Contacts of the helix formed by residues 442 - 464 (chain B) in PDB entry 6MZL
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 442 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B TYR* 3.8 5.7 + - - -
431B LEU* 5.8 0.2 - - - -
432B HIS* 3.9 8.1 + - - -
441B LEU* 1.3 74.7 - - - +
443B TRP* 1.3 54.2 + - - +
444B GLU* 3.1 15.3 + - - +
445B TYR* 2.5 38.2 + - - +
446B TYR* 2.5 38.9 + - - +
969B CYS* 5.1 1.3 - - - -
973B ASP* 3.7 32.3 - - - -
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Residues in contact with TRP 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B TYR* 3.7 31.4 - + - -
314B VAL* 3.6 32.8 - - + -
441B LEU 5.3 2.0 - - - -
442B SER* 1.3 73.0 - - - +
444B GLU* 1.3 55.4 + - + +
446B TYR* 4.0 27.8 - + + +
447B SER* 2.5 42.8 + - - -
924B HIS* 3.3 29.6 - + + +
928B ASN* 5.5 8.3 - - - +
966B ARG* 3.3 50.1 - - + +
969B CYS* 5.9 1.1 - - + -
973B ASP* 5.2 0.6 + - - -
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Residues in contact with GLU 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B TYR* 3.3 34.0 + - + -
408B LYS* 4.6 13.2 + - - +
442B SER* 3.1 10.3 + - - +
443B TRP* 1.3 77.3 - - + +
445B TYR* 1.3 58.8 + - - +
447B SER* 2.6 20.3 + - - -
448B MET* 3.0 19.2 + - + +
928B ASN* 3.6 25.0 - - - +
931B THR* 5.4 6.1 - - - +
932B LYS* 3.7 24.2 + - - +
973B ASP* 6.4 1.3 - - - -
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Residues in contact with TYR 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B TYR* 4.0 16.3 + + - +
411B GLY 3.5 22.2 + - - -
412B VAL* 3.5 25.9 - - + +
413B LEU* 3.1 31.5 + - - +
428B ALA* 5.8 4.1 - - + +
432B HIS* 4.6 12.3 - + + +
434B SER* 4.5 14.1 + - - -
441B LEU* 3.6 43.5 - - + -
442B SER* 2.5 29.5 + - - +
444B GLU* 1.3 74.5 - - - +
446B TYR* 1.3 57.1 + - - +
448B MET* 3.3 1.4 + - - +
449B PHE* 2.9 36.3 + + + +
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Residues in contact with TYR 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B TYR* 3.2 29.9 - + - +
183B GLN* 3.4 14.7 + - - +
352B GLN* 5.0 0.3 + - - -
364B TRP* 4.1 14.8 - + - -
371B LYS* 2.3 40.8 + - + -
441B LEU* 5.0 8.5 - - + -
442B SER 2.5 19.7 + - - +
443B TRP* 4.0 38.4 - + + +
445B TYR* 1.3 72.9 - - - +
447B SER* 1.3 65.9 + - - +
449B PHE* 3.2 14.5 - + + +
450B GLN* 3.1 45.0 + - - +
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Residues in contact with SER 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B LYS* 5.6 4.3 - - - -
443B TRP* 2.5 28.2 + - - -
444B GLU* 2.6 19.8 + - - -
446B TYR* 1.3 79.9 - - - +
448B MET* 1.3 70.3 + - - +
450B GLN* 3.0 13.4 + - - +
451B CYS* 3.0 32.4 + - - -
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Residues in contact with MET 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B LYS* 3.4 62.4 - - + +
402B ILE* 3.8 12.6 - - + -
405B TYR* 3.5 25.1 - - + -
406B GLU* 6.0 0.7 - - + -
412B VAL* 3.9 21.3 - - + -
444B GLU* 3.0 16.6 + - - +
445B TYR 3.9 0.4 - - - +
447B SER* 1.3 103.2 + - - +
449B PHE* 1.3 61.7 + - - +
451B CYS* 3.6 4.9 - - - +
452B LYS* 2.9 34.9 + - + +
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Residues in contact with PHE 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B TRP* 5.4 14.1 - + - -
367B GLU* 4.4 11.7 - - + -
368B TRP* 3.6 31.4 - + + -
371B LYS* 3.8 33.4 - - + -
412B VAL* 3.7 16.1 - - + +
413B LEU 4.9 3.8 - - - -
414B LEU* 3.5 33.6 - - + +
441B LEU* 6.4 1.1 - - + -
445B TYR* 2.9 22.7 + + + +
446B TYR* 3.2 25.6 - + - +
448B MET* 1.3 75.7 - - - +
450B GLN* 1.3 60.6 + - + +
