Contacts of the helix formed by residues 431 - 458 (chain B) in PDB entry 2W8D
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 431 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A THR* 4.2 11.5 - - - +
429B PHE 3.4 0.2 - - - -
430B GLY* 1.3 80.5 - - - +
432B SER* 1.3 57.5 + - - +
433B VAL* 2.9 40.5 + - - +
434B VAL* 3.3 7.8 + - + +
435B ASP* 2.8 33.0 + - - +
478B ASN 4.7 1.2 - - - +
479B HIS* 2.8 33.5 + - - +
482B ALA* 3.4 23.1 + - + +
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Residues in contact with SER 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ASN* 5.0 1.7 + - - -
346A THR* 3.5 29.2 - - - +
348A THR* 3.9 6.9 + - - -
349A PHE* 4.6 7.1 - - - -
431B ASP* 1.3 73.0 + - - +
433B VAL* 1.3 63.6 + - - +
435B ASP* 3.8 11.0 + - - -
436B ASN* 3.0 45.9 + - - +
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Residues in contact with VAL 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A PHE* 3.7 32.5 - - + -
413B PHE* 3.6 26.7 - - + -
414B PRO* 4.2 15.7 - - + -
415B PHE* 3.5 26.4 - - + -
431B ASP* 2.9 11.3 + - - +
432B SER* 1.3 77.2 + - - +
434B VAL* 1.3 64.5 + - - +
436B ASN* 3.5 0.5 + - - -
437B TYR* 3.1 19.9 + - - +
474B GLY 5.6 0.2 - - - +
475B ILE* 4.5 5.2 - - + -
479B HIS* 3.7 26.2 - - + +
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Residues in contact with VAL 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B PHE* 4.1 10.3 - - + -
431B ASP* 3.3 9.0 + - - +
433B VAL* 1.3 73.6 - - - +
435B ASP* 1.3 67.2 + - - +
436B ASN 3.1 0.9 + - - -
437B TYR* 3.3 13.8 + - + +
438B PHE* 3.1 26.5 - - + -
475B ILE* 4.2 17.5 - - + -
479B HIS* 3.8 31.4 - - + +
482B ALA* 3.8 18.2 - - + +
483B MSE 4.7 6.5 - - + -
486B VAL* 3.5 32.1 - - + -
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Residues in contact with ASP 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B ALA* 3.8 9.5 - - + -
427B GLY* 3.0 45.6 + - - +
428B ASP* 4.3 2.8 - - - +
429B PHE* 2.7 33.1 + - - +
430B GLY* 4.2 1.7 + - - -
431B ASP 2.8 32.4 + - - +
432B SER* 3.6 11.4 - - - +
434B VAL* 1.3 73.6 - - - +
436B ASN* 1.3 65.0 + - - +
438B PHE* 3.6 8.4 + - - +
439B GLN 4.4 0.5 + - - -
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Residues in contact with ASN 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B PRO 4.1 6.3 + - - +
415B PHE* 3.4 27.1 + - - +
416B GLY 3.4 8.9 - - - +
426B ALA* 4.3 6.2 - - - +
432B SER* 3.0 31.8 + - - +
434B VAL 3.2 0.2 - - - -
435B ASP* 1.3 77.0 - - - +
437B TYR* 1.3 67.4 + - - +
438B PHE 3.0 3.7 + - - -
439B GLN* 3.0 33.6 + - - +
440B SER* 3.3 10.0 + - - -
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Residues in contact with TYR 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B SER 2.6 30.2 + - - -
255B LEU* 3.4 3.3 - - - +
256B GLN* 2.9 25.6 + - - +
258B PHE* 3.7 30.3 - + - -
259B ILE* 3.7 18.8 - - + -
411B ASN* 3.7 15.0 - - - -
415B PHE* 3.4 40.7 - + + +
433B VAL 3.1 14.5 + - - +
434B VAL* 3.4 13.0 - - + +
436B ASN* 1.3 75.2 - - - +
438B PHE* 1.3 62.9 + + + +
440B SER* 3.6 1.6 + - - -
441B ALA* 3.0 32.0 + - + +
474B GLY* 4.3 2.0 - - - -
475B ILE* 3.6 20.2 - - + -
