Contacts of the helix formed by residues 466 - 486 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341D GLU* 4.8 5.7 + - - -
425D LEU* 3.6 40.2 - - + +
465D ASP* 1.3 86.6 + - - +
467D PRO* 1.3 70.7 - - + +
468D LYS* 3.0 34.4 + - + +
469D VAL* 2.9 21.0 + - + +
470D ALA 3.1 6.4 + - - -
514D PHE* 3.6 38.1 - + - -
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Residues in contact with PRO 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465D ASP 3.4 3.6 - - - +
466D HIS* 1.3 101.5 - - + +
468D LYS* 1.3 61.1 + - - +
470D ALA* 3.7 6.3 - - + -
471D THR* 3.0 28.4 + - - -
509D ARG* 3.9 17.5 - - - +
513D GLU* 3.3 34.3 - - + +
514D PHE* 4.1 10.8 - - + -
516D ALA* 3.4 15.8 - - + +
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Residues in contact with LYS 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340D PRO 3.2 29.0 + - - +
341D GLU* 3.8 14.3 - - + +
342D ASP 5.5 0.2 - - - +
343D ASP* 5.4 11.1 - - - +
425D LEU* 4.5 9.4 - - + -
429D GLU* 3.5 37.4 + - - +
466D HIS* 3.0 24.8 + - + +
467D PRO* 1.3 78.3 - - - +
469D VAL* 1.3 63.4 + - - +
471D THR* 3.6 6.1 - - - -
472D ASN* 3.6 19.8 + - - +
514D PHE* 3.7 37.6 - - + +
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Residues in contact with VAL 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420D MET* 3.9 17.0 - - + -
425D LEU* 3.6 23.3 - - + -
428D LYS* 3.7 14.6 - - + +
429D GLU* 3.5 30.1 - - - +
432D ALA* 4.2 0.8 - - + +
462D GLY* 3.7 26.7 - - - +
465D ASP* 4.0 13.9 - - + +
466D HIS 2.9 9.2 + - - +
468D LYS* 1.3 75.4 - - - +
470D ALA* 1.3 65.4 + - - +
472D ASN* 3.0 14.7 + - - +
473D CYS* 3.1 13.9 + - - -
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Residues in contact with ALA 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462D GLY 3.5 21.3 + - - +
463D LEU* 3.7 24.1 - - + +
466D HIS 3.1 10.5 + - - +
467D PRO* 3.3 13.2 + - + +
469D VAL* 1.3 75.7 - - - +
471D THR* 1.3 63.3 + - - +
473D CYS* 3.4 3.3 + - - +
474D SER* 3.0 27.2 + - - -
506D ALA* 5.2 1.8 - - + -
509D ARG* 4.2 9.2 - - - +
516D ALA* 4.3 8.1 - - + -
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Residues in contact with THR 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C TYR* 6.0 0.9 - - - +
467D PRO 3.0 11.3 + - - -
468D LYS* 3.6 6.7 - - - -
470D ALA* 1.3 76.9 - - - +
472D ASN* 1.3 70.6 + - - +
474D SER* 3.3 5.0 + - - -
475D TRP* 3.2 22.1 + - + +
514D PHE 2.5 28.2 + - - +
515D ASN* 3.0 19.1 - - + +
516D ALA* 3.0 5.1 + - - +
519D SER* 3.2 22.4 - - - +
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Residues in contact with ASN 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429D GLU* 2.7 39.4 + - - +
432D ALA* 3.6 18.8 - - + -
433D TRP* 3.5 23.1 - - - +
468D LYS 3.6 6.7 + - - +
469D VAL* 3.0 7.1 + - - +
471D THR* 1.3 86.9 - - - +
473D CYS* 1.3 58.5 + - - +
475D TRP* 3.6 13.5 + - + +
476D THR* 3.0 31.1 + - - -
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Residues in contact with CYS 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420D MET* 4.4 4.5 - - - -
432D ALA* 4.0 16.6 - - - -
