Contacts of the helix formed by residues 428 - 456 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B VAL* 4.7 7.1 - - - +
365B ASP 4.9 0.8 - - - +
366B GLN* 4.5 21.8 - - - -
426B VAL* 3.7 4.7 + - - +
427B GLN* 1.3 78.4 - - - +
429B TRP* 1.3 66.2 + - - +
430B LYS* 3.2 15.5 + - - +
431B GLU* 3.3 18.6 + - - +
432B LEU* 3.2 17.7 + - - +
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Residues in contact with TRP 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B MET* 3.6 39.0 - - + -
264B GLU* 3.4 44.1 + - + +
265B GLY* 3.7 28.3 - - - +
268B GLN* 4.5 14.2 - - + +
315B LEU* 4.2 0.2 - - + -
317B ARG* 4.3 7.0 - - - -
364B VAL* 3.7 33.8 - - + +
366B GLN* 3.8 23.8 + - + +
428B SER* 1.3 75.2 - - - +
430B LYS* 1.3 58.6 + - - +
432B LEU* 3.1 42.5 + - + +
433B ALA* 2.7 28.7 + - - +
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Residues in contact with LYS 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B GLN* 3.7 27.1 + - - +
272B ALA* 6.2 1.4 - - - +
428B SER* 3.2 9.5 + - - +
429B TRP* 1.3 77.0 - - - +
431B GLU* 1.3 52.2 + - - +
433B ALA* 2.8 9.9 + - + +
434B ASP* 2.6 60.8 + - - +
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Residues in contact with GLU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ILE 3.9 3.5 - - - +
426B VAL* 3.2 29.0 - - + +
427B GLN* 2.8 46.8 + - - +
428B SER* 3.3 17.0 + - - +
430B LYS* 1.3 77.6 - - - +
432B LEU* 1.3 64.3 + - - +
434B ASP* 3.0 8.4 + - - +
435B PHE* 2.9 30.2 + - + +
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Residues in contact with LEU 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LEU* 6.0 0.2 - - + -
265B GLY 5.3 1.8 - - - +
269B LEU* 3.8 31.0 - - + -
315B LEU* 3.5 24.9 - - + -
362B VAL* 4.4 20.2 - - + -
364B VAL* 4.9 4.3 - - + -
426B VAL* 4.7 11.2 - - + +
428B SER 3.2 10.0 + - - +
429B TRP* 3.1 45.7 + - + +
431B GLU* 1.3 79.0 - - - +
433B ALA* 1.3 55.9 + - - +
435B PHE* 4.6 2.0 - - - +
436B THR* 2.1 38.3 + - - +
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Residues in contact with ALA 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B GLN* 4.1 27.8 - - + +
269B LEU* 4.3 16.1 - - + +
272B ALA* 4.4 9.4 - - + +
273B LEU* 5.2 0.2 - - - +
429B TRP 2.7 13.8 + - - +
430B LYS* 2.8 15.6 + - + +
432B LEU* 1.3 77.6 - - + +
434B ASP* 1.4 58.4 + - - +
436B THR* 2.9 24.4 - - - +
437B CYS* 3.1 14.1 + - - -
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Residues in contact with ASP 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A LEU* 4.5 14.7 - - + +
272B ALA* 5.7 1.4 - - - +
430B LYS* 2.6 50.0 + - - +
431B GLU* 3.0 7.5 + - - +
433B ALA* 1.4 70.9 - - - +
435B PHE* 1.3 65.0 - - - +
436B THR 2.9 1.6 - - - -
437B CYS* 3.0 23.0 + - - +
438B ALA* 3.2 12.5 + - - +
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Residues in contact with PHE 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A LEU* 4.7 10.1 - - + -
389A THR* 4.0 18.2 - - + -
392A GLN* 3.6 17.7 - - - -
401A ARG* 3.1 32.3 - - - -
313B LEU* 4.0 11.9 - - + -
360B SER* 5.4 0.7 - - - -
362B VAL* 4.5 13.5 - - + -
424B GLN* 3.3 27.6 - - - +
426B VAL* 5.6 6.3 - - + -
431B GLU* 2.9 18.1 + - + +
432B LEU* 4.6 2.7 - - + +
434B ASP* 1.3 74.3 - - - +
436B THR* 1.3 57.1 + - - +
