Contacts of the helix formed by residues 428 - 456 (chain D) in PDB entry 4P0S
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 SER 428 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364D VAL* 4.6 8.7 - - - +
365D ASP 4.8 0.4 - - - -
366D GLN* 4.5 20.2 - - - -
426D VAL* 3.7 4.9 + - - +
427D GLN* 1.3 79.7 - - - +
429D TRP* 1.3 65.0 + - - +
430D LYS* 3.4 14.5 + - - +
431D GLU* 3.2 18.6 + - - +
432D LEU* 3.1 18.5 + - - +
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Residues in contact with TRP 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D MET* 3.6 41.1 - - + -
264D GLU* 3.6 41.4 - - + +
265D GLY* 3.5 31.6 - - - +
268D GLN* 4.5 14.2 - - + +
315D LEU* 4.3 0.2 - - + -
317D ARG* 4.3 7.2 - - - -
364D VAL* 3.6 33.9 - - + +
366D GLN* 3.6 24.7 + - - +
428D SER* 1.3 72.5 - - - +
430D LYS* 1.3 60.9 + - - +
432D LEU* 3.1 39.4 + - + +
433D ALA* 2.6 28.5 + - - +
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Residues in contact with LYS 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D GLN* 3.7 28.7 + - - +
272D ALA* 6.1 2.4 - - - +
428D SER* 3.2 9.1 + - - +
429D TRP* 1.3 77.6 - - - +
431D GLU* 1.3 52.8 + - - +
433D ALA* 2.7 12.1 + - + +
434D ASP* 2.6 62.2 + - - +
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Residues in contact with GLU 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C ARG* 5.7 5.0 - - - -
425D ILE 4.1 2.9 - - - +
426D VAL* 3.2 29.9 - - + +
427D GLN* 2.7 47.9 + - - +
428D SER* 3.2 16.1 + - - +
430D LYS* 1.3 76.0 - - - +
432D LEU* 1.3 65.0 + - - +
434D ASP* 4.3 8.5 - - - +
435D PHE* 3.0 29.3 + - + +
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Residues in contact with LEU 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D GLY 5.2 1.6 - - - +
269D LEU* 3.7 33.7 - - + -
313D LEU* 6.5 0.4 - - + -
315D LEU* 3.4 29.6 - - + -
362D VAL* 4.3 21.1 - - + -
364D VAL* 5.0 4.5 - - + -
426D VAL* 4.7 10.5 - - + +
428D SER 3.1 10.2 + - - +
429D TRP* 3.2 40.4 - - + +
430D LYS 3.0 0.4 - - - -
431D GLU* 1.3 82.4 - - - +
433D ALA* 1.3 53.9 + - + +
435D PHE* 4.6 3.6 - - + +
436D THR* 2.2 37.7 + - - +
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Residues in contact with ALA 433 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D GLN* 4.0 28.5 - - + +
269D LEU* 4.3 14.7 - - + +
272D ALA* 4.4 9.5 - - + +
273D LEU* 5.1 0.2 - - - +
429D TRP 2.6 17.1 + - - +
430D LYS* 2.7 19.1 + - + +
432D LEU* 1.3 72.3 - - - +
434D ASP* 1.3 59.3 + - - +
436D THR* 3.0 24.2 - - - +
437D CYS* 3.1 14.5 + - - -
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Residues in contact with ASP 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C GLU* 4.7 9.9 - - - +
385C LEU* 3.7 28.2 - - + +
272D ALA* 5.6 1.9 - - - +
430D LYS* 2.6 52.1 + - - +
431D GLU* 3.9 5.9 + - - +
433D ALA* 1.3 69.7 - - - +
435D PHE* 1.3 64.7 + - - +
436D THR 2.9 1.8 - - - -
437D CYS* 3.0 22.9 + - - +
438D ALA* 3.2 8.7 + - - +
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Residues in contact with PHE 435 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C LEU* 4.4 10.9 - - + +
389C THR* 3.9 21.1 - - + -
392C GLN* 3.4 21.3 - - - -
401C ARG* 3.2 27.4 - - - +
313D LEU* 4.0 12.3 - - + -
360D SER* 5.4 1.1 - - - -
