Contacts of the helix formed by residues 424 - 442 (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 SER 424 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383D TRP* 3.4 35.3 - - - +
386D ARG* 3.9 2.0 - - - +
422D ASP* 3.2 6.3 + - - -
423D GLN* 1.3 77.6 - - - +
425D LEU* 1.3 65.2 + - - +
426D GLN* 3.6 12.1 + - - +
427D VAL* 3.5 26.0 + - - +
428D LYS* 3.2 27.2 + - - +
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Residues in contact with LEU 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340D PRO* 3.7 24.9 - - + -
341D GLU* 6.5 0.2 - - + -
423D GLN 3.6 4.8 + - - -
424D SER* 1.3 72.3 + - - +
426D GLN* 1.3 67.9 + - - +
428D LYS* 3.1 10.6 + - - +
429D GLU* 2.9 32.1 + - + +
465D ASP* 5.0 1.6 - - - +
466D HIS* 3.6 59.2 - - + +
468D LYS* 4.5 9.9 - - + -
469D VAL* 3.6 16.4 - - + -
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Residues in contact with GLN 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D GLN* 5.9 2.0 - - + -
337D ASN 4.2 3.5 + - - +
338D GLU* 3.3 21.4 + - - -
340D PRO* 3.2 37.4 - - + +
383D TRP* 3.3 51.2 - - + -
387D GLU* 3.9 8.5 - - + -
424D SER* 3.3 4.2 + - - -
425D LEU* 1.3 80.3 + - - +
427D VAL* 1.3 62.6 + - - +
429D GLU* 3.5 14.4 + - - +
430D THR* 3.0 30.3 + - - -
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Residues in contact with VAL 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383D TRP* 3.6 26.0 - - + +
386D ARG* 3.9 11.9 - - + +
387D GLU* 3.7 15.5 - - + +
390D VAL* 4.3 1.0 - - + +
419D LEU* 4.1 16.4 - - + +
422D ASP* 3.5 33.2 - - + +
424D SER* 3.4 26.7 + - - +
425D LEU 3.2 0.2 - - - -
426D GLN* 1.3 77.7 - - - +
428D LYS* 1.3 53.4 + - - +
430D THR* 3.9 1.4 - - - -
431D THR* 2.4 45.4 + - - +
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Residues in contact with LYS 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419D LEU 3.6 16.4 - - - +
420D MET* 3.2 29.4 - - + +
421D ASN 4.7 0.4 - - - -
422D ASP* 3.2 24.9 + - + +
423D GLN 4.7 3.6 + - - -
424D SER 3.2 17.4 + - - +
425D LEU* 3.1 11.9 + - - +
427D VAL* 1.3 72.8 - - - +
429D GLU* 1.3 66.8 + - - +
431D THR* 3.3 7.1 + - - -
432D ALA* 3.0 25.5 + - - +
465D ASP* 2.7 39.4 + - - +
469D VAL* 3.7 14.5 - - + +
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Residues in contact with GLU 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340D PRO 4.6 3.6 - - - +
425D LEU* 2.9 18.0 + - + +
426D GLN* 3.6 17.7 + - - +
428D LYS* 1.3 76.7 - - - +
430D THR* 1.3 60.1 + - - +
432D ALA* 3.5 2.1 + - - +
433D TRP 3.2 12.0 + - - -
468D LYS* 3.5 47.1 + - - +
469D VAL* 3.5 18.9 - - + +
472D ASN* 2.7 37.9 + - - +
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Residues in contact with THR 430 (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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387D GLU* 2.9 29.8 + - - +
390D VAL* 3.9 5.2 - - + -
391D MET* 3.5 41.2 - - + +
426D GLN 3.0 15.1 + - - -
427D VAL 4.1 1.8 - - - -
429D GLU* 1.3 79.0 - - - +
431D THR* 1.3 55.8 + - - +
433D TRP* 3.2 17.4 + - + +
434D CYS* 2.7 32.7 + - - +
472D ASN* 4.9 0.2 - - - +
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Residues in contact with THR 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390D VAL* 3.9 13.1 - - + +
416D ILE* 3.1 37.5 - - + +
419D LEU* 3.4 21.3 - - + +
420D MET* 4.0 16.8 - - + -
427D VAL* 2.4 27.1 + - - +
428D LYS* 3.5 8.0 - - - -
430D THR* 1.3 75.3 - - - +
432D ALA* 1.3 64.5 + - - +
434D CYS* 3.1 9.0 + - - +
435D ILE* 3.0 28.4 + - + +
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Residues in contact with ALA 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420D MET* 4.2 8.0 - - - -
428D LYS 3.0 16.8 + - - +
429D GLU 3.5 5.8 - - - +
430D THR 3.3 0.2 - - - -
431D THR* 1.3 75.3 - - - +
433D TRP* 1.3 62.1 + - - +
435D ILE* 3.2 18.2 + - - +
436D GLY 3.4 0.2 + - - -
469D VAL* 4.2 4.3 - - + +
472D ASN* 3.6 17.0 - - + -
473D CYS* 4.0 26.0 - - - +
476D THR* 2.9 23.1 + - - -
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Residues in contact with TRP 433 (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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356D GLN* 4.1 13.5 - - - -
390D VAL 4.3 0.4 - - - -
391D MET* 3.8 37.9 - - + -
394D GLY* 4.0 18.4 - - - -
395D SER* 3.8 19.3 - - - -
429D GLU 3.2 3.5 + - - +
430D THR* 3.4 23.6 - - + +
432D ALA* 1.3 80.3 - - - +
434D CYS* 1.3 71.8 + - - +