438B ALA* 3.3 5.8 + - - +
439B PHE* 2.7 71.1 + + + +
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Residues in contact with THR 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B LEU* 6.3 0.7 - - + -
269B LEU* 3.3 31.3 - - + +
273B LEU* 3.7 13.4 - - + +
313B LEU* 5.9 4.9 - - + +
432B LEU* 2.1 30.9 + - - +
433B ALA 2.9 12.3 - - - -
435B PHE* 1.3 80.8 - - - +
437B CYS* 1.3 63.6 + - - +
439B PHE* 4.0 7.0 - - + +
440B THR* 3.0 27.3 + - - +
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Residues in contact with CYS 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ALA* 3.7 43.1 - - - -
273B LEU* 3.9 9.4 - - - +
276B MET* 3.9 20.8 - - + +
433B ALA 3.1 9.6 + - - -
434B ASP* 3.0 17.8 + - - +
436B THR* 1.3 76.2 - - - +
438B ALA* 1.3 59.4 + - - +
440B THR* 3.1 8.0 + - - -
441B LYS* 3.0 23.6 + - - +
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Residues in contact with ALA 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A LEU* 4.3 19.5 - - + +
386A GLN* 3.3 29.1 + - - +
389A THR* 3.7 18.8 - - + +
434B ASP 3.2 8.4 + - - +
435B PHE* 3.6 7.6 - - - +
437B CYS* 1.3 77.7 - - - +
439B PHE* 1.3 54.7 + - - +
441B LYS* 3.0 2.8 + - - -
442B ALA* 2.7 33.8 + - - +
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Residues in contact with PHE 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A THR* 3.5 11.1 - - + +
392A GLN* 4.0 4.7 - - - -
393A VAL* 3.2 32.8 - - + -
293B TRP* 3.3 40.4 - + + -
311B THR* 4.0 11.4 - - + -
313B LEU* 3.3 24.5 - - + -
360B SER* 3.5 26.5 - - - -
435B PHE* 2.7 53.8 + + + +
436B THR* 4.0 7.2 - - + +
437B CYS 3.4 0.2 - - - -
438B ALA* 1.3 71.6 - - - +
440B THR* 1.3 57.7 + - - +
442B ALA* 3.0 2.4 + - - +
443B VAL* 2.7 37.6 + - + +
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Residues in contact with THR 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B LEU* 4.6 9.0 - - + -
252B ILE* 5.0 6.0 - - + +
254B VAL* 4.0 21.1 - - + +
273B LEU* 4.0 14.2 - - - +
276B MET* 3.7 22.9 - - + -
278B CYS* 4.9 1.6 - - + -
293B TRP* 3.7 26.0 + - + +
436B THR* 3.0 13.9 + - - +
437B CYS 3.1 10.8 + - - -
439B PHE* 1.3 78.5 - - - +
441B LYS* 1.3 61.7 + - - +
443B VAL* 3.2 1.9 + - - +
444B ALA* 3.1 24.7 + - + +
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Residues in contact with LYS 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A SER* 5.8 6.7 + - - -
386A GLN* 3.0 40.0 + - - +
249B LEU* 5.1 18.6 - - + -
276B MET* 4.9 13.0 - - - -
437B CYS 3.0 12.9 + - - +
438B ALA* 3.0 3.8 + - - +
440B THR* 1.3 76.5 - - - +
442B ALA* 1.3 58.8 + - - +
444B ALA* 3.8 5.2 - - - +
445B GLU* 3.3 34.6 + - - +
2I A 3.9 29.7 + - - +
3I A 6.1 0.2 - - - -
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Residues in contact with ALA 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A GLN* 3.7 0.8 - - - +
389A THR* 3.6 21.1 - - + +
390A ASN* 2.9 33.3 - - - +
393A VAL* 4.7 7.2 - - + -
394A ILE* 4.0 3.5 - - - +
438B ALA 2.7 12.0 + - - +
439B PHE* 3.2 8.7 - - - +
441B LYS* 1.3 75.3 - - - +
443B VAL* 1.3 59.0 + - - +
444B ALA 3.1 1.8 - - - -
445B GLU* 2.9 4.9 + - - +
446B ALA* 2.9 28.5 + - - +
----------------------------------------------------------
