Contacts of the helix formed by residues 466 - 486 (chain B) in PDB entry 2BKU
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 HIS 466 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341B GLU* 4.3 12.3 + - - -
425B LEU* 3.7 36.5 - - + +
465B ASP* 1.3 84.0 + - - +
467B PRO* 1.3 76.4 - - + +
468B LYS* 3.1 52.4 + - + +
469B VAL* 2.9 20.1 + - - +
470B ALA 3.0 9.5 + - - -
514B PHE* 4.0 16.0 - + - -
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Residues in contact with PRO 467 (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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465B ASP 3.4 3.6 - - - +
466B HIS* 1.3 101.9 - - + +
468B LYS* 1.3 55.2 + - - +
470B ALA* 4.2 4.9 - - + -
471B THR* 2.9 35.1 + - - -
509B ARG* 4.2 15.7 - - - +
513B GLU* 3.4 38.1 - - + +
514B PHE* 4.2 9.4 - - + -
516B ALA* 3.6 15.5 - - + +
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Residues in contact with LYS 468 (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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340B PRO 3.5 21.7 + - - +
341B GLU* 3.9 21.6 - - + +
343B ASP* 5.3 11.6 - - - +
425B LEU* 4.5 6.7 - - + -
429B GLU* 3.3 43.8 + - - +
466B HIS* 3.1 25.9 + - + +
467B PRO* 1.3 77.1 - - - +
469B VAL* 1.3 61.9 + - - +
471B THR* 3.7 6.4 - - - -
472B ASN* 3.7 20.8 + - - +
514B PHE* 3.9 34.9 - - + +
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Residues in contact with VAL 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B MET* 3.9 15.9 - - + -
425B LEU* 3.7 22.0 - - + -
428B LYS* 3.7 15.3 - - + +
429B GLU* 3.6 28.5 - - - +
432B ALA* 4.2 0.8 - - + +
462B GLY* 3.4 29.6 - - - +
465B ASP* 3.9 16.2 - - + +
466B HIS 2.9 8.4 + - - +
468B LYS* 1.3 76.0 - - - +
470B ALA* 1.3 64.1 + - - +
472B ASN* 3.2 13.9 + - - +
473B CYS* 3.2 12.7 + - - -
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Residues in contact with ALA 470 (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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462B GLY 3.2 20.6 - - - +
463B LEU* 3.7 25.3 - - + +
466B HIS 3.0 10.7 + - - +
467B PRO* 3.1 12.5 + - + +
469B VAL* 1.3 76.7 - - - +
471B THR* 1.3 63.1 + - - +
473B CYS* 3.2 4.3 + - - +
474B SER* 3.1 26.0 + - - -
506B ALA* 5.3 1.6 - - + -
509B ARG* 4.2 9.4 - - - +
516B ALA* 4.4 8.3 - - + +
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Residues in contact with THR 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A TYR* 5.9 0.9 - - - +
467B PRO 2.9 15.1 + - - -
468B LYS* 3.7 7.4 - - - -
469B VAL 3.2 0.2 - - - -
470B ALA* 1.3 76.7 - - - +
472B ASN* 1.3 66.4 + - - +
474B SER* 3.3 5.7 + - - -
475B TRP* 2.9 42.3 + - + +
514B PHE 2.6 28.6 + - - +
515B ASN* 4.5 4.0 - - + +
516B ALA* 3.2 12.4 + - - +
519B SER* 3.2 24.4 + - - +
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Residues in contact with ASN 472 (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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429B GLU* 2.6 41.6 + - - +
432B ALA* 3.6 17.5 - - + -
433B TRP* 3.8 22.8 - - - +
468B LYS 3.7 6.9 + - - +
469B VAL 3.2 6.5 + - - +
471B THR* 1.3 83.5 - - - +
473B CYS* 1.3 61.0 + - - +
475B TRP* 3.3 11.8 + - - +
476B THR* 2.9 32.2 + - - -
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Residues in contact with CYS 473 (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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420B MET* 4.4 4.0 - - - -