436D GLY 3.3 2.4 + - - -
437D ARG* 3.1 49.1 + - + +
472D ASN* 3.5 24.3 - - - +
475D TRP* 3.3 37.3 - + - -
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Residues in contact with CYS 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390D VAL* 3.6 28.0 - - + +
393D PHE* 3.9 19.3 - - - -
394D GLY* 3.9 13.9 - - - -
416D ILE* 4.1 20.6 - - + -
430D THR 2.7 16.2 + - - +
431D THR* 3.1 14.3 + - - +
433D TRP* 1.3 78.4 - - + +
435D ILE* 1.3 63.1 + - - +
437D ARG* 3.4 6.8 + - - +
438D ILE* 3.1 28.5 + - - +
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Residues in contact with ILE 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413D LEU* 4.4 7.9 - - + -
416D ILE* 3.8 24.0 - - + -
417D LEU* 3.7 29.6 - - + +
420D MET* 5.6 1.1 - - - -
431D THR* 3.0 19.0 + - + +
432D ALA* 3.2 12.5 + - - +
434D CYS* 1.3 75.6 - - - +
436D GLY* 1.3 57.7 + - - +
438D ILE* 3.2 10.6 + - + +
439D ALA* 2.8 27.3 + - + +
455D VAL* 3.7 32.3 - - + +
458D ALA* 5.2 7.0 - - + -
459D CYS* 5.1 3.4 - - - -
476D THR* 3.7 14.1 - - + -
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Residues in contact with GLY 436 (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 5.3 + - - -
435D ILE* 1.3 72.7 - - - +
437D ARG* 1.3 57.1 + - - +
439D ALA* 4.0 3.1 - - - -
440D ASP* 2.6 38.8 + - - +
475D TRP* 4.1 3.1 - - - -
476D THR* 3.1 31.5 + - - -
479D ASN* 3.2 18.6 + - - -
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Residues in contact with ARG 437 (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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356D GLN* 4.0 22.9 + - - +
394D GLY* 3.3 35.1 + - - +
395D SER 4.4 4.4 + - - -
397D MET* 3.7 9.9 - - + +
398D ASP* 4.0 25.7 - - - +
433D TRP* 3.1 53.1 + - + +
434D CYS* 3.6 9.4 - - - +
435D ILE 3.3 0.2 - - - -
436D GLY* 1.3 75.8 - - - +
438D ILE* 1.3 61.5 + - - +
440D ASP* 4.8 5.4 + - - +
441D SER* 3.1 53.0 + - - -
475D TRP* 4.0 9.8 - - - -
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Residues in contact with ILE 438 (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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393D PHE* 4.4 4.3 - - + -
397D MET* 4.1 22.7 - - + -
409D VAL* 3.6 32.8 - - + -
413D LEU* 4.0 24.7 - - + -
416D ILE* 4.4 10.3 - - + -
434D CYS* 3.1 27.6 + - - +
435D ILE* 3.4 14.4 - - + +
437D ARG* 1.3 73.9 - - - +
439D ALA* 1.3 59.0 + - - +
442D VAL* 2.7 40.7 + - + -
445D SER* 3.9 4.7 - - - +
446D ILE* 3.8 18.6 - - + -
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Residues in contact with ALA 439 (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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435D ILE* 2.8 16.7 + - + +
436D GLY* 3.5 6.5 - - - +
438D ILE* 1.3 79.7 - - - +
440D ASP* 1.3 62.9 + - - +
441D SER 3.2 1.4 + - - -
443D ALA* 3.4 30.7 + - - +
446D ILE* 5.5 2.0 - - - -
476D THR* 4.5 1.8 - - + +
479D ASN* 4.0 3.8 - - + -
480D LEU* 3.7 44.9 - - + +
483D GLN* 3.6 6.4 - - - +
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Residues in contact with ASP 440 (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 2.6 21.7 + - - +
437D ARG* 4.4 6.4 + - - +
439D ALA* 1.3 74.0 - - - +
441D SER* 1.3 61.7 + - - +
475D TRP* 5.3 4.9 - - + -
479D ASN* 3.6 32.2 - - - +
482D GLU* 4.3 9.9 - - - +
483D GLN* 3.1 26.1 + - - +
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Residues in contact with SER 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397D MET* 3.4 25.0 + - - -
398D ASP* 4.7 3.7 - - - +
405D ARG* 3.8 10.7 + - - -
437D ARG* 3.1 35.5 + - - -
438D ILE 3.4 0.8 + - - -
439D ALA 3.2 0.2 - - - -
440D ASP* 1.3 82.4 + - - +
442D VAL* 1.3 68.4 + - - +
444D GLU* 4.4 2.1 - - - +
483D GLN* 3.5 11.7 + - - -
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Residues in contact with VAL 442 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397D MET* 4.4 4.7 - - - -
402D LYS* 4.6 10.3 - - + +
405D ARG* 3.7 43.5 - - + +
406D THR* 4.8 1.1 - - - +
409D VAL* 4.1 13.0 - - + -
438D ILE* 2.7 37.6 + - + +
441D SER* 1.3 82.4 - - - +
443D ALA* 1.3 60.3 + - - +
444D GLU* 3.3 16.6 - - - +
445D SER* 2.5 45.1 + - - +
446D ILE* 4.2 0.7 - - - +
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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) + - + + + + + -
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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