Contacts of the helix formed by residues 419 - 446 (chain E) in PDB entry 6I53
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 ASP 419 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417E LEU* 3.1 30.2 - - + +
418E THR* 1.3 78.6 + - - +
420E VAL* 1.3 65.1 + - - +
421E ASN* 3.4 2.0 - - + +
422E ALA* 3.4 20.8 + - + +
423E ILE* 3.3 26.6 + - - +
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Residues in contact with VAL 420 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244E TYR* 3.6 42.4 - - + -
302E VAL* 3.7 21.0 - - + +
305E ILE* 4.6 5.8 - - + -
306E PHE* 3.6 41.3 - - + +
418E THR 4.5 6.7 - - - +
419E ASP* 1.3 73.0 - - - +
421E ASN* 1.3 65.4 + - - +
422E ALA 3.4 0.3 + - - -
423E ILE* 3.6 13.5 + - + +
424E ASP* 3.7 15.6 + - - +
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Residues in contact with ASN 421 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244E TYR* 5.6 5.5 - - + -
419E ASP* 3.4 1.9 - - + +
420E VAL* 1.3 78.9 - - - +
422E ALA* 1.3 57.4 + - - +
424E ASP* 3.6 9.0 + - - +
425E ARG* 3.1 68.1 + - - +
428E ARG* 5.1 5.0 + - - -
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Residues in contact with ALA 422 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416E ASP* 3.7 11.5 - - + +
417E LEU* 4.7 10.5 - - + +
419E ASP* 3.4 28.0 + - + +
420E VAL 3.2 1.0 - - - -
421E ASN* 1.3 78.3 - - - +
423E ILE* 1.3 59.6 + - - +
425E ARG* 3.8 7.0 - - - +
426E TRP* 3.0 28.6 + - - +
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Residues in contact with ILE 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298E GLU* 3.3 20.2 - - + +
301E PHE* 3.8 23.1 - - + -
302E VAL* 4.0 15.3 - - + -
305E ILE* 3.7 31.0 - - + -
416E ASP* 3.3 20.4 - - - +
417E LEU 3.8 12.1 - - - +
418E THR* 4.5 1.6 - - - -
419E ASP 3.3 20.3 + - - +
420E VAL* 4.1 7.0 - - - +
421E ASN 3.3 0.4 - - - -
422E ALA* 1.3 74.2 - - - +
424E ASP* 1.3 61.3 + - - +
426E TRP* 3.3 8.1 + - + +
427E SER* 2.9 35.4 + - - +
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Residues in contact with ASP 424 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E PHE* 3.9 21.5 - - - +
242E ILE 4.8 2.8 - - - +
244E TYR* 4.5 10.2 + - - +
250E ARG* 3.1 39.8 + - - -
298E GLU* 3.3 14.1 - - - +
302E VAL* 4.1 5.8 - - - +
420E VAL* 3.7 13.8 + - - +
421E ASN* 3.6 13.6 + - - +
422E ALA 3.3 0.2 - - - -
423E ILE* 1.3 78.3 - - - +
425E ARG* 1.3 58.6 + - - +
427E SER* 3.1 4.4 + - - -
428E ARG* 2.9 38.6 + - - +
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Residues in contact with ARG 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421E ASN* 3.1 51.5 + - - +
422E ALA* 4.1 6.1 - - - +
424E ASP* 1.3 74.6 - - - +
426E TRP* 1.3 59.9 + - - +
428E ARG* 3.9 29.2 + - - +
429E ILE* 3.6 25.6 - - - +
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Residues in contact with TRP 426 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298E GLU* 6.2 1.1 - - + -
415E PRO* 4.2 34.8 + - + +
416E ASP* 3.6 25.4 - - + +
422E ALA 3.0 19.5 + - - +
423E ILE* 3.5 9.6 - - + +
424E ASP 3.1 0.2 - - - -
425E ARG* 1.3 78.1 - - - +
427E SER* 1.3 77.7 + - - +
429E ILE* 3.3 6.9 + - + +
430E VAL* 3.2 58.6 + - + +
431E PHE* 6.0 5.8 - + - -
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Residues in contact with SER 427 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E PHE* 3.6 36.8 - - - -
298E GLU* 3.4 18.9 + - - +
423E ILE* 2.9 20.3 + - - +
424E ASP 3.1 1.5 + - - -
426E TRP* 1.3 86.7 - - - +
428E ARG* 1.3 63.8 + - - +
429E ILE 3.2 2.1 + - - -
430E VAL* 4.1 5.6 - - - +
431E PHE* 3.6 30.4 + - - +
432E PRO* 3.9 1.7 - - - +