362D VAL* 4.3 14.8 - - + -
424D GLN* 3.0 30.3 - - - -
426D VAL* 5.5 6.5 - - + -
431D GLU* 3.0 19.0 + - + +
432D LEU* 4.6 3.8 - - + +
434D ASP* 1.3 73.3 - - - +
436D THR* 1.3 56.1 + - - +
438D ALA* 3.4 3.6 + - - +
439D PHE* 2.7 71.1 + + - +
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Residues in contact with THR 436 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D LEU* 6.2 0.7 - - + -
269D LEU* 3.3 32.0 - - + +
273D LEU* 3.7 13.4 - - + +
313D LEU* 5.9 4.5 - - + +
432D LEU* 2.2 30.9 + - - +
433D ALA 3.0 13.0 - - - -
435D PHE* 1.3 81.3 - - - +
437D CYS* 1.3 63.2 + - - +
439D PHE* 4.0 7.0 - - + +
440D THR* 3.0 27.4 + - - +
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Residues in contact with CYS 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C GLN* 5.9 0.2 - - - +
272D ALA* 3.6 45.8 - - - -
273D LEU* 3.8 8.3 - - - +
276D MET* 3.7 19.2 - - - +
433D ALA 3.1 10.7 + - - -
434D ASP* 3.0 17.4 + - - +
436D THR* 1.3 75.0 - - - +
438D ALA* 1.3 58.9 + - - +
440D THR* 3.1 8.3 + - - -
441D LYS* 3.0 22.4 + - - +
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Residues in contact with ALA 438 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C LEU* 4.4 6.5 - - + +
386C GLN* 3.2 40.8 + - - +
389C THR* 3.6 24.0 - - - +
434D ASP 3.2 8.6 + - - +
435D PHE* 3.6 6.3 - - - +
437D CYS* 1.3 77.4 - - - +
439D PHE* 1.3 55.5 + - - +
440D THR 3.1 1.6 - - - -
441D LYS* 3.0 1.3 + - - -
442D ALA* 2.8 33.8 + - - +
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Residues in contact with PHE 439 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C THR* 3.6 9.2 - - + +
392C GLN* 4.6 2.2 - - - -
393C VAL* 3.4 28.5 - - + -
293D TRP* 3.4 30.7 - + + -
311D THR* 4.1 14.1 - - + -
313D LEU* 3.4 24.9 - - + -
360D SER* 3.6 27.4 - - - -
435D PHE* 2.7 53.1 + + - +
436D THR* 4.0 7.9 - - + +
437D CYS 3.4 0.2 - - - -
438D ALA* 1.3 72.2 - - - +
440D THR* 1.3 57.0 - - - +
442D ALA* 3.1 3.2 + - - +
443D VAL* 2.8 57.7 + - + +
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Residues in contact with THR 440 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D LEU* 4.6 9.6 - - + +
252D ILE* 5.0 6.9 - - + +
254D VAL* 3.9 22.4 - - + +
273D LEU* 3.9 14.2 - - - +
276D MET* 3.7 21.5 - - + -
278D CYS* 5.0 1.3 - - + -
293D TRP* 3.8 24.2 + - + +
436D THR* 3.0 14.1 + - - +
437D CYS 3.1 9.8 + - - -
438D ALA 3.1 0.6 - - - -
439D PHE* 1.3 80.2 - - - +
441D LYS* 1.3 60.4 + - - +
443D VAL* 3.4 2.0 + - - +
444D ALA* 3.2 23.8 + - + +
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Residues in contact with LYS 441 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C SER* 5.9 3.0 + - - -
386C GLN* 3.1 42.0 + - + +
249D LEU* 5.0 18.8 - - + -
276D MET* 4.9 12.7 - - - -
437D CYS 3.0 11.9 + - - +
438D ALA* 3.0 2.3 + - - +
440D THR* 1.3 76.9 - - - +
442D ALA* 1.3 59.5 + - - +
444D ALA* 3.8 5.2 - - - +
445D GLU* 3.2 40.3 + - - +
2U A 3.9 19.9 + - - -
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Residues in contact with ALA 442 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C THR* 4.2 8.5 - - + -
390C ASN* 3.1 32.5 + - - +
393C VAL* 4.5 14.8 - - + -
394C ILE* 4.5 6.1 - - + +
438D ALA 2.8 10.9 + - - +
439D PHE* 3.1 13.0 + - - +
441D LYS* 1.3 74.4 - - - +