432B ALA* 3.9 15.9 - - - -
458B ALA 5.2 0.2 - - - -
459B CYS* 3.8 29.2 - - + +
462B GLY* 3.6 29.2 - - - -
463B LEU* 4.1 9.0 - - + -
469B VAL* 3.2 15.8 + - - -
470B ALA 3.2 6.7 + - - +
472B ASN* 1.3 73.2 - - - +
474B SER* 1.3 60.8 + - - +
476B THR* 3.3 8.0 + - - +
477B ILE* 2.8 36.0 + - - +
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Residues in contact with SER 474 (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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463B LEU* 3.6 13.2 - - - +
470B ALA 3.1 12.4 + - - -
471B THR 3.4 9.9 - - - -
473B CYS* 1.3 77.7 - - - +
475B TRP* 1.3 57.0 + - - +
477B ILE* 3.2 11.0 + - - +
478B ILE* 2.9 33.6 + - - +
503B LEU* 3.8 1.9 - - - +
516B ALA 4.8 1.2 + - - -
519B SER* 3.6 28.6 - - - -
520B ALA* 3.7 17.3 + - - +
523B ALA* 4.0 7.1 - - - +
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Residues in contact with TRP 475 (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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155A TYR* 4.4 23.4 + + - -
471B THR* 2.9 45.2 + - + +
472B ASN* 3.3 12.1 + - - +
474B SER* 1.3 76.0 - - - +
476B THR* 1.3 57.0 + - - +
478B ILE* 3.4 36.5 + - + +
479B ASN* 3.0 34.9 + - - +
518B ALA 5.7 0.2 - - - -
519B SER* 3.5 18.8 + - - -
522B SER* 4.2 20.0 - - - -
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Residues in contact with THR 476 (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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432B ALA* 2.7 23.7 + - - +
433B TRP* 4.4 1.7 + - - -
435B ILE* 3.6 31.9 - - + +
436B GLY* 3.1 22.4 + - - +
439B ALA* 4.5 0.2 - - - +
459B CYS* 3.8 16.6 - - - -
472B ASN 2.9 15.7 + - - -
473B CYS* 3.5 6.5 - - - -
475B TRP* 1.3 76.2 - - - +
477B ILE* 1.3 61.0 + - - +
479B ASN* 3.2 3.4 + - - +
480B LEU* 2.9 32.4 + - + +
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Residues in contact with ILE 477 (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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459B CYS* 4.0 24.2 - - + -
463B LEU* 4.0 28.3 - - + -
473B CYS 2.8 22.7 + - - +
474B SER 3.6 4.7 - - - +
476B THR* 1.3 72.3 - - - +
478B ILE* 1.3 66.5 + - - +
480B LEU* 3.4 9.2 + - + +
481B VAL* 2.9 26.7 + - + +
499B LEU* 4.0 25.8 - - + -
503B LEU* 4.1 21.3 - - + -
523B ALA* 4.9 2.7 - - + -
527B MET* 4.0 25.8 - - - -
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Residues in contact with ILE 478 (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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474B SER 2.9 18.5 + - - +
475B TRP* 3.4 43.5 - - + +
476B THR 3.2 0.2 - - - -
477B ILE* 1.3 75.9 - - - +
479B ASN* 1.3 64.0 + - - +
481B VAL* 3.3 3.1 + - - +
482B GLU* 2.9 42.3 + - - +
519B SER 4.6 1.1 - - - +
522B SER* 3.9 7.0 - - - +
523B ALA* 3.6 35.2 - - + +
526B THR* 3.6 26.0 - - + +
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Residues in contact with ASN 479 (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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436B GLY* 3.3 34.1 + - - +
439B ALA* 4.0 4.0 - - + -
440B ASP* 3.1 34.1 - - + +
475B TRP* 3.0 24.0 + - - +
476B THR* 3.2 7.5 + - - +
478B ILE* 1.3 76.5 - - - +
480B LEU* 1.3 64.7 + - - +
482B GLU* 3.1 12.6 + - - +
483B GLN* 2.9 27.4 + - - +
