Contacts of the helix formed by residues 401 - 419 (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 ASP 401 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364D ASN* 2.6 36.6 + - - +
399D GLY 3.9 0.2 + - - -
400D PRO* 1.3 73.9 - - - +
402D LYS* 1.3 64.9 + - - +
403D VAL* 3.3 12.6 + - - +
404D GLN* 3.0 21.8 + - - +
405D ARG* 3.0 21.0 + - - +
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Residues in contact with LYS 402 (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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401D ASP* 1.3 73.4 - - - +
403D VAL* 1.3 72.5 + - + +
405D ARG* 3.3 24.4 + - - +
406D THR* 2.9 53.7 + - - +
441D SER 6.0 0.2 - - - +
442D VAL* 4.6 4.0 - - + +
444D GLU* 3.7 32.4 + - + +
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Residues in contact with VAL 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401D ASP* 3.2 10.5 - - - +
402D LYS* 1.3 92.1 - - + +
404D GLN* 1.3 69.8 + - - +
406D THR* 3.4 4.3 + - - -
407D TYR* 3.0 30.2 + - + +
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Residues in contact with GLN 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364D ASN* 3.4 28.1 - - - +
367D LEU* 3.5 20.6 - - + +
400D PRO* 4.5 1.3 - - + -
401D ASP* 3.0 23.0 + - - +
403D VAL* 1.3 84.8 - - - +
405D ARG* 1.3 65.1 + - - +
407D TYR* 3.4 8.0 + - - +
408D TYR* 3.1 53.9 + - - -
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Residues in contact with ARG 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367D LEU* 5.7 2.7 - - + -
396D ILE 4.3 5.4 - - - +
397D MET* 3.1 43.1 + - + +
398D ASP* 4.7 5.9 + - - +
399D GLY 5.0 2.0 - - - +
400D PRO* 2.9 38.6 + - + +
401D ASP* 3.0 12.3 + - - +
402D LYS* 3.3 30.4 - - - +
404D GLN* 1.3 76.1 - - - +
406D THR* 1.3 63.4 + - - +
408D TYR* 4.2 2.3 - - - +
409D VAL* 3.1 31.4 + - - +
441D SER* 3.8 13.1 + - - +
442D VAL* 3.7 34.5 - - + +
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Residues in contact with THR 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402D LYS* 2.9 39.8 + - - +
403D VAL* 3.6 6.1 - - - -
405D ARG* 1.3 74.1 - - - +
407D TYR* 1.3 68.0 + - - +
409D VAL* 3.8 0.7 - - - +
410D HIS* 2.9 33.0 + - + +
442D VAL* 4.8 1.6 - - - +
444D GLU* 3.6 13.0 + - - +
445D SER* 3.7 29.3 - - - +
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Residues in contact with TYR 407 (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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403D VAL* 3.0 17.0 + - + +
404D GLN* 3.4 10.1 + - - +
406D THR* 1.3 83.9 - - - +
408D TYR* 1.3 103.1 + + - +
410D HIS* 3.5 7.4 + - - +
411D GLN* 3.3 40.9 + - + +
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Residues in contact with TYR 408 (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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367D LEU* 3.9 24.8 - - + +
368D GLU* 5.7 1.4 + - - -
371D LEU* 3.3 45.6 - - + +
393D PHE* 4.2 6.3 - - + -
396D ILE* 6.3 0.2 - - + -
397D MET* 6.0 2.2 - - + -
404D GLN* 3.1 44.0 + - - +
405D ARG* 4.5 2.0 - - - +
407D TYR* 1.3 103.7 - + - +
409D VAL* 1.3 61.8 + - - +
411D GLN* 3.3 18.2 + - - +
412D ALA* 2.9 33.3 + - - +
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Residues in contact with VAL 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393D PHE* 4.1 14.4 - - + -
397D MET* 3.5 30.1 - - + -
405D ARG 3.1 25.1 + - - +
406D THR 3.8 2.0 - - - +
408D TYR* 1.3 71.8 - - - +
410D HIS* 1.3 71.5 + - - +
411D GLN 3.0 0.3 + - - -
412D ALA 3.1 0.2 + - - -
413D LEU* 2.8 37.3 + - + +
416D ILE* 6.2 0.4 - - - -
438D ILE* 3.6 25.8 - - + -
442D VAL* 4.1 4.3 - - + -
445D SER* 3.5 20.9 - - - +
446D ILE* 4.1 11.2 - - + -
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Residues in contact with HIS 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406D THR* 2.9 24.8 + - + +
407D TYR* 3.5 8.2 + - - +
409D VAL* 1.3 79.5 - - - +
411D GLN* 1.3 63.4 + - - +
414D PRO* 4.0 7.4 - - - +
445D SER 4.8 7.4 - - - +
447D ASP* 5.7 4.0 + - + -
450D GLN* 5.7 2.8 + - - -
451D HIS* 3.7 41.9 + + - -
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Residues in contact with GLN 411 (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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407D TYR* 3.3 39.4 + - + +
