Contacts of the helix formed by residues 442 - 465 (chain B) in PDB entry 1BK6
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 ASN 442 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359A LYS* 5.4 5.4 + - - -
441B ASP* 1.3 72.5 - - - +
443B ARG* 1.3 63.1 + - - +
445B ILE* 3.1 16.6 + - - +
446B GLU* 3.3 14.4 + - - +
492B ASN* 3.7 11.7 + - - -
493B GLU* 3.1 25.1 + - - +
494B ASN* 3.7 25.6 - - + +
497B ILE* 3.6 21.0 - - + +
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Residues in contact with ARG 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B LYS* 6.4 0.7 - - - -
405B TRP* 3.7 35.3 - - + -
441B ASP* 3.1 8.7 + - - +
442B ASN* 1.3 78.0 - - - +
444B ILE* 1.3 65.9 + - + +
446B GLU* 3.1 41.9 + - - +
447B VAL* 3.3 21.3 + - - +
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Residues in contact with ILE 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B TYR* 3.5 21.3 - - + +
401B LYS* 3.5 41.3 - - + +
404B CYS* 4.1 6.5 - - + -
405B TRP* 3.5 27.8 - - + +
436B LEU* 3.8 24.5 - - + -
440B ALA* 3.7 16.8 - - + -
441B ASP* 3.0 14.7 + - - +
443B ARG* 1.3 76.5 - - + +
445B ILE* 1.3 60.8 + - - +
447B VAL* 3.5 5.4 + - + +
448B THR* 2.8 26.6 + - - +
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Residues in contact with ILE 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B LEU* 3.8 33.7 - - + +
440B ALA* 4.0 24.2 - - + +
441B ASP 3.1 18.4 + - - +
442B ASN* 3.1 11.7 + - - +
444B ILE* 1.3 76.9 - - - +
446B GLU* 1.3 60.1 + - - +
448B THR* 3.8 0.9 - - - -
449B LEU* 2.9 35.2 + - + +
489B CYS* 4.0 11.0 - - - -
492B ASN* 4.2 20.2 - - - +
497B ILE* 3.9 26.7 - - + -
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Residues in contact with GLU 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B ASN* 3.3 12.3 + - - +
443B ARG* 3.1 39.3 + - - +
445B ILE* 1.3 79.7 - - - +
447B VAL* 1.3 57.3 + - - +
449B LEU* 3.4 6.7 + - - +
450B ASP* 3.0 39.2 + - - +
494B ASN* 4.5 9.9 + - - +
496B LYS* 4.2 24.0 - - + +
497B ILE* 4.0 16.7 - - + +
500B LYS* 6.0 0.4 - - - +
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Residues in contact with VAL 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B CYS* 4.0 14.4 - - - -
405B TRP* 3.6 53.6 - - + -
408B SER* 2.9 48.7 + - - +
443B ARG* 3.3 22.1 + - - +
444B ILE* 3.9 7.9 - - + +
445B ILE 3.3 0.2 - - - -
446B GLU* 1.3 74.8 - - - +
448B THR* 1.3 62.8 + - - +
450B ASP* 3.6 5.5 + - - +
451B ALA* 3.3 10.0 + - - +
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Residues in contact with THR 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B CYS* 3.5 18.3 - - - -
433B LEU* 3.5 35.7 - - + +
436B LEU* 3.8 12.0 - - - +
437B LEU* 3.6 25.7 - - + +
444B ILE* 2.8 21.3 + - - +
445B ILE 3.8 0.2 - - - -
447B VAL* 1.3 78.5 - - - +
449B LEU* 1.3 58.2 + - - +
451B ALA* 3.3 5.5 + - - +
452B LEU* 2.9 38.6 + - + +
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Residues in contact with LEU 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B LEU* 4.1 26.0 - - + -
445B ILE* 2.9 40.7 + - + +
446B GLU* 3.9 5.4 - - - +
448B THR* 1.3 74.5 - - - +
450B ASP* 1.3 61.6 + - - +
452B LEU* 4.4 6.3 - - + -
453B GLU* 2.9 31.2 + - - +
486B ILE* 4.3 18.8 - - + -
489B CYS* 4.7 8.1 - - + -
497B ILE* 4.1 21.1 - - + +
500B LYS* 3.9 30.7 - - + -
501B ALA* 4.6 4.7 - - + +
504B ILE* 3.9 13.5 - - + +
