Contacts of the helix formed by residues 512 - 537 (chain B) in PDB entry 3K5N
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 512 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B VAL* 3.7 13.3 - - - +
438B LEU* 3.2 18.1 - - + +
503B LEU 4.4 0.4 + - - +
510B PHE 3.5 3.4 + - - -
511B PHE* 1.3 84.3 - - - +
513B PRO* 1.3 79.1 - - - +
514B ARG* 2.9 48.2 + - - +
515B LEU* 2.8 36.9 + - + +
516B ALA* 3.4 4.7 + - - +
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Residues in contact with PRO 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B VAL* 3.5 13.7 - - + -
395B PRO 3.5 19.7 - - - +
396B PRO* 3.9 12.6 - - + -
397B HIS* 3.9 22.4 - - + +
455B LEU* 4.7 6.3 - - + -
511B PHE* 3.9 11.2 - - + -
512B ASP* 1.3 96.1 - - - +
514B ARG* 1.3 58.3 + - + +
516B ALA* 3.5 3.2 + - + +
517B SER* 2.3 37.4 + - - +
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Residues in contact with ARG 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B LEU* 3.5 30.7 - - + +
442B MET* 3.9 21.6 - - - +
455B LEU* 4.3 37.7 - - + +
457B ALA* 4.4 12.3 - - + +
459B PHE* 4.6 0.2 - - - -
512B ASP* 2.9 38.4 + - - +
513B PRO* 1.3 78.1 - - + +
515B LEU* 1.3 57.3 + - - +
517B SER* 4.2 2.7 - - - -
518B SER* 2.4 35.2 + - - -
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Residues in contact with LEU 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B ILE* 3.9 23.9 - - + +
434B ASP 4.0 4.7 - - - +
435B PRO* 3.7 42.0 - - + -
438B LEU* 5.0 6.0 - - + +
459B PHE* 4.2 7.2 - - + -
503B LEU* 4.0 22.9 - - + +
510B PHE 2.8 30.7 - - - +
512B ASP* 2.8 26.4 + - + +
514B ARG* 1.3 81.7 - - - +
516B ALA* 1.3 58.8 + - - +
518B SER* 4.3 1.1 - - - -
519B ILE* 3.5 20.8 + - - +
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Residues in contact with ALA 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B TYR* 5.2 11.7 - - + +
503B LEU* 4.1 22.4 + - - +
504B GLY* 4.3 12.8 - - - +
511B PHE* 5.7 2.0 - - + -
512B ASP 3.4 4.0 + - - +
513B PRO* 3.5 6.0 + - + +
515B LEU* 1.3 78.8 - - - +
517B SER* 1.3 61.5 + - - +
519B ILE* 2.9 29.9 + - - +
520B THR* 3.1 10.4 + - - +
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Residues in contact with SER 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B PHE* 5.0 1.1 - - - -
455B LEU* 4.1 23.4 - - - +
513B PRO* 2.3 29.6 + - - +
514B ARG* 4.3 1.6 - - - -
516B ALA* 1.3 73.0 - - - +
518B SER* 1.3 68.7 + - - +
519B ILE 2.8 1.3 - - - -
520B THR* 2.7 19.6 + - - -
521B MET* 2.8 29.6 + - - +
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Residues in contact with SER 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B ILE* 3.4 25.5 - - - +
453B GLY* 4.5 3.4 - - - -
454B PHE* 3.8 25.6 + - - +
457B ALA* 3.6 9.2 - - - +
459B PHE* 3.5 21.4 - - - -
514B ARG 2.4 27.8 + - - -
515B LEU 4.3 0.7 - - - -
517B SER* 1.3 78.7 - - - +
519B ILE* 1.3 65.1 + - - +
522B ARG* 3.5 23.0 + - - +
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Residues in contact with ILE 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B TYR* 3.0 37.8 - - + +
427B ILE* 3.7 14.7 - - + +
428B ILE* 2.5 45.1 - - + -
433B ILE* 4.1 12.8 - - + -
500B TYR* 3.6 25.1 - - + -
503B LEU* 4.9 7.6 - - + -
515B LEU 3.5 13.7 + - - +
516B ALA* 2.9 15.1 + - - +
517B SER 2.8 1.2 - - - -
518B SER* 1.3 83.5 - - - +
520B THR* 1.3 58.9 + - - +
522B ARG* 4.0 0.2 - - - +
523B GLY 3.7 8.5 + - - -
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Residues in contact with THR 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B TYR* 2.9 34.3 - - + +