452B LYS* 3.4 3.6 + - - +
453B ALA* 3.0 27.7 + - + +
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Residues in contact with GLN 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B GLN* 5.8 2.8 + - - +
352B GLN* 3.9 11.3 + - - +
371B LYS* 3.6 30.7 - - + +
446B TYR* 3.1 45.8 + - - +
447B SER* 3.0 12.0 + - - +
449B PHE* 1.3 78.8 - - + +
451B CYS* 1.3 63.6 + - - +
453B ALA* 3.2 10.3 + - - +
454B HIS* 3.0 36.1 + - + +
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Residues in contact with CYS 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B GLU* 3.2 22.6 - - - +
401B LYS* 4.1 27.8 - - - -
402B ILE* 3.5 22.0 - - + -
447B SER* 3.0 23.6 + - - -
448B MET* 3.2 11.2 + - - +
450B GLN* 1.3 76.8 - - - +
452B LYS* 1.3 64.9 + - - +
454B HIS* 3.2 14.9 + - - +
455B LEU* 3.1 26.5 + - - +
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Residues in contact with LYS 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B ILE* 3.7 25.1 - - + -
406B GLU* 3.7 17.0 + - - +
412B VAL* 2.4 44.3 + - + +
413B LEU* 4.6 0.8 - - - +
414B LEU* 5.2 12.9 - - + +
448B MET 2.9 14.4 + - - +
449B PHE* 3.9 4.3 - - - +
451B CYS* 1.3 75.3 - - - +
453B ALA* 1.3 57.8 + - - +
455B LEU* 4.4 2.7 - - - +
456B VAL* 2.9 41.9 + - + +
522B TRP* 3.8 18.2 + - - -
525B GLN 5.0 0.2 + - - -
526B SER* 3.5 24.7 - - - +
527B GLY 4.9 0.8 - - - +
637B LEU* 4.6 18.6 - - + +
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Residues in contact with ALA 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B TRP* 4.0 13.7 - - + +
371B LYS* 3.7 8.1 - - + -
372B GLY* 3.4 31.1 - - - +
414B LEU* 5.7 5.3 - - - +
449B PHE* 3.0 15.5 + - + +
450B GLN* 3.2 16.2 - - - +
451B CYS 3.1 0.2 - - - -
452B LYS* 1.3 76.8 - - - +
454B HIS* 1.3 60.8 + - - +
456B VAL* 4.1 3.1 - - - +
457B MET* 3.2 28.9 + - - +
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Residues in contact with HIS 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B GLN* 5.9 0.4 + - - -
371B LYS 5.2 1.1 - - - -
372B GLY* 4.6 4.7 - - - -
375B GLY* 3.4 41.8 + - - -
376B TYR* 4.5 5.9 - - - +
378B TYR* 4.1 8.6 + + - -
394B TRP* 3.6 29.2 - + + -
398B GLU* 3.5 26.8 + - - -
450B GLN* 3.0 30.9 + - + +
451B CYS* 3.2 9.0 + - - +
453B ALA* 1.3 74.2 - - - +
455B LEU* 1.3 75.0 + - + +
457B MET* 3.2 6.1 + - - +
458B ARG* 3.1 26.8 + - - +
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Residues in contact with LEU 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B TRP* 6.1 0.2 - - + -
395B ILE* 4.0 14.1 - - + -
398B GLU* 4.0 20.4 - - + -
399B LEU* 3.8 27.4 - - + -
402B ILE* 3.6 25.1 - - + -
451B CYS 3.1 12.2 + - - +
452B LYS* 4.2 4.0 - - - +
453B ALA 3.3 0.4 - - - -
454B HIS* 1.3 85.5 - - + +
456B VAL* 1.3 59.7 + - + +
458B ARG* 3.2 32.8 + - - +
459B LEU* 3.0 29.4 + - - +
635B SER 5.2 1.0 - - - +
637B LEU* 4.1 15.7 - - + +
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Residues in contact with VAL 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B TRP* 4.4 5.6 - - + -
414B LEU* 5.2 6.3 - - + -
452B LYS* 2.9 30.5 + - + +
453B ALA* 4.2 3.6 - - - +
455B LEU* 1.3 78.0 - - + +
457B MET* 1.3 77.4 + - + +
459B LEU* 3.0 13.7 + - + +
460B ILE* 3.0 27.6 + - + +
518B LEU* 5.5 4.0 - - + -
522B TRP* 4.2 29.4 - - + +
523B VAL* 4.1 24.2 - - + -
637B LEU* 5.7 5.4 - - + -
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Residues in contact with MET 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B TRP* 3.6 32.8 - - + -
369B VAL* 5.0 2.5 - - - -
372B GLY* 3.4 23.1 - - - +
373B ILE* 3.8 25.1 - - + +
