* 5.1 1.0 + - - -
501E 67S 4.1 13.2 - - - +
----------------------------------------------------------
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Residues in contact with VAL 439 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435E HIS* 3.0 41.9 + - + +
436E SER* 3.1 9.8 + - - +
438E GLN* 1.3 75.0 - - - +
440E PHE* 1.3 63.1 + - - +
442E LEU* 3.1 22.8 + - + +
443E ARG* 3.1 24.7 + - + +
449E LEU* 5.2 5.2 - - + -
457E TRP* 4.9 15.9 - - + +
458E ASP 5.6 0.9 - - - +
459E VAL* 3.9 28.3 - - + -
501E 67S 4.3 5.8 - - - +
----------------------------------------------------------
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Residues in contact with PHE 440 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436E SER 3.0 12.6 + - - +
437E GLU* 3.5 15.0 - - - +
439E VAL* 1.3 77.5 - - - +
441E ALA* 1.3 66.2 + - - +
443E ARG* 3.4 30.0 + - - +
444E LEU* 3.2 37.1 + - + +
----------------------------------------------------------
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Residues in contact with ALA 441 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346E GLN* 3.7 30.5 - - - +
437E GLU 3.3 4.0 + - - +
438E GLN* 3.1 12.6 + - - +
440E PHE* 1.3 83.9 - - + +
442E LEU* 1.3 56.6 + - - +
444E LEU* 3.3 12.4 + - + +
445E GLN* 2.9 45.7 + - - +
----------------------------------------------------------
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Residues in contact with LEU 442 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E PHE* 4.2 17.7 - - + -
344E GLY 3.9 16.2 - - - +
438E GLN* 3.1 31.5 + - - +
439E VAL* 3.1 14.6 + - + +
441E ALA* 1.3 73.0 - - - +
443E ARG* 1.3 67.0 + - - +
445E GLN* 3.1 7.8 + - - +
446E ASP 3.0 4.3 + - - -
447E LYS* 2.9 47.5 + - + +
449E LEU* 4.3 22.2 - - + -
501E 67S 3.9 34.3 - - - +
----------------------------------------------------------
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Residues in contact with ARG 443 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439E VAL* 3.1 17.2 + - - +
440E PHE* 3.6 41.5 + - - +
442E LEU* 1.3 76.2 - - - +
444E LEU* 1.3 57.9 + - - +
446E ASP* 2.9 26.8 + - - +
447E LYS 4.5 4.0 + - - -
458E ASP 5.3 2.8 + - - -
459E VAL* 4.3 29.3 + - + +
----------------------------------------------------------
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Residues in contact with LEU 444 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440E PHE* 3.2 31.4 + - + +
441E ALA* 3.3 14.8 - - + +
443E ARG* 1.3 80.5 - - - +
445E GLN* 1.3 61.5 + - + +
446E ASP* 3.3 8.2 + - - +
----------------------------------------------------------
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Residues in contact with GLN 445 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344E GLY* 4.6 14.9 + - - +
346E GLN* 5.6 4.2 - - - +
438E GLN* 5.1 0.9 + - - -
441E ALA* 2.9 35.1 + - - +
442E LEU* 3.1 11.6 + - - +
444E LEU* 1.3 78.6 - - + +
446E ASP* 1.3 72.9 + - - +
447E LYS* 3.3 28.0 + - + +
----------------------------------------------------------
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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