Contacts of the helix formed by residues 424 - 443 (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 SER 424 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B TRP* 3.5 37.7 - - - +
386B ARG* 4.4 1.5 - - - +
422B ASP* 3.1 15.4 + - - -
423B GLN* 1.3 77.6 - - - +
425B LEU* 1.3 64.4 + - - +
426B GLN* 3.7 10.6 + - - -
427B VAL* 3.5 14.8 - - - +
428B LYS* 3.3 27.0 + - - +
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B PRO* 3.5 28.3 - - + -
341B GLU* 5.6 2.2 - - - +
423B GLN 3.6 4.4 + - - -
424B SER* 1.3 70.0 + - - +
426B GLN* 1.3 67.3 + - - +
428B LYS* 3.3 9.4 + - - +
429B GLU* 2.9 34.2 + - - +
465B ASP* 5.0 1.1 - - - +
466B HIS* 3.7 57.0 - - + +
468B LYS* 4.5 12.3 - - + -
469B VAL* 3.7 15.9 - - + -
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Residues in contact with GLN 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B GLN* 5.8 2.2 - - + -
337B ASN 3.8 4.9 + - - +
338B GLU 3.1 26.1 + - - -
340B PRO* 3.2 39.8 - - + +
383B TRP* 3.3 45.5 - - + -
387B GLU* 4.0 8.7 - - + -
424B SER* 3.4 4.2 + - - -
425B LEU* 1.3 79.5 + - - +
427B VAL* 1.3 57.5 + - - +
429B GLU* 3.4 12.7 + - - +
430B THR* 2.9 35.0 + - - +
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Residues in contact with VAL 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B TRP* 3.6 27.8 - - + +
386B ARG* 4.0 7.6 - - + -
387B GLU* 3.9 17.9 - - + +
390B VAL* 4.3 1.4 - - + +
419B LEU* 4.0 17.5 - - + +
422B ASP* 3.6 30.1 - - + +
424B SER* 3.5 26.8 + - - +
425B LEU 3.3 0.2 - - - -
426B GLN* 1.3 77.3 - - - +
428B LYS* 1.3 54.8 + - - +
430B THR* 3.8 1.0 - - - -
431B THR* 2.5 45.7 + - - +
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Residues in contact with LYS 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B LEU 3.8 10.5 - - - +
420B MET* 3.3 33.9 - - + +
421B ASN 4.9 0.2 - - - -
422B ASP* 3.3 23.4 + - + +
423B GLN* 4.6 3.7 + - - +
424B SER 3.3 20.4 + - - +
425B LEU* 3.3 10.4 + - - +
427B VAL* 1.3 74.7 - - - +
429B GLU* 1.3 66.3 + - - +
431B THR* 3.2 8.0 + - - -
432B ALA* 2.9 25.8 + - - +
465B ASP* 2.8 40.2 + - - +
469B VAL* 3.7 17.7 - - + +
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Residues in contact with GLU 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B PRO 4.3 4.9 - - - +
425B LEU* 2.9 20.7 + - - +
426B GLN* 3.5 12.0 - - - +
428B LYS* 1.3 77.4 - - - +
430B THR* 1.3 62.0 + - - +
432B ALA* 3.5 1.8 + - - +
433B TRP 3.3 6.6 + - - -
468B LYS* 3.3 52.4 + - - +
469B VAL* 3.6 17.1 - - + +
472B ASN* 2.6 37.1 + - - +
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Residues in contact with THR 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B GLU* 2.5 34.3 + - - +
390B VAL* 4.0 5.8 - - + -
391B MET* 3.6 42.2 - - + +
426B GLN* 2.9 15.6 + - - +
427B VAL 4.1 1.3 - - - -
429B GLU* 1.3 76.5 - - - +
431B THR* 1.3 60.2 + - - +
433B TRP* 3.3 14.2 + - + +
434B CYS* 2.9 26.0 + - - +
472B ASN* 4.9 0.2 - - - +
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Residues in contact with THR 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B VAL* 3.9 11.2 - - - +
416B ILE* 3.3 34.0 - - + +
419B LEU* 3.3 21.1 - - + +
420B MET* 3.7 22.0 - - + -
427B VAL* 2.5 27.6 + - - +
428B LYS* 3.2 6.7 + - - -
430B THR* 1.3 74.3 - - - +
432B ALA* 1.3 64.2 + - - +
434B CYS* 3.2 8.7 + - - +
435B ILE* 3.1 25.1 + - + +
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Residues in contact with ALA 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B MET* 4.1 8.5 - - + -
428B LYS 2.9 15.9 + - - +
429B GLU 3.7 1.1 - - - +
431B THR* 1.3 75.8 - - - +
433B TRP* 1.3 58.4 + - - +
435B ILE* 3.3 17.8 + - - +
436B GLY 3.3 0.5 + - - -
469B VAL* 4.2 3.1 - - + +
472B ASN* 3.6 22.0 - - + -
473B CYS* 3.9 26.5 - - - +
476B THR* 2.7 26.4 + - - -
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Residues in contact with TRP 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B GLN* 4.0 21.1 - - - -
390B VAL 4.2 0.7 - - - -
391B MET* 3.8 35.9 - - + -
394B GLY* 3.8 28.9 - - - -
395B SER* 4.0 4.0 - - - -
429B GLU 3.3 4.1 + - - +
430B THR* 3.5 22.2 - - + +
431B THR 3.3 0.2 - - - -
432B ALA* 1.3 76.8 - - - +
434B CYS* 1.3 76.6 + - + +
436B GLY* 3.0 3.6 + - - -
437B ARG* 3.0 52.2 + - + +
472B ASN* 3.8 25.2 - - - +
476B THR* 4.4 2.9 - - - -
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Residues in contact with CYS 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B VAL* 3.3 29.2 - - + +