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Residues in contact with PHE 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B PHE* 4.2 18.8 - + - -
259B ILE* 4.2 7.2 - - + -
262B TYR* 3.8 20.9 - + - -
264B ILE* 3.9 29.2 - - + -
269B VAL* 3.6 23.2 - - + +
424B PHE* 4.0 8.9 - - + -
425B PRO 4.6 0.4 - - - +
427B GLY* 4.1 8.1 - - - +
429B PHE* 3.5 27.1 - + - -
434B VAL* 3.1 32.5 - - + -
435B ASP 3.6 10.8 - - - +
436B ASN 3.0 1.2 - - - -
437B TYR* 1.3 81.3 - + + +
439B GLN* 1.3 56.7 + - - +
441B ALA* 4.6 0.2 - - - -
442B HIS* 3.1 29.3 + - - +
486B VAL* 3.9 25.8 - - + -
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Residues in contact with GLN 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B GLY 4.1 9.4 - - - +
417B MSE 4.4 6.0 + - - +
422B THR* 4.0 26.5 + - + +
424B PHE* 3.3 26.6 + - - +
425B PRO* 3.7 16.1 - - - +
426B ALA* 4.0 21.0 - - + +
435B ASP 4.6 0.9 - - - +
436B ASN* 3.0 30.3 + - - +
438B PHE* 1.3 76.8 - - - +
440B SER* 1.3 56.0 + - - +
442B HIS* 3.7 2.7 + - - +
443B TYR* 3.0 24.4 + - - +
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Residues in contact with SER 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B SER 4.2 10.9 - - - -
411B ASN* 2.7 25.2 + - - +
415B PHE* 3.4 24.8 - - - +
416B GLY 3.9 11.9 - - - -
417B MSE 4.1 18.8 - - - -
436B ASN 3.3 3.8 + - - -
437B TYR 3.8 0.9 + - - -
439B GLN* 1.3 77.8 - - - +
441B ALA* 1.3 60.0 + - - +
443B TYR* 3.6 6.6 - - - +
444B LEU* 2.8 28.8 + - - +
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Residues in contact with ALA 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU* 4.1 21.2 - - + +
259B ILE* 5.0 2.9 - - + -
269B VAL* 4.0 15.9 - - + -
270B THR* 3.8 6.4 - - + +
411B ASN* 3.5 11.5 + - - +
437B TYR* 3.0 28.4 + - + +
438B PHE* 4.0 3.6 - - - +
440B SER* 1.3 75.1 - - - +
442B HIS* 1.3 57.7 + - - +
444B LEU* 3.2 6.7 + - - +
445B ASP* 2.9 29.1 + - - +
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Residues in contact with HIS 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B GLU 3.7 8.3 + - - -
269B VAL 3.2 27.1 + - - +
271B PRO* 4.3 14.1 - - + +
422B THR* 3.9 9.0 - - - -
423B ASP 5.7 0.2 - - - -
424B PHE* 3.2 49.6 + + + +
438B PHE 3.1 19.3 + - - +
439B GLN 3.9 3.8 - - - +
441B ALA* 1.3 73.9 - - - +
443B TYR* 1.3 62.2 + - - +
445B ASP* 3.5 2.0 + - - +
446B GLN* 3.3 48.9 + - + +
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Residues in contact with TYR 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B LYS* 3.5 17.2 - - + +
384B ASP 4.1 6.1 - - - -
385B LYS* 3.4 51.7 + - + +
386B PRO* 4.1 1.4 - - - +
410B SER* 3.8 25.6 - - - -
417B MSE 3.8 35.2 - - + -
421B ASP* 3.8 36.5 + - + -
422B THR* 4.5 4.5 - - - -
439B GLN 3.0 19.7 + - - +
440B SER 3.7 4.5 - - - +
441B ALA 3.3 0.4 - - - -
442B HIS* 1.3 77.5 - - - +
444B LEU* 1.3 56.7 + - - +
446B GLN* 3.4 11.6 + - - +
447B SER* 2.6 40.2 + - - -
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Residues in contact with LEU 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LEU* 4.1 17.0 - - + -
253B GLU 3.9 29.8 - - - +
255B LEU* 4.3 18.2 - - + -
273B LEU* 5.7 0.9 - - + -
384B ASP* 3.7 21.5 - - - +
388B PHE* 5.4 0.4 - - + -
408B THR* 4.2 19.7 - - + +
410B SER* 5.9 0.2 - - - -
411B ASN* 4.2 10.3 - - + +