443D VAL* 1.3 54.0 + - - +
444D ALA 3.1 1.8 - - - -
445D GLU* 2.8 6.4 + - - +
446D ALA* 2.8 34.8 + - - +
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Residues in contact with VAL 443 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C VAL* 5.1 7.4 - - + -
252D ILE* 5.4 2.0 - - + -
293D TRP* 3.4 57.4 - - + +
295D ARG* 3.4 13.0 + - - +
309D GLU* 3.9 16.5 - - + +
311D THR* 4.8 7.2 - - + +
439D PHE* 2.8 49.5 + - + +
440D THR 3.9 3.4 - - - +
442D ALA* 1.3 71.3 - - - +
444D ALA* 1.3 62.3 + - - +
446D ALA* 3.3 18.9 + - - +
447D PRO* 3.5 0.2 - - - +
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Residues in contact with ALA 444 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D GLN* 5.2 2.6 - - - +
248D CYS* 3.9 25.2 - - - +
249D LEU* 4.7 9.4 - - + -
252D ILE* 4.2 21.3 - - + -
295D ARG* 3.5 18.3 + - - +
440D THR 3.2 15.1 + - - +
441D LYS* 3.8 7.6 - - - +
442D ALA 3.1 0.2 - - - -
443D VAL* 1.3 80.9 - - - +
445D GLU* 1.3 58.7 + - - +
446D ALA 3.1 3.9 + - - -
447D PRO* 3.2 12.8 - - - +
448D PHE* 4.6 2.6 + - - +
----------------------------------------------------------
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Residues in contact with GLU 445 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C GLN* 4.9 1.4 + - - +
390C ASN* 4.3 15.8 + - - +
394C ILE* 4.8 7.6 - - + +
243D GLN 5.4 0.2 - - - +
245D PRO* 3.7 31.5 - - + +
248D CYS* 4.4 15.7 - - - -
441D LYS* 3.2 32.9 + - - +
442D ALA* 2.8 8.0 + - - +
444D ALA* 1.3 78.3 - - - +
446D ALA* 1.3 67.1 + - - +
447D PRO 3.5 0.4 - - - -
448D PHE* 3.2 30.5 + - + +
449D LYS* 3.3 26.0 + - - +
----------------------------------------------------------
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Residues in contact with ALA 446 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C VAL* 5.0 8.7 - - + -
394C ILE* 4.6 16.9 - - + +
309D GLU* 4.7 4.9 - - - +
442D ALA 2.8 9.1 + - - +
443D VAL* 3.4 13.9 - - - +
444D ALA 3.1 0.2 - - - -
445D GLU* 1.3 78.8 - - - +
447D PRO* 1.4 73.7 - - + +
448D PHE 3.0 1.4 + - - -
449D LYS* 3.3 1.6 + - - +
450D LYS* 3.1 40.3 + - - +
----------------------------------------------------------
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Residues in contact with PRO 447 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D GLN* 3.5 25.3 - - + +
295D ARG* 3.1 42.2 - - - +
309D GLU* 3.8 10.5 - - - +
443D VAL 3.5 0.9 - - - +
444D ALA 3.2 6.7 - - - +
446D ALA* 1.4 93.5 - - + +
448D PHE* 1.3 54.5 + - - +
450D LYS* 3.9 8.3 - - + -
451D LEU* 3.1 35.8 + - + +
----------------------------------------------------------
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Residues in contact with PHE 448 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D GLN* 2.8 43.3 + - + +
244D ARG* 4.8 2.2 - - + -
245D PRO* 3.8 31.9 - - + -
445D GLU* 3.2 23.2 + - + +
446D ALA 3.0 1.0 + - - -
447D PRO* 1.3 78.5 - - - +
449D LYS* 1.3 103.4 + - + +
451D LEU* 3.6 2.4 + - - +
452D ARG* 3.3 55.3 + - + +
----------------------------------------------------------
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Residues in contact with LYS 449 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C ARG* 4.6 19.9 - - - +
390C ASN* 4.8 8.1 - - - +