408D TYR* 3.7 20.7 - - - +
409D VAL 3.1 0.8 - - - -
410D HIS* 1.3 83.5 - - - +
412D ALA* 1.3 61.9 + - - +
413D LEU 3.5 0.2 - - - -
414D PRO* 3.8 9.5 - - - +
415D SER* 4.5 3.3 + - - -
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Residues in contact with ALA 412 (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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371D LEU* 5.6 2.7 - - + -
374D VAL* 5.8 4.9 - - + -
393D PHE* 3.9 24.7 - - + -
408D TYR 2.9 17.9 + - - +
411D GLN* 1.3 78.5 - - + +
413D LEU* 1.3 63.7 + - - +
414D PRO* 3.4 2.9 - - - -
415D SER* 3.1 14.4 + - - +
416D ILE* 3.1 28.1 + - + +
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Residues in contact with LEU 413 (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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409D VAL* 2.8 20.8 + - + +
412D ALA* 1.3 73.6 - - - +
414D PRO* 1.4 65.2 - - + +
416D ILE* 3.1 6.7 + - + +
417D LEU* 2.8 63.5 + - + +
435D ILE* 4.4 7.9 - - + -
438D ILE* 4.0 26.9 - - + -
446D ILE* 3.6 28.7 - - + -
451D HIS* 3.8 32.3 - - + +
455D VAL* 4.4 10.5 - - + -
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Residues in contact with PRO 414 (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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410D HIS 4.0 9.6 - - - +
411D GLN 3.8 12.1 - - - +
412D ALA 3.5 3.4 - - - -
413D LEU* 1.4 92.2 - - + +
415D SER* 1.3 57.4 + - - +
417D LEU* 3.9 8.8 - - + +
418D ASN* 3.0 29.6 + - - +
451D HIS* 4.7 9.4 - - + +
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Residues in contact with SER 415 (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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378D ILE* 4.4 23.2 - - - +
379D THR* 6.1 2.5 - - - -
411D GLN 4.5 2.8 + - - -
412D ALA* 3.1 20.3 + - - +
414D PRO* 1.3 77.4 - - - +
416D ILE* 1.3 63.1 + - - +
418D ASN* 3.4 19.5 + - - +
419D LEU* 3.5 15.0 + - - +
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Residues in contact with ILE 416 (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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374D VAL* 6.2 1.8 - - + -
378D ILE* 4.8 7.9 - - + -
390D VAL* 4.2 17.0 - - + -
393D PHE* 3.7 42.0 - - + -
409D VAL* 6.2 0.4 - - - -
412D ALA* 3.1 21.5 + - + +
413D LEU* 3.1 10.9 + - + +
415D SER* 1.3 73.9 - - - +
417D LEU* 1.3 68.2 + - - +
418D ASN 3.1 1.3 - - - -
419D LEU* 3.0 17.2 + - - +
431D THR* 3.1 29.3 - - + +
434D CYS* 4.1 14.4 - - - -
435D ILE* 3.8 22.2 - - + -
438D ILE* 4.4 7.6 - - + -
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Residues in contact with LEU 417 (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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413D LEU* 2.8 44.8 + - + +
414D PRO* 3.9 6.3 - - + +
416D ILE* 1.3 72.7 - - - +
418D ASN* 1.3 62.2 + - - +
419D LEU 3.2 1.0 + - - -
420D MET* 3.3 22.2 + - - +
421D ASN* 5.1 1.2 - - - +
435D ILE* 3.7 24.0 - - + -
451D HIS* 4.6 7.0 - - + +
454D GLY* 3.6 39.0 - - - +
455D VAL* 3.7 19.1 - - + +
458D ALA* 3.8 11.2 - - + +
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Residues in contact with ASN 418 (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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379D THR* 5.8 5.9 - - - +
414D PRO 3.0 20.0 + - - +
415D SER* 3.4 12.3 + - - +
417D LEU* 1.3 77.7 - - - +
419D LEU* 1.3 61.8 + - - +
420D MET 3.1 5.4 + - - -
421D ASN* 3.2 34.7 + - - +
422D ASP 4.6 0.5 + - - -
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Residues in contact with LEU 419 (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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378D ILE* 3.5 49.1 - - + +
379D THR* 6.0 1.8 - - + -
386D ARG* 4.3 5.6 - - - +
390D VAL* 3.5 26.0 - - + -
415D SER 3.6 11.9 - - - +
416D ILE 3.0 11.9 + - - +
418D ASN* 1.3 78.4 - - - +
420D MET* 1.3 58.9 + - - +
421D ASN 3.1 6.3 - - - -
422D ASP* 3.2 42.5 - - - +
427D VAL* 4.1 9.3 - - + +
428D LYS* 3.6 6.6 - - - +
431D THR* 3.4 17.6 + - - +
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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