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Residues in contact with LEU 480 (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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435B ILE* 5.6 0.7 - - + -
439B ALA* 3.6 22.8 - - + +
443B ALA* 5.9 1.3 - - + -
446B ILE* 5.3 10.3 - - + -
452B LEU* 4.4 13.2 - - + -
455B VAL* 3.6 32.3 - - + -
456B VAL* 5.0 6.7 - - + -
459B CYS* 4.9 7.6 - - - -
476B THR* 2.9 20.8 + - + +
477B ILE* 3.5 17.0 - - + +
479B ASN* 1.3 72.9 - - - +
481B VAL* 1.3 63.2 + - + +
483B GLN* 3.9 0.4 - - - -
484B LEU* 2.9 53.2 + - + +
492B ILE* 4.6 11.9 - - + -
499B LEU* 5.7 2.7 - - + -
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Residues in contact with VAL 481 (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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477B ILE* 2.9 25.6 + - + +
478B ILE* 3.9 3.8 - - - +
480B LEU* 1.3 76.9 - - + +
482B GLU* 1.3 61.4 + - - +
484B LEU* 4.9 0.9 - - - -
485B ALA* 3.2 25.1 + - + +
492B ILE* 4.0 26.9 - - + -
496B TYR* 4.0 13.7 - - + +
499B LEU* 5.0 0.4 - - + -
526B THR* 4.3 12.1 - - + +
527B MET* 3.8 25.6 - - + -
530B TYR* 3.7 34.6 - - + -
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Residues in contact with GLU 482 (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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440B ASP* 4.3 7.2 - - - +
478B ILE* 2.9 34.0 + - + +
479B ASN* 3.5 18.1 - - - +
481B VAL* 1.3 79.9 - - - +
483B GLN* 1.3 64.5 + - + +
484B LEU 3.3 0.5 + - - -
485B ALA 3.8 2.8 + - - -
486B GLU* 3.7 15.8 + - - +
526B THR* 4.5 2.7 + - + +
530B TYR* 3.6 37.6 + - + +
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Residues in contact with GLN 483 (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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439B ALA 3.4 17.6 + - - +
440B ASP* 3.4 33.0 + - - +
441B SER* 3.7 19.8 + - - +
443B ALA* 3.5 21.4 - - + +
444B GLU* 5.3 4.8 + - - +
479B ASN 2.9 13.9 + - - +
480B LEU* 5.6 0.2 - - - -
482B GLU* 1.3 75.2 - - + +
484B LEU* 1.3 57.2 - - - +
486B GLU* 3.0 38.7 - - - +
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Residues in contact with LEU 484 (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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443B ALA* 4.0 29.2 - - + +
444B GLU* 5.6 0.9 - - - -
446B ILE* 5.0 8.7 - - + +
452B LEU* 3.8 31.2 - - + -
480B LEU* 2.9 35.3 + - + +
483B GLN* 1.3 76.7 - - - +
485B ALA* 1.3 57.5 + - - +
486B GLU 3.1 4.7 - - - -
487B ALA* 2.9 30.8 + - + +
490B SER* 3.6 13.1 + - - +
491B PRO* 4.6 16.4 - - + -
492B ILE* 4.0 23.1 - - + -
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Residues in contact with ALA 485 (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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481B VAL* 3.2 20.4 + - + +
484B LEU* 1.3 77.7 - - - +
486B GLU* 1.3 58.5 + - - +
487B ALA 3.2 8.3 + - - +
490B SER* 3.3 15.5 + - - +
492B ILE* 4.6 5.6 - - + +
493B TYR* 3.9 21.8 + - + +
530B TYR* 3.8 23.8 - - + -
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Residues in contact with GLU 486 (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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444B GLU* 5.8 4.3 - - - +
482B GLU 3.7 13.8 + - - +
483B GLN* 3.0 40.2 - - - +
485B ALA* 1.3 78.4 - - - +
487B ALA* 1.3 75.8 + - - +
488B THR* 3.9 2.8 + - - -
530B TYR* 5.6 1.7 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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