394C ILE* 4.5 31.8 - - + +
445D GLU* 3.3 25.7 + - - +
446D ALA 4.4 1.3 - - - +
448D PHE* 1.3 107.0 - - + +
450D LYS* 1.3 62.7 + - - +
452D ARG* 4.2 6.5 - - + +
453D ASP* 2.8 42.6 + - - +
1U G 4.1 19.0 + - - -
----------------------------------------------------------
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Residues in contact with LYS 450 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C VAL 5.2 4.6 + - - -
394C ILE* 4.0 34.6 + - + +
446D ALA* 3.1 33.4 + - - +
447D PRO* 4.0 6.5 - - + +
449D LYS* 1.3 79.0 - - - +
451D LEU* 1.3 67.5 + - + +
452D ARG 3.4 0.2 + - - -
453D ASP* 4.9 3.2 - - - +
454D GLU* 3.2 33.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 451 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D MET* 3.6 26.2 - - + -
243D GLN* 3.6 27.1 - - - +
447D PRO* 3.1 23.9 + - + +
448D PHE 4.1 3.4 - - - +
450D LYS* 1.3 87.1 - - + +
452D ARG* 1.4 59.4 + - + +
454D GLU* 3.8 15.0 - - - +
455D THR* 3.5 21.7 + - - -
----------------------------------------------------------
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Residues in contact with ARG 452 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C ARG* 5.8 6.7 - - - +
488C GLU* 4.7 16.6 - - - -
448D PHE* 3.3 47.5 + - + +
449D LYS* 3.2 10.3 + - + +
451D LEU* 1.4 74.8 - - + +
453D ASP* 1.3 69.5 + - - +
454D GLU 2.9 2.8 + - - -
455D THR* 3.0 4.0 + - - +
456D THR* 3.0 45.1 + - + +
----------------------------------------------------------
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Residues in contact with ASP 453 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C PHE* 6.5 1.8 - - + -
357C LYS* 4.0 20.9 + - - +
394C ILE* 5.6 3.3 - - - +
395C ASP* 5.1 4.0 - - - +
449D LYS* 2.8 31.0 + - - +
450D LYS* 4.9 3.2 - - - +
452D ARG* 1.3 74.8 - - - +
454D GLU* 1.3 61.8 + - + +
456D THR* 3.5 20.5 - - - +
----------------------------------------------------------
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Residues in contact with GLU 454 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450D LYS* 3.2 28.3 + - - +
451D LEU* 3.8 18.1 - - - +
452D ARG 2.9 1.6 - - - -
453D ASP* 1.3 81.1 - - + +
455D THR* 1.3 62.0 + - - +
456D THR 4.0 1.7 - - - +
457D PHE* 5.9 1.0 - - - -
----------------------------------------------------------
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Residues in contact with THR 455 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488C GLU* 4.2 30.3 - - + +
491C ALA* 4.6 10.7 - - + +
526C GLY* 4.8 13.2 - - - +
451D LEU 3.5 13.6 + - - -
452D ARG* 3.0 8.0 + - - -
454D GLU* 1.3 77.5 - - - +
456D THR* 1.3 67.3 + - - +
457D PHE* 3.8 17.0 - - - -
----------------------------------------------------------
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Residues in contact with THR 456 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C GLY* 4.3 15.0 + - - -
488C GLU* 4.9 7.8 + - - +
452D ARG* 3.0 45.6 + - + +
453D ASP* 3.5 23.3 - - - +
454D GLU 4.0 1.7 - - - +
455D THR* 1.3 82.9 - - - +
457D PHE* 1.3 71.8 + - - +
460D CYS* 4.1 14.0 - - - +
----------------------------------------------------------
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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