376B TYR* 3.7 24.2 - - + -
453B ALA 3.2 17.7 + - - +
454B HIS 3.6 7.2 - - - +
456B VAL* 1.3 81.1 - - + +
458B ARG* 1.3 57.9 + - - +
460B ILE* 3.1 29.6 + - + +
461B GLU* 3.0 22.7 + - - +
469B MET* 3.9 11.8 - - + +
473B PHE* 5.8 2.5 - - - -
503B PHE* 5.4 6.3 - - + -
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Residues in contact with ARG 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B TYR* 4.7 12.2 - - + +
379B GLY* 4.9 3.2 - - - -
391B TYR* 2.3 49.9 + - - -
392B ARG* 4.5 5.8 - - - +
394B TRP* 3.7 18.0 - - - -
395B ILE* 3.3 35.4 - - - +
454B HIS* 3.1 16.1 + - - +
455B LEU* 3.2 34.1 + - - +
457B MET* 1.3 78.0 - - - +
459B LEU* 1.3 56.3 + - + +
461B GLU* 3.2 24.7 + - - +
462B ASN* 2.7 35.7 + - - +
633B ASP 5.9 3.8 - - - +
634B MET 5.6 6.7 - - - +
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Residues in contact with LEU 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B LEU 3.0 16.4 + - - +
456B VAL* 3.0 15.8 + - + +
458B ARG* 1.3 76.2 - - - +
460B ILE* 1.3 59.5 + - - +
462B ASN* 2.9 33.8 + - + +
463B ARG* 3.0 17.2 + - - +
518B LEU* 3.8 18.3 - - + +
522B TRP* 3.5 45.8 - - + +
635B SER* 3.3 37.2 - - - +
636B VAL* 5.0 3.8 - - + -
637B LEU* 5.5 4.9 - - + -
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Residues in contact with ILE 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B TRP* 5.4 4.7 - - + -
456B VAL* 3.0 12.9 + - + +
457B MET* 3.1 40.1 + - + +
459B LEU* 1.3 72.1 - - - +
461B GLU* 1.3 62.0 + - - +
463B ARG* 3.8 1.7 - - - +
464B ILE* 2.9 47.3 + - + +
469B MET* 4.5 13.7 - - + -
503B PHE* 5.3 5.4 - - + -
507B ILE* 4.9 23.1 - - + -
515B ILE* 6.3 2.0 - - + -
518B LEU* 3.7 22.7 - - + -
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Residues in contact with GLU 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B TYR* 2.4 44.5 + - - +
383B LYS* 3.8 18.9 + - - -
391B TYR* 4.5 2.9 + - - -
392B ARG* 5.7 3.3 + - - -
457B MET 3.0 11.2 + - - +
458B ARG* 3.2 23.7 + - - +
460B ILE* 1.3 76.9 - - - +
462B ASN* 1.3 64.8 + - - +
463B ARG 4.0 0.2 - - - -
464B ILE 2.8 24.6 + - - +
466B MET* 4.4 12.7 - - + +
469B MET* 3.6 16.9 - - + +
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Residues in contact with ASN 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B ARG* 2.7 28.4 + - - +
459B LEU* 2.9 35.8 + - + +
461B GLU* 1.3 80.0 - - - +
463B ARG* 1.3 63.1 + - + +
633B ASP* 4.9 15.6 + - - +
634B MET 5.0 0.2 + - - -
635B SER* 3.7 22.8 - - - +
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Residues in contact with ARG 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B LEU 3.0 13.2 + - - +
460B ILE* 4.5 2.9 - - - +
461B GLU 4.0 0.2 - - - -
462B ASN* 1.3 83.1 - - + +
464B ILE* 1.3 68.4 + - + +
513B LYS* 3.6 26.0 + - + +
514B ASP* 2.3 38.8 + - - +
515B ILE* 4.1 18.6 - - + -
517B PRO* 4.0 6.9 - - - +
518B LEU* 3.1 43.1 - - + +
521B GLN* 4.1 17.4 + - - +
564B LEU* 6.3 0.8 - - - +
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Residues in contact with ILE 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B ILE* 2.9 26.0 + - + +
461B GLU* 2.8 23.8 + - - +
463B ARG* 1.3 88.2 - - + +
465B SER* 1.3 76.6 + - - +
466B MET 3.6 0.3 + - - -
468B PHE* 3.6 21.3 - - + -
469B MET* 4.1 8.1 - - + +
472B VAL* 6.2 2.2 - - + -
507B ILE* 3.8 30.5 - - + +
510B VAL* 5.9 0.7 - - + -
511B SER* 4.0 21.8 - - - +
513B LYS* 4.4 15.0 - - + +
515B ILE* 4.4 15.7 - - + -
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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