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Residues in contact with ASP 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B SER* 4.6 4.0 - - - +
446B GLU* 3.0 26.3 + - - +
447B VAL* 4.0 7.9 - - - +
448B THR 3.2 0.2 - - - -
449B LEU* 1.3 77.1 - - - +
451B ALA* 1.3 58.3 + - - +
453B GLU* 3.4 9.4 + - - +
454B ASN* 2.8 40.8 + - - +
500B LYS* 3.4 20.3 - - - +
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Residues in contact with ALA 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B CYS* 6.4 0.2 - - - -
407B ILE* 5.3 1.6 - - + +
408B SER* 3.7 19.0 + - - +
411B SER* 3.6 19.9 + - - +
433B LEU* 4.2 20.2 - - + -
447B VAL 3.3 12.0 + - - +
448B THR* 3.3 8.7 + - - +
450B ASP* 1.3 76.7 - - - +
452B LEU* 1.3 60.1 + - - +
454B ASN* 3.1 3.2 + - - +
455B ILE* 2.9 37.3 + - + +
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Residues in contact with LEU 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B ILE* 4.6 4.5 - - + +
433B LEU* 4.3 18.4 - - + -
434B CYS* 4.0 25.8 - - - -
437B LEU* 4.1 19.7 - - + -
448B THR* 2.9 38.3 + - + +
449B LEU* 4.0 7.6 - - + +
451B ALA* 1.3 75.5 - - - +
453B GLU* 1.3 57.4 + - - +
455B ILE* 3.5 10.8 + - + +
456B ILE* 3.0 35.1 + - - +
477B ILE* 3.8 25.6 - - + +
486B ILE* 4.4 15.9 - - + -
504B ILE* 5.4 2.9 - - + -
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Residues in contact with GLU 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B LEU 2.9 18.9 + - - +
450B ASP* 3.5 10.5 - - - +
451B ALA 3.1 0.2 - - - -
452B LEU* 1.3 75.1 - - - +
454B ASN* 1.3 67.5 + - - +
456B ILE* 3.1 7.9 + - - +
457B LYS* 2.9 58.8 + - + +
500B LYS* 3.1 31.6 - - - +
503B LYS* 5.7 3.8 - - - +
504B ILE* 4.1 19.8 - - + +
508B TYR* 5.1 7.7 - - + -
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Residues in contact with ASN 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B SER* 4.7 1.0 + - - -
411B SER* 3.4 43.9 + - - +
412B SER* 4.3 10.3 + - - +
421B ILE* 4.6 6.0 - - + +
450B ASP* 2.8 33.9 + - - +
451B ALA 3.7 3.1 - - - +
453B GLU* 1.3 75.9 - - - +
455B ILE* 1.3 64.3 + - - +
457B LYS* 3.2 32.9 + - - +
458B MET* 3.3 13.5 + - - +
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Residues in contact with ILE 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B SER* 4.9 4.9 - - - -
421B ILE* 3.9 20.3 - - + +
424B LEU* 6.0 3.4 - - + -
425B VAL* 3.6 26.7 - - + -
429B CYS* 4.1 16.6 - - - -
430B ILE* 4.3 14.1 - - + -
433B LEU* 3.9 26.9 - - + -
451B ALA* 2.9 29.2 + - + +
452B LEU* 3.5 11.2 - - + +
454B ASN* 1.3 76.9 - - - +
456B ILE* 1.3 61.2 + - - +
458B MET* 3.6 2.9 + - - +
459B GLY 3.3 6.4 + - - -
473B ASN* 3.2 30.1 + - + -
477B ILE* 5.2 4.7 - - + -
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Residues in contact with ILE 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B LEU 3.0 21.7 + - - +
453B GLU* 3.1 7.2 + - - +
455B ILE* 1.3 76.9 - - - +
457B LYS* 1.3 64.4 + - - +
459B GLY 3.4 0.9 + - - +
460B GLU* 3.0 21.0 + - - +
471B ASN* 3.4 4.6 + - - +
473B ASN* 4.1 3.6 - - + -
474B ALA* 3.6 34.5 - - + +
477B ILE* 3.6 27.4 - - + -
504B ILE* 5.6 4.5 - - + -
508B TYR* 3.0 49.4 - - + -
509B PHE* 4.5 10.5 - - + -
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Residues in contact with LYS 457 (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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453B GLU* 2.9 53.0 + - + +
454B ASN* 3.2 21.8 + - - +
456B ILE* 1.3 74.3 - - - +
458B MET* 1.3 59.2 + - - +