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Residues in contact with VAL 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A VAL* 4.4 11.9 - - + -
252B ILE* 5.4 2.2 - - + -
293B TRP* 3.4 70.0 - - + -
295B ARG* 3.1 13.5 + - - +
309B GLU* 3.7 16.8 - - + +
311B THR* 4.7 2.7 - - + +
439B PHE* 2.7 33.6 + - + +
440B THR 3.7 4.0 - - - +
442B ALA* 1.3 71.2 - - - +
444B ALA* 1.3 63.4 + - - +
446B ALA* 3.4 16.8 + - - +
447B PRO* 3.6 0.2 - - - +
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Residues in contact with ALA 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ALA 5.1 0.5 - - - +
243B GLN* 5.4 2.3 - - - -
248B CYS* 3.9 25.1 - - - +
249B LEU* 4.7 9.4 - - + -
252B ILE* 4.1 22.0 - - + -
295B ARG* 3.3 18.8 + - - +
440B THR* 3.1 14.5 + - + +
441B LYS* 3.8 7.4 - - - +
443B VAL* 1.3 81.9 - - - +
445B GLU* 1.3 57.2 + - - +
446B ALA 3.2 4.4 + - - -
447B PRO* 3.3 12.6 - - - +
448B PHE* 4.8 1.7 + - - +
----------------------------------------------------------
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Residues in contact with GLU 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A GLN* 4.2 0.2 + - - -
390A ASN* 4.0 12.8 + - - +
394A ILE* 3.9 7.9 - - + +
243B GLN 5.4 0.7 - - - +
245B PRO* 3.7 31.9 - - + +
248B CYS* 4.4 15.9 - - - -
441B LYS* 3.3 25.2 + - - +
442B ALA 2.9 6.0 + - - +
444B ALA* 1.3 78.5 - - - +
446B ALA* 1.3 66.5 + - - +
447B PRO 3.5 0.7 - - - -
448B PHE* 3.2 30.5 + - + +
449B LYS* 3.4 13.3 + - - +
2I A 2.7 39.0 + - - +
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Residues in contact with ALA 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A VAL* 4.7 8.3 - - + -
394A ILE* 3.4 34.6 - - + +
309B GLU* 4.6 4.3 - - - +
442B ALA 2.9 6.1 + - - +
443B VAL* 3.6 12.8 - - - +
444B ALA 3.2 0.2 - - - -
445B GLU* 1.3 80.0 - - - +
447B PRO* 1.3 73.8 - - + +
448B PHE 3.0 1.4 + - - -
449B LYS 3.4 0.2 + - - -
450B LYS* 3.1 31.7 + - - +
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Residues in contact with PRO 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B GLN* 3.5 24.8 - - + +
295B ARG* 3.2 41.1 - - - +
309B GLU* 3.8 9.9 - - - +
444B ALA 3.3 6.1 - - - +
446B ALA* 1.3 94.7 - - + +
448B PHE* 1.3 54.8 + - - +
450B LYS* 4.2 7.6 - - + -
451B LEU* 3.0 37.1 + - + +
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Residues in contact with PHE 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ARG* 5.6 1.6 - - - -
243B GLN* 2.9 43.3 + - + +
244B ARG* 4.9 1.6 - - + -
245B PRO* 3.8 33.2 - - + -
444B ALA 4.8 0.2 + - - -
445B GLU* 3.3 21.5 - - + +
446B ALA 3.0 1.6 + - - -
447B PRO* 1.3 80.2 - - - +
449B LYS* 1.3 99.2 + - + +
451B LEU* 3.5 2.9 + - - +
452B ARG* 3.2 62.6 + - + +
----------------------------------------------------------
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Residues in contact with LYS 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ARG* 4.0 19.5 - - - +
390A ASN* 4.0 3.8 - - - +
394A ILE* 4.5 17.5 - - + -
445B GLU* 3.4 12.0 + - - +
446B ALA 3.4 2.4 + - - -
448B PHE* 1.3 105.2 - - + +
450B LYS* 1.3 61.8 + - - +
452B ARG* 3.5 6.7 - - + +
453B ASP* 2.8 41.6 + - - +
1I G 3.1 68.6 + - - +
2I A 3.6 8.6 + - - -
----------------------------------------------------------