459D CYS* 3.7 30.5 - - + +
462D GLY* 3.6 30.1 - - - -
463D LEU* 4.2 7.0 - - + -
469D VAL* 3.1 19.7 + - - -
470D ALA 3.7 6.5 - - - +
471D THR 3.3 0.2 - - - -
472D ASN* 1.3 72.3 - - - +
474D SER* 1.3 61.5 + - - +
476D THR* 3.2 7.4 + - - -
477D ILE* 2.9 36.3 + - - +
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Residues in contact with SER 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463D LEU* 3.5 13.5 - - - +
470D ALA 3.0 15.4 + - - -
471D THR 3.3 8.5 + - - -
473D CYS* 1.3 76.9 - - - +
475D TRP* 1.3 63.8 + - - +
477D ILE* 3.2 12.7 + - - +
478D ILE* 3.0 27.1 + - - +
503D LEU* 4.0 1.1 - - - +
506D ALA* 5.2 0.2 - - - +
516D ALA 4.7 1.4 + - - -
519D SER* 3.6 32.6 - - - -
520D ALA* 3.8 10.4 + - - +
523D ALA* 3.8 9.3 - - - +
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Residues in contact with TRP 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433D TRP* 3.3 59.0 - + - -
436D GLY* 4.1 4.7 - - - -
437D ARG* 4.0 17.5 - - - -
440D ASP* 5.3 4.9 - - + -
471D THR* 3.2 11.2 + - + +
472D ASN* 3.7 24.5 - - + +
474D SER* 1.3 80.0 - - - +
476D THR* 1.3 67.9 + - - +
478D ILE* 3.0 23.5 - - + +
479D ASN* 3.0 47.8 + - - -
519D SER* 5.2 0.8 - - - -
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Residues in contact with THR 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432D ALA 2.9 22.5 + - - -
435D ILE* 3.7 30.5 - - + -
436D GLY* 3.1 23.4 + - - +
439D ALA* 4.9 0.7 - - + -
459D CYS* 4.0 14.4 - - - -
472D ASN 3.0 17.4 + - - -
473D CYS* 3.2 7.6 + - - -
475D TRP* 1.3 76.6 - - - +
477D ILE* 1.3 61.3 + - - +
479D ASN* 2.9 6.4 + - - +
480D LEU* 2.8 35.4 + - + +
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Residues in contact with ILE 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459D CYS* 3.9 26.0 - - + -
463D LEU* 4.0 16.8 - - + -
473D CYS 2.9 21.2 + - - +
474D SER 3.5 5.6 - - - +
476D THR* 1.3 75.6 - - - +
478D ILE* 1.3 64.4 + - - +
480D LEU* 3.3 11.3 + - + +
481D VAL* 3.0 27.1 + - + +
499D LEU* 4.0 26.5 - - + -
503D LEU* 3.8 31.2 - - + -
523D ALA* 5.1 1.6 - - + -
527D MET* 4.0 27.6 - - - -
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Residues in contact with ILE 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474D SER 3.0 22.3 + - - +
475D TRP* 3.0 25.1 - - + +
477D ILE* 1.3 77.7 - - - +
479D ASN* 1.3 65.8 + - - +
481D VAL* 3.2 4.3 + - - +
482D GLU* 3.0 50.1 + - - +
519D SER* 4.7 1.8 - - - +
522D SER* 4.2 11.4 - - - -
523D ALA* 3.7 26.5 - - - +
526D THR* 3.5 29.8 - - + +
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Residues in contact with ASN 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436D GLY* 3.2 21.2 + - - -
439D ALA* 4.0 4.7 - - + -
440D ASP* 3.6 37.3 - - + +
475D TRP* 3.0 58.5 + - - +
476D THR 2.9 7.0 + - - +
478D ILE* 1.3 80.3 - - - +
480D LEU* 1.3 66.6 + - - +
482D GLU* 3.1 10.1 + - - +
483D GLN* 3.0 27.5 + - - +
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Residues in contact with LEU 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439D ALA* 3.7 23.5 - - + +