393B PHE* 3.8 22.0 - - - -
394B GLY* 3.7 16.1 - - - -
416B ILE* 4.4 17.3 - - + -
430B THR 2.9 14.3 + - - +
431B THR* 3.4 12.8 - - - +
433B TRP* 1.3 83.6 - - + +
435B ILE* 1.3 62.7 + - - +
437B ARG* 3.2 5.4 + - - +
438B ILE* 3.1 28.1 + - - +
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Residues in contact with ILE 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B LEU* 4.6 6.1 - - + -
416B ILE* 4.2 15.9 - - + -
417B LEU* 3.4 34.8 - - + -
420B MET* 5.5 1.3 - - - -
431B THR* 3.1 19.8 + - + +
432B ALA* 3.4 12.8 - - - +
434B CYS* 1.3 75.7 - - - +
436B GLY* 1.3 56.8 + - - +
438B ILE* 3.2 12.2 + - + +
439B ALA* 2.9 26.7 + - + +
455B VAL* 3.8 26.0 - - + +
458B ALA* 4.7 8.1 - - + -
459B CYS* 4.8 4.3 - - - -
476B THR* 3.6 19.5 - - + -
480B LEU* 5.6 0.7 - - + -
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Residues in contact with GLY 436 (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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433B TRP 3.0 7.3 + - - -
435B ILE* 1.3 77.4 - - - +
437B ARG* 1.3 60.5 + - - +
439B ALA* 4.2 3.8 - - - -
440B ASP* 2.8 33.3 + - - +
476B THR* 3.1 26.6 + - - -
479B ASN* 3.3 18.1 + - - -
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Residues in contact with ARG 437 (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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356B GLN* 4.3 16.9 + - - +
394B GLY* 3.2 35.6 + - - +
395B SER 4.3 7.1 + - - -
397B MET* 3.7 8.6 - - + +
398B ASP* 4.0 23.4 - - - +
433B TRP* 3.0 60.0 + - + +
434B CYS 3.6 6.7 - - - +
435B ILE 3.2 0.2 - - - -
436B GLY* 1.3 75.8 - - - +
438B ILE* 1.3 64.4 + - - +
440B ASP* 4.6 7.9 + - - +
441B SER* 3.3 52.3 + - - -
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Residues in contact with ILE 438 (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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393B PHE* 4.1 18.6 - - + -
397B MET* 4.2 19.1 - - + -
409B VAL* 3.7 21.1 - - + -
413B LEU* 3.8 26.2 - - + -
416B ILE* 4.4 8.5 - - + -
434B CYS 3.1 17.3 + - - +
435B ILE* 3.4 13.0 - - + +
437B ARG* 1.3 74.5 - - - +
439B ALA* 1.3 61.1 + - - +
442B VAL* 2.8 38.4 + - + +
445B SER* 4.0 5.4 - - - +
446B ILE* 3.6 30.5 - - + -
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Residues in contact with ALA 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B ILE 2.9 16.0 + - - +
436B GLY* 3.8 6.3 - - - +
438B ILE* 1.3 80.0 - - - +
440B ASP* 1.3 63.3 + - - +
441B SER 3.1 1.6 + - - -
443B ALA* 3.3 22.4 + - - +
446B ILE* 5.5 1.8 - - - -
476B THR 4.5 0.4 - - - +
479B ASN* 4.0 3.1 - - + -
480B LEU* 3.6 49.6 - - + +
483B GLN* 3.4 14.2 - - - +
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Residues in contact with ASP 440 (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 2.8 22.2 + - - +
437B ARG* 4.4 9.6 + - - +
439B ALA* 1.3 74.0 - - - +
441B SER* 1.3 61.6 + - - +
479B ASN* 3.1 30.8 - - - +
482B GLU* 4.3 9.0 - - - +
483B GLN* 3.4 24.4 + - - +
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Residues in contact with SER 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B MET* 3.2 29.2 + - - -
398B ASP* 4.5 5.3 - - - +
405B ARG* 3.5 9.8 + - - -
437B ARG* 3.3 30.1 + - - -
438B ILE 3.3 1.4 + - - -
439B ALA 3.1 0.2 - - - -
440B ASP* 1.3 85.0 + - - +
442B VAL* 1.3 68.8 + - - +
444B GLU* 4.8 2.1 - - - +
483B GLN* 3.7 12.4 + - - +
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Residues in contact with VAL 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B MET* 4.3 10.1 - - - -
402B LYS* 4.6 16.2 - - + +
405B ARG* 3.4 41.5 - - + +
406B THR* 4.8 1.8 - - - +
409B VAL* 4.0 19.7 - - + -
438B ILE* 2.8 28.2 + - + +
441B SER* 1.3 79.9 - - - +
443B ALA* 1.3 59.9 + - - +
444B GLU* 3.3 9.6 - - - +
445B SER* 2.3 50.2 + - - +
446B ILE* 4.2 0.3 - - - +
483B GLN* 4.8 0.2 - - - +
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Residues in contact with ALA 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B ILE 4.4 0.7 - - - -
439B ALA* 3.3 22.1 + - + +
441B SER 4.0 0.8 - - - -
442B VAL* 1.3 69.2 - - - +
444B GLU* 1.3 59.4 + - + +
445B SER 3.0 4.7 - - - -
446B ILE* 2.9 36.3 + - - +
480B LEU* 5.9 1.3 - - + -
483B GLN* 3.5 39.7 - - + +
484B LEU* 4.0 21.2 - - + +
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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