500B TYR* 3.7 19.0 + - + +
516B ALA* 3.2 12.0 + - - +
517B SER* 2.7 15.5 + - - -
519B ILE* 1.3 71.4 - - - +
521B MET* 1.3 54.5 + - - +
522B ARG 2.8 5.4 - - - -
523B GLY* 2.3 27.5 + - - +
524B HIS* 2.9 28.4 + - + -
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Residues in contact with MET 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B PHE* 2.6 75.0 - - + -
455B LEU* 4.9 10.5 - - + +
517B SER* 2.8 25.5 + - - +
520B THR* 1.3 72.9 - - - +
522B ARG* 1.3 56.6 + - - +
524B HIS* 3.4 24.1 + - + +
525B GLN* 2.9 24.8 + - - +
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Residues in contact with ARG 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B ILE* 3.7 9.6 - - + +
431B PHE* 2.4 78.3 - - - +
433B ILE* 5.4 1.8 - - - +
451B THR* 6.0 0.6 - - - +
452B GLU 3.3 24.2 + - - -
453B GLY* 4.5 1.8 - - - -
454B PHE* 3.7 24.0 - - + -
518B SER* 3.5 20.9 + - - +
519B ILE 4.0 2.0 - - - +
520B THR 2.8 0.8 - - - -
521B MET* 1.3 78.0 - - - +
523B GLY* 1.3 60.8 + - - +
525B GLN* 3.3 21.8 + - - +
526B ILE* 2.8 46.9 + - + +
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Residues in contact with GLY 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B LEU* 4.8 10.0 - - - +
424B TYR* 5.0 5.8 - - - -
427B ILE* 3.9 16.8 - - - +
519B ILE 3.7 4.1 + - - -
520B THR* 2.3 23.4 + - - -
522B ARG* 1.3 66.6 - - - +
524B HIS* 1.3 66.9 + - - -
526B ILE* 3.0 6.9 + - - +
527B MET* 2.8 24.3 + - - +
546B THR 5.3 5.2 - - - -
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Residues in contact with HIS 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B TYR* 5.5 0.7 - - - -
520B THR* 2.9 26.7 + - + -
521B MET* 3.6 30.9 + - + +
523B GLY* 1.3 75.6 - - - +
525B GLN* 1.3 50.6 + - - +
527B MET* 2.7 24.6 + - - +
528B ARG* 2.4 33.6 + - - +
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Residues in contact with GLN 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B PHE* 5.4 0.8 - - - -
454B PHE* 4.0 19.3 - - + -
521B MET 2.9 15.1 + - - +
522B ARG* 3.3 30.1 + - - +
524B HIS* 1.3 76.9 - - - +
526B ILE* 1.3 68.1 + - + +
528B ARG* 3.1 17.9 + - - +
529B GLN* 3.2 22.8 + - + +
577B TRP* 4.5 20.1 - - + -
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Residues in contact with ILE 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B TYR* 3.8 20.6 - - + +
423B LEU* 5.1 4.7 - - + -
427B ILE* 4.6 7.4 - - + -
431B PHE* 4.2 11.0 - - + -
522B ARG* 2.8 46.6 + - + +
523B GLY* 3.5 6.1 - - - +
525B GLN* 1.3 78.5 - - + +
527B MET* 1.3 58.2 + - - +
529B GLN* 4.0 0.2 - - - +
530B THR* 2.4 45.8 + - - +
577B TRP* 3.5 27.1 - - + -
590B LEU* 3.9 32.8 - - + -
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Residues in contact with MET 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B TYR* 4.5 12.1 - - + -
423B LEU* 5.7 2.5 - - - -
523B GLY 2.8 10.2 + - - +
524B HIS* 2.7 15.7 + - - +
526B ILE* 1.3 78.7 - - - +
528B ARG* 1.3 66.3 + - + +
530B THR* 3.1 12.9 + - - +
531B LYS* 3.0 21.4 + - - +
544B GLY* 5.3 4.7 - - - -
545B ASP 3.6 17.5 - - - +
546B THR* 3.7 20.0 - - - +
547B ASP* 4.1 7.9 - - - -
548B SER 4.0 10.5 - - - +
549B THR* 2.9 38.6 - - + -
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Residues in contact with ARG 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B HIS* 2.4 40.7 + - - +
525B GLN* 3.1 20.8 + - - +
527B MET* 1.3 76.4 - - + +
529B GLN* 1.3 59.1 + - - +
531B LYS* 2.4 40.7 + - + +
532B ALA* 2.8 6.6 + - - +