443D ALA* 5.8 2.2 - - + -
446D ILE* 5.3 10.3 - - + -
452D LEU* 4.2 18.2 - - + -
455D VAL* 3.8 28.5 - - + -
456D VAL* 4.7 8.3 - - + -
459D CYS* 5.1 4.3 - - - -
476D THR* 2.8 20.0 + - + +
477D ILE* 3.4 18.6 - - + +
479D ASN* 1.3 72.0 - - - +
481D VAL* 1.3 59.8 + - + +
483D GLN* 3.8 0.6 - - - -
484D LEU* 2.8 59.9 + - + +
492D ILE* 4.6 10.8 - - + -
499D LEU* 5.6 2.0 - - + -
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Residues in contact with VAL 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477D ILE* 3.0 24.1 + - + +
478D ILE* 3.8 4.0 - - - +
480D LEU* 1.3 76.5 - - + +
482D GLU* 1.3 58.8 + - - +
484D LEU* 4.1 1.8 - - - -
485D ALA* 3.1 28.6 + - + +
492D ILE* 3.9 27.6 - - + -
493D TYR* 5.9 0.2 - - + -
496D TYR* 3.8 16.4 - - + +
499D LEU* 5.1 0.2 - - + -
526D THR* 4.6 11.0 - - + +
527D MET* 4.2 23.1 - - + -
530D TYR* 3.7 33.4 - - + -
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Residues in contact with GLU 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C LYS* 5.9 0.7 + - - -
440D ASP* 4.3 12.8 - - - +
478D ILE* 3.0 37.4 + - + +
479D ASN* 3.6 8.0 - - - +
481D VAL* 1.3 80.9 - - - +
483D GLN* 1.3 64.5 + - + +
484D LEU 3.5 0.2 + - - -
486D GLU* 3.8 18.2 + - - +
526D THR* 4.3 9.5 - - + +
530D TYR* 3.8 34.6 + - + +
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Residues in contact with GLN 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439D ALA 3.6 9.8 + - - +
440D ASP* 3.1 36.5 + - - +
441D SER 3.5 22.6 + - - -
442D VAL* 4.5 0.2 - - - +
443D ALA* 3.6 26.5 - - + +
444D GLU* 5.3 1.4 + - - -
479D ASN 3.0 11.2 + - - +
480D LEU* 4.4 0.4 - - - +
482D GLU* 1.3 78.4 - - + +
484D LEU* 1.3 58.6 + - - +
486D GLU* 2.9 33.9 - - - +
487D ALA* 5.2 0.2 - - - +
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Residues in contact with LEU 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443D ALA* 4.0 30.3 - - + +
444D GLU* 5.7 1.1 - - - -
446D ILE* 5.3 7.2 - - + +
452D LEU* 4.0 22.2 - - + -
480D LEU* 2.8 50.7 + - + +
483D GLN* 1.3 74.6 - - - +
485D ALA* 1.3 59.6 + - - +
486D GLU 3.2 2.5 - - - -
487D ALA* 3.0 31.8 + - + +
490D SER* 3.8 7.0 + - - +
491D PRO* 5.0 15.3 - - + +
492D ILE* 4.2 25.4 - - + +
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Residues in contact with ALA 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481D VAL* 3.1 23.8 + - + +
484D LEU* 1.3 77.3 - - - +
486D GLU* 1.3 60.3 + - - +
487D ALA 3.2 8.9 + - - +
490D SER* 3.5 15.5 + - - +
492D ILE* 4.6 2.4 - - + +
493D TYR* 3.6 24.9 + - + +
530D TYR* 3.8 20.6 - - + -
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Residues in contact with GLU 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D GLU 3.8 14.9 + - - +
483D GLN* 2.9 35.0 - - - +
485D ALA* 1.3 76.6 - - - +
487D ALA* 1.3 77.7 + - - +
488D THR* 3.8 3.1 + - - -
530D TYR* 5.5 2.1 - - + -
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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
------------------------------------------------------------
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