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Residues in contact with ARG 428 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A TYR* 4.1 15.6 + - - -
240E PHE* 2.8 43.1 + - + -
241E TRP* 3.5 68.0 + - + +
242E ILE 5.5 0.4 + - - -
421E ASN* 5.1 5.3 + - - -
424E ASP* 2.9 24.0 + - - +
425E ARG* 4.1 30.9 - - - +
426E TRP 3.3 0.8 - - - -
427E SER* 1.3 77.3 - - - +
429E ILE* 1.3 61.9 + - + +
432E PRO* 3.4 21.6 - - - +
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Residues in contact with ILE 429 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425E ARG 3.6 17.7 - - - +
426E TRP* 3.3 6.9 + - + +
427E SER 3.2 0.4 - - - -
428E ARG* 1.3 85.3 - - + +
430E VAL* 1.3 68.4 + - + +
431E PHE 3.6 0.4 - - - -
432E PRO* 3.8 3.6 - - - +
433E PHE* 3.3 23.8 + - + +
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Residues in contact with VAL 430 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426E TRP* 3.2 60.6 + - + +
427E SER* 4.7 2.7 - - - -
429E ILE* 1.3 81.6 - - + +
431E PHE* 1.3 67.9 + - + +
433E PHE* 2.9 8.0 + - + +
434E THR* 2.6 51.7 + - - +
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Residues in contact with PHE 431 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237E TRP* 3.2 33.5 - + + +
240E PHE* 3.4 36.1 - + + -
291E PHE* 4.9 18.0 - + + -
294E LEU* 4.1 42.0 - - + -
295E ALA* 4.1 6.7 - - + -
298E GLU* 4.6 7.9 - - + -
426E TRP* 6.0 5.6 - + - -
427E SER* 3.6 16.8 + - - +
430E VAL* 1.3 96.4 - - + +
432E PRO* 1.3 66.7 - - + +
434E THR* 4.4 6.3 - - + +
435E PHE* 3.2 17.8 + - - +
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Residues in contact with PRO 432 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237E TRP* 3.8 35.7 - - + -
240E PHE* 6.2 0.4 - - + -
427E SER 3.9 1.6 - - - +
428E ARG* 3.4 31.6 - - - +
429E ILE 3.8 3.4 - - - +
431E PHE* 1.3 91.2 - - + +
433E PHE* 1.3 56.4 + - - +
436E SER* 3.0 23.1 + - - -
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Residues in contact with PHE 433 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429E ILE* 3.3 21.6 + - + +
430E VAL* 2.9 7.7 + - + +
432E PRO* 1.3 78.3 - - - +
434E THR* 1.3 66.7 + - - +
436E SER* 2.7 21.3 + - - -
437E LEU* 2.9 37.1 + - + +
508E POV 4.5 12.3 - - - -
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Residues in contact with THR 434 (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* 3.6 23.3 - - + -
430E VAL* 2.6 38.0 + - - +
431E PHE* 4.6 5.6 - - + -
433E PHE* 1.3 76.1 - - - +
435E PHE* 1.3 54.3 + - - +
437E LEU* 3.1 13.8 + - + +
438E PHE* 2.7 32.9 + - - +
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Residues in contact with PHE 435 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E ILE* 4.2 22.9 - - + -
233E THR* 3.8 22.0 - - + -
234E ILE* 5.0 2.2 - - + -
237E TRP* 3.5 28.3 - + + -
284E TYR* 4.1 6.5 - - - -
288E CYS* 3.6 30.3 - - - -
291E PHE* 3.6 36.0 - + + -
431E PHE 3.2 18.6 + - - +
434E THR* 1.3 75.6 - - - +
436E SER* 1.3 65.5 + - - +
438E PHE* 3.6 8.1 - + - +
439E ASN* 3.2 46.0 + - - -
508E POV 4.5 9.9 - - + -
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Residues in contact with SER 436 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432E PRO 3.0 19.1 + - - -
433E PHE* 2.7 24.8 + - - -
435E PHE* 1.3 80.3 - - - +
437E LEU* 1.3 60.5 + - - +
439E ASN* 3.7 8.3 + - - +
440E LEU* 3.3 20.6 + - - +
508E POV 3.8 47.8 - - - +
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Residues in contact with LEU 437 (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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433E PHE* 2.9 40.1 + - + +
434E THR* 3.4 14.4 - - + +
436E SER* 1.3 76.7 + - - +
438E PHE* 1.3 63.2 + - - +
440E LEU* 3.4 17.6 + - + +
441E VAL* 3.2 34.9 + - + +