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Residues in contact with GLN 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B GLN* 3.2 15.8 + - + +
526B ILE 4.0 0.2 - - - +
528B ARG* 1.3 76.1 - - - +
530B THR* 1.3 71.0 + - - +
531B LYS 2.9 1.6 - - - -
532B ALA* 4.1 10.8 - - - +
533B LEU* 2.9 46.4 + - + +
576B TRP* 3.1 36.2 - - + -
577B TRP* 4.0 16.2 - - + -
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Residues in contact with THR 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B LEU* 6.3 0.4 - - + -
420B TYR* 3.2 32.5 + - + +
526B ILE* 2.4 32.3 + - - +
527B MET* 3.1 12.8 + - - -
529B GLN* 1.3 75.6 - - - +
531B LYS* 1.3 58.7 + - - +
533B LEU* 3.5 7.6 + - - +
534B ILE* 2.9 32.6 + - + +
549B THR* 4.7 12.1 - - + +
573B VAL* 4.0 18.6 - - + +
577B TRP* 4.4 3.6 - - - -
592B LEU* 4.1 13.5 - - + -
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Residues in contact with LYS 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527B MET 3.0 10.0 + - - +
528B ARG* 2.4 34.7 + - + +
529B GLN 2.9 0.6 - - - -
530B THR* 1.3 76.5 - - - +
532B ALA* 1.3 77.5 - - + +
534B ILE* 3.1 6.7 + - - +
535B GLU* 3.1 50.1 + - - +
541B VAL* 4.0 36.1 + - + +
549B THR* 6.0 4.9 - - + -
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Residues in contact with ALA 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B ARG 2.8 9.0 + - - +
529B GLN* 3.1 17.7 + - - +
531B LYS* 1.3 84.1 - - + +
533B LEU* 1.3 68.2 + - + +
535B GLU* 3.3 11.2 + - - +
536B ALA* 2.9 22.9 + - - +
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Residues in contact with LEU 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B GLN* 2.9 51.8 + - + +
530B THR* 3.6 4.5 - - - +
532B ALA* 1.3 80.3 - - + +
534B ILE* 1.3 64.9 + - - +
536B ALA* 2.8 24.2 + - - +
537B GLN* 3.4 3.6 + - - +
572B HIS* 4.0 27.0 - - + +
573B VAL* 4.5 18.8 - - + -
576B TRP* 3.4 52.5 - - + -
577B TRP* 5.4 1.6 - - - +
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Residues in contact with ILE 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B LEU* 4.8 13.5 - - + -
530B THR* 2.9 23.3 + - + +
531B LYS* 3.1 4.5 + - - +
533B LEU* 1.3 76.7 - - - +
535B GLU* 1.3 66.9 + - + +
537B GLN* 3.3 14.6 + - - +
539B TYR* 3.9 20.0 + - + +
540B ASP 4.9 1.8 - - - +
541B VAL* 3.8 28.3 - - + -
549B THR* 5.5 3.6 - - - +
551B VAL* 4.9 6.3 - - + -
569B LEU* 3.4 51.6 - - + -
572B HIS* 5.8 1.6 - - - +
573B VAL* 4.7 13.2 - - + -
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Residues in contact with GLU 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B LYS* 3.1 39.8 + - - +
532B ALA* 3.7 10.5 - - - +
534B ILE* 1.3 80.9 - - + +
536B ALA* 1.3 53.8 + - - +
537B GLN 2.5 6.1 + - - -
538B GLY* 2.4 32.7 + - - -
539B TYR 3.4 23.7 + - - +
540B ASP* 4.8 4.7 - - - +
541B VAL* 4.8 12.4 + - + +
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Residues in contact with ALA 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B ALA 2.9 13.4 + - - +
533B LEU* 2.8 18.5 + - - +
535B GLU* 1.3 76.8 - - - +
537B GLN* 1.3 61.0 + - + +
538B GLY 3.3 1.0 + - - -
572B HIS* 5.8 1.6 - - + -
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Residues in contact with GLN 537 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B LEU 3.4 1.5 + - - +
534B ILE* 3.3 11.3 + - - +
535B GLU 2.5 5.9 + - - -
536B ALA* 1.3 79.7 - - + +
538B GLY* 1.3 57.7 + - - -
539B TYR* 3.6 12.2 + - + -
568B ALA* 5.3 2.4 + - - +
569B LEU* 3.2 35.3 - - + +
572B HIS* 4.2 39.5 + - + +
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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