460B GLU* 3.3 6.2 + - - +
461B ALA* 2.9 26.9 + - - +
508B TYR* 3.4 20.9 - - - +
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Residues in contact with MET 458 (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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414B GLY 5.7 2.0 - - - +
418B PRO* 5.1 11.4 - - + +
421B ILE* 3.8 36.6 - - + -
422B ARG* 5.7 1.8 - - + +
454B ASN 3.3 6.2 + - - +
455B ILE 3.8 1.3 - - - +
456B ILE 3.2 0.4 - - - -
457B LYS* 1.3 75.5 - - - +
459B GLY* 1.3 63.6 + - - +
460B GLU 2.9 4.3 - - - -
461B ALA* 2.9 17.8 + - - +
462B ASP* 2.9 23.0 + - - +
473B ASN* 5.0 0.2 - - - +
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Residues in contact with GLY 459 (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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455B ILE 3.3 8.7 + - - -
456B ILE 3.4 0.9 + - - -
458B MET* 1.3 78.8 - - - +
460B GLU* 1.3 58.3 + - - +
462B ASP* 3.7 9.3 + - - +
463B LYS* 3.4 16.1 + - - +
471B ASN* 3.1 23.4 + - - -
472B GLU* 4.6 4.6 + - - +
473B ASN* 3.0 25.9 - - - +
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Residues in contact with GLU 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B ILE 3.0 7.0 + - - +
457B LYS* 3.3 10.8 - - - +
458B MET 2.9 0.2 - - - -
459B GLY* 1.3 74.8 - - - +
461B ALA* 1.3 58.0 + - - +
462B ASP 3.0 4.3 - - - -
463B LYS* 2.9 36.9 + - - +
464B GLU* 3.4 5.5 + - - +
471B ASN* 2.8 36.7 + - - +
507B THR 5.1 1.6 - - - +
508B TYR* 3.4 30.0 - - + +
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Residues in contact with ALA 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B LYS 2.9 13.3 + - - +
458B MET* 2.9 12.0 + - - +
460B GLU* 1.3 75.1 - - - +
462B ASP* 1.3 60.5 + - - +
464B GLU* 3.5 8.6 - - - +
465B ALA* 3.5 19.4 + - - +
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Residues in contact with ASP 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B PRO* 5.5 2.3 - - - +
422B ARG* 3.6 31.7 + - - +
458B MET* 2.9 27.3 + - - +
459B GLY* 3.8 9.2 - - - +
460B GLU 3.0 0.4 - - - -
461B ALA* 1.3 79.3 - - - +
463B LYS* 1.3 66.1 + - - +
464B GLU 2.9 2.2 - - - -
465B ALA* 4.5 5.8 - - - +
466B ARG* 3.0 34.4 + - + +
468B LEU* 4.7 1.1 - - - +
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Residues in contact with LYS 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B GLY 3.4 9.7 + - - +
460B GLU* 2.9 26.4 + - - +
462B ASP* 1.3 77.0 - - - +
464B GLU* 1.3 62.6 + - - +
467B GLY* 3.2 1.9 - - - -
468B LEU* 2.7 62.6 + - - +
469B ASN 4.3 5.4 - - - +
470B ILE 3.6 23.3 - - - +
471B ASN* 4.7 1.3 - - - +
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Residues in contact with GLU 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B GLU 3.4 4.6 + - - +
461B ALA* 3.5 15.3 - - - +
462B ASP 2.9 0.4 - - - -
463B LYS* 1.3 76.8 - - - +
465B ALA* 1.3 58.9 + - - +
467B GLY* 2.7 26.7 + - - -
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Residues in contact with ALA 465 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B ALA 3.5 12.0 + - - +
462B ASP* 3.5 5.8 + - - +
464B GLU* 1.3 78.9 - - - +
466B ARG* 1.3 56.3 + - - +
467B GLY* 2.7 12.0 + - - -
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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) + - + + + + + -
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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