508E POV 5.3 4.5 - - - -
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Residues in contact with PHE 438 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283E MET* 4.2 13.0 - - + -
284E TYR* 3.9 27.1 - + - -
287E GLY* 3.7 34.3 - - - -
288E CYS* 4.5 1.6 - - - -
291E PHE* 3.7 27.6 - + + -
434E THR 2.7 18.4 + - - +
435E PHE* 3.6 12.3 - + - +
436E SER 3.3 0.4 - - - -
437E LEU* 1.3 74.5 - - - +
439E ASN* 1.3 67.0 + - - +
441E VAL* 3.5 6.2 + - + +
442E TYR* 3.0 34.1 + + + +
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Residues in contact with ASN 439 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284E TYR* 3.1 34.9 + - - -
435E PHE* 3.2 44.5 + - - +
436E SER* 4.1 4.5 - - - +
437E LEU 3.3 0.2 - - - -
438E PHE* 1.3 77.3 - - - +
440E LEU* 1.3 60.6 + - - +
442E TYR* 4.2 1.8 - - - -
443E TRP* 2.9 48.1 + - + +
508E POV 3.4 40.3 - - + +
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Residues in contact with LEU 440 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436E SER 3.3 15.7 + - - +
437E LEU* 3.8 19.7 - - + +
438E PHE 3.3 0.6 - - - -
439E ASN* 1.3 77.0 - - - +
441E VAL* 1.3 64.8 + - + +
443E TRP* 5.4 0.4 - - - -
444E LEU* 3.3 47.7 + - + +
508E POV 4.4 41.7 - - + +
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Residues in contact with VAL 441 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437E LEU* 3.2 29.4 + - + +
438E PHE* 4.0 7.0 - - + +
440E LEU* 1.3 77.6 - - + +
442E TYR* 1.3 64.1 + - - +
444E LEU* 3.6 1.2 + - - +
445E TYR* 3.1 28.3 + - + +
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Residues in contact with TYR 442 (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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145E LEU* 4.5 4.8 - - + +
226E TYR* 2.9 33.0 + + - -
280E ALA* 2.3 37.6 + - + +
283E MET* 5.0 5.8 - - + -
284E TYR* 3.6 37.4 - + + +
438E PHE* 3.0 28.6 + + + +
439E ASN* 3.9 4.9 - - - +
440E LEU 3.4 0.4 - - - -
441E VAL* 1.3 79.1 - - - +
443E TRP* 1.3 86.2 + + - +
444E LEU 3.1 5.0 + - - -
445E TYR* 3.4 1.5 + - - -
446E TYR* 3.4 57.9 + + - +
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Residues in contact with TRP 443 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E LEU* 4.1 23.8 - - + -
218E ILE* 5.5 3.1 - - + -
222E ILE* 5.1 4.0 - - + -
226E TYR* 3.7 48.2 - + + -
230E ILE* 5.6 0.9 - - + +
284E TYR* 4.5 4.3 + + - -
439E ASN* 2.9 51.5 + - + +
440E LEU 5.2 0.2 - - - +
442E TYR* 1.3 87.5 - + - +
444E LEU* 1.3 60.6 + - - +
447E VAL* 3.4 40.0 - - + +
508E POV 3.1 96.1 - - + +
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Residues in contact with LEU 444 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440E LEU* 3.3 44.3 + - + +
441E VAL* 3.6 2.1 + - - +
442E TYR 3.1 0.8 - - - -
443E TRP* 1.3 84.5 - - + +
445E TYR* 1.3 64.2 + - - +
446E TYR 3.5 0.4 - - - -
447E VAL* 4.4 10.4 + - + +
508E POV 4.2 12.1 - - + +
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Residues in contact with TYR 445 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E ARG* 3.9 18.1 + - - -
441E VAL* 3.1 22.8 + - + +
442E TYR* 3.4 3.1 + - - +
444E LEU* 1.3 79.8 - - - +
446E TYR* 1.3 97.2 + + + +
447E VAL 5.1 0.6 - - - -
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Residues in contact with TYR 446 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E ARG 4.3 9.4 + - - -
142E ARG* 2.4 48.0 + - + +
145E LEU* 3.7 31.2 - - + +
279E LYS 4.6 0.9 + - - -
280E ALA* 3.6 28.4 - - + -
283E MET* 4.1 24.9 - - + +
442E TYR* 3.4 50.2 + + - +
445E TYR* 1.3 108.1 - + + +
447E VAL* 1.3 62.8 + - - +
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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