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Residues in contact with LYS 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LYS* 4.5 17.5 - - - +
393A VAL 4.4 3.6 + - - -
394A ILE* 2.6 53.8 + - + +
395A ASP* 4.7 1.3 - - - +
446B ALA* 3.1 32.7 + - - +
447B PRO* 3.9 7.6 - - + +
449B LYS* 1.3 74.6 - - - +
451B LEU* 1.3 73.5 + - + +
452B ARG 3.4 0.3 + - - -
453B ASP* 4.8 2.8 - - - +
454B GLU* 3.1 34.1 + - - +
----------------------------------------------------------
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Residues in contact with LEU 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B MET* 3.7 26.9 - - + -
243B GLN* 3.6 26.9 - - - +
447B PRO* 3.0 23.7 + - + +
448B PHE 3.9 4.7 - - - +
449B LYS 3.2 0.2 - - - -
450B LYS* 1.3 87.8 - - + +
452B ARG* 1.3 59.8 + - + +
454B GLU* 3.8 14.8 - - - +
455B THR* 3.5 21.7 + - - -
----------------------------------------------------------
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Residues in contact with ARG 452 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ARG* 4.3 27.4 - - - +
488A GLU* 5.5 7.6 - - - -
448B PHE* 3.2 51.2 + - + +
449B LYS* 3.2 7.6 + - + +
451B LEU* 1.3 75.2 - - + +
453B ASP* 1.3 64.4 + - - +
454B GLU 2.9 5.2 - - - -
455B THR* 2.8 16.9 + - - +
456B THR* 3.0 33.9 + - + +
----------------------------------------------------------
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Residues in contact with ASP 453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ARG* 4.0 29.5 + - - +
353A LYS* 5.2 4.9 + - - -
354A PHE* 5.3 20.0 - - + -
357A LYS* 4.8 12.2 + - - +
394A ILE* 6.0 0.2 - - - +
395A ASP* 4.1 15.8 - - - +
449B LYS* 2.8 28.8 + - - +
450B LYS* 4.9 2.8 - - - +
452B ARG* 1.3 72.5 - - - +
454B GLU* 1.3 62.5 - - + +
456B THR* 3.6 18.3 - - - +
1I G 5.7 0.3 + - - -
----------------------------------------------------------
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Residues in contact with GLU 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B LYS* 3.1 28.4 - - - +
451B LEU* 3.8 17.8 - - - +
452B ARG 2.8 1.4 + - - -
453B ASP* 1.3 82.1 - - + +
455B THR* 1.3 63.0 + - - +
456B THR 3.9 1.9 - - - +
457B PHE* 5.8 1.4 - - - -
----------------------------------------------------------
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Residues in contact with THR 455 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A GLY 4.8 1.0 - - - +
488A GLU* 2.8 44.0 + - + +
491A ALA* 5.4 1.2 - - - +
526A GLY* 4.6 11.8 - - - -
451B LEU 3.5 12.0 + - - -
452B ARG* 2.8 13.4 + - - -
454B GLU* 1.3 74.0 - - - +
456B THR* 1.3 66.5 + - - +
457B PHE* 3.8 16.6 - - - -
----------------------------------------------------------
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Residues in contact with THR 456 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ARG* 5.5 7.6 - - - +
486A SER* 5.7 1.4 - - - -
487A GLY* 4.6 4.3 + - - -
488A GLU* 4.4 14.5 - - - +
452B ARG* 3.0 38.2 + - + +
453B ASP* 3.6 21.5 - - - +
454B GLU 3.9 1.9 - - - +
455B THR* 1.3 86.5 - - - +
457B PHE* 1.3 74.0 + - - +
460B CYS* 4.0 14.5 - - + +
----------------------------------------------------------
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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