440B SER 2.8 20.9 + - - +
441B ALA 3.2 4.7 + - - +
443B TYR* 1.3 76.5 - - - +
445B ASP* 1.3 63.5 + - - +
447B SER* 3.1 19.4 + - - -
448B ILE* 3.2 37.5 + - + +
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Residues in contact with ASP 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B VAL 4.2 1.6 - - - +
270B THR* 3.3 26.4 - - + -
271B PRO* 3.2 11.5 - - + +
272B PHE* 2.8 30.8 + - - +
273B LEU* 2.9 42.5 + - - +
441B ALA 2.9 16.8 + - - +
442B HIS 3.8 5.2 - - - +
443B TYR 3.3 0.6 - - - -
444B LEU* 1.3 75.8 - - - +
446B GLN* 1.3 62.8 + - + +
448B ILE* 3.5 10.4 + - - +
449B GLU* 3.2 19.4 + - - +
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Residues in contact with GLN 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PRO* 6.3 1.8 - - + -
385B LYS* 3.4 30.5 + - - -
421B ASP 4.5 4.2 - - - +
422B THR* 4.9 3.8 + - - +
442B HIS* 3.3 45.0 + - + +
443B TYR* 3.4 11.6 + - - +
444B LEU 3.3 0.4 - - - -
445B ASP* 1.3 75.6 - - + +
447B SER* 1.3 61.1 + - - +
449B GLU* 3.3 19.6 + - - +
450B GLN* 2.9 28.1 + - - +
----------------------------------------------------------
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Residues in contact with SER 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ASP* 3.8 32.1 - - - +
385B LYS* 4.2 10.6 - - - +
388B PHE* 3.8 17.3 - - - +
443B TYR* 2.6 25.6 + - - -
444B LEU* 3.1 12.6 + - - -
446B GLN* 1.3 78.0 - - - +
448B ILE* 1.3 57.2 + - - +
450B GLN* 3.4 8.7 + - - +
451B PHE* 3.0 25.8 + - - +
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Residues in contact with ILE 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B VAL* 5.1 0.9 - - + -
252B LEU* 3.6 33.0 - - + -
272B PHE* 3.7 15.9 - - + -
273B LEU* 4.3 12.6 - - + -
388B PHE* 4.9 11.0 - - + -
444B LEU* 3.2 37.9 + - + +
445B ASP* 3.8 8.7 - - - +
446B GLN 3.3 0.2 - - - -
447B SER* 1.3 74.1 - - - +
449B GLU* 1.3 55.6 + - - +
451B PHE* 3.1 9.0 + - + +
452B PHE* 2.8 58.0 + - + -
468B MSE 3.7 16.6 - - + -
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Residues in contact with GLU 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PHE* 3.6 42.2 - - + +
445B ASP 3.2 13.4 + - - +
446B GLN* 3.3 21.0 - - - +
448B ILE* 1.3 74.1 - - - +
450B GLN* 1.3 63.3 + - - +
452B PHE* 3.4 1.2 + - - +
453B ASN* 3.0 42.2 + - - +
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Residues in contact with GLN 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B LYS* 3.1 48.3 + - + +
388B PHE* 3.7 10.3 - - - +
389B LYS* 3.5 30.6 - - - +
446B GLN 2.9 13.5 + - - +
447B SER* 3.4 9.0 - - - +
449B GLU* 1.3 76.5 - - - +
451B PHE* 1.3 63.2 + - - +
452B PHE 3.3 0.2 + - - -
453B ASN* 3.3 8.4 + - - +
454B ASP* 3.0 38.0 + - - +
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Residues in contact with PHE 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ILE* 4.0 7.9 - - + -
250B VAL* 3.8 24.7 - - + -
388B PHE* 3.3 44.4 - + + -
392B MSE 3.8 25.4 - - - -
395B LEU* 4.5 0.4 - - + -
406B PHE* 3.9 32.1 - + - -
447B SER 3.0 13.9 + - - +
448B ILE* 3.1 13.0 + - + +
450B GLN* 1.3 76.0 - - - +
452B PHE* 1.3 67.7 + + - +
454B ASP* 3.0 8.3 + - - +
455B LEU* 2.8 61.1 + - + +
466B ILE* 5.6 0.4 - - + -
----------------------------------------------------------
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Residues in contact with PHE 452 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PHE* 3.5 23.1 - + + -
276B LEU* 4.0 21.3 - - + -
448B ILE* 2.8 39.1 + - + +
449B GLU 3.8 3.6 - - - +
451B PHE* 1.3 80.8 - + - +
453B ASN* 1.3 68.7 + - - +
454B ASP 3.0 1.6 - - - -
455B LEU* 2.9 7.7 + - + +
456B LYS* 2.8 39.7 + - - +
461B TYR* 3.9 20.9 - + + -
466B ILE* 3.6 42.6 - - + -
468B MSE 3.8 24.0 - - + -
508B HIS* 5.2 7.2 - + + -
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Residues in contact with ASN 453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PHE* 5.1 2.8 - - - -
449B GLU* 3.0 31.5 + - - +
450B GLN* 3.5 8.4 - - - +
452B PHE* 1.3 76.1 - - - +
454B ASP* 1.3 60.3 + - - +
456B LYS* 3.8 16.5 + - - +
457B LYS* 3.3 35.1 + - + +
----------------------------------------------------------
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Residues in contact with ASP 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B PHE 5.2 0.3 - - - +
389B LYS* 4.8 5.2 - - - +
392B MSE 3.7 34.6 - - + +
450B GLN* 3.0 35.2 + - - +
451B PHE* 3.4 8.6 - - - +
453B ASN* 1.3 78.9 - - - +
455B LEU* 1.3 65.5 + - - +
456B LYS 3.2 1.3 - - - -
457B LYS* 3.1 16.4 + - - +
458B ASP* 3.0 23.7 + - - +
----------------------------------------------------------
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Residues in contact with LEU 455 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ILE* 3.8 24.2 - - + -
392B MSE 3.6 21.3 - - + -
395B LEU* 3.7 21.5 - - + -
451B PHE* 2.8 46.5 + - + +
452B PHE* 3.7 8.7 - - + +
454B ASP* 1.3 73.2 - - - +
456B LYS* 1.3 60.1 + - - +
458B ASP* 3.5 3.5 - - - +
459B GLY 3.5 1.4 + - - -
460B LEU* 2.9 23.6 + - + -
461B TYR* 2.8 35.0 + - + +
466B ILE* 4.0 24.2 - - + -
----------------------------------------------------------
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Residues in contact with LYS 456 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PHE* 5.0 9.1 - - - -
275B LYS* 6.2 0.2 - - - +
452B PHE* 2.8 32.7 + - - +
453B ASN* 3.9 14.6 + - - +
455B LEU* 1.3 76.5 - - - +
457B LYS* 1.3 60.7 + - + +
459B GLY* 3.6 11.3 + - - -
461B TYR* 3.5 53.5 + - + +
----------------------------------------------------------
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Residues in contact with LYS 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B ASN* 3.3 20.8 + - + +
454B ASP* 3.1 13.4 + - - +
456B LYS* 1.3 80.3 - - + +
458B ASP* 1.3 57.6 + - - +
459B GLY 3.5 1.3 - - - -
----------------------------------------------------------
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Residues in contact with ASP 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B MSE 3.9 7.1 - - - +
396B GLU* 2.9 47.9 - - + +
454B ASP* 3.0 22.3 - - - +
455B LEU* 3.5 9.5 - - - +
456B LYS 3.5 0.2 - - - -
457B LYS* 1.3 76.6 - - - +
459B GLY* 1.3 55.6 + - - +
460B LEU* 2.9 35.7 + - - +
463B LYS* 5.1 3.5 + - - -
----------------------------------------------------------
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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