Contacts of the helix formed by residues 429 - 438 (chain B) in PDB entry 1BK6
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 CYS 429 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385B ILE* 6.2 0.2 - - + -
389B VAL* 4.2 21.1 - - + -
392B LEU* 5.7 1.1 - - + -
407B ILE* 4.3 21.3 - - + -
424B LEU* 3.5 34.4 + - + +
425B VAL 4.4 1.5 + - - -
427B GLN 3.8 0.2 - - - -
428B GLY* 1.3 75.9 - - - +
430B ILE* 1.3 71.5 + - - +
432B PRO* 3.0 6.5 - - - +
433B LEU* 2.9 43.1 + - + +
455B ILE* 4.1 15.5 - - - -
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Residues in contact with ILE 430 (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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425B VAL* 3.7 43.5 - - + +
428B GLY* 3.4 1.5 - - - -
429B CYS* 1.3 80.2 - - - +
431B LYS* 1.3 61.1 + - - +
433B LEU* 3.1 9.0 + - - +
434B CYS* 2.9 33.1 + - - -
452B LEU* 4.8 2.0 - - + -
455B ILE* 4.3 20.9 - - + -
473B ASN* 4.3 5.6 - - - +
476B PHE* 3.8 29.2 - - + +
477B ILE* 3.7 36.3 - - + +
480B ALA* 4.9 0.9 - - + -
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Residues in contact with LYS 431 (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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428B GLY* 4.5 3.2 + - - +
430B ILE* 1.3 78.2 - - - +
432B PRO* 1.3 73.6 - - + +
434B CYS* 3.3 0.9 + - - +
435B ASP* 3.1 50.6 + - - +
479B LYS 4.9 0.6 + - - -
480B ALA* 3.1 50.1 + - + +
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Residues in contact with PRO 432 (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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389B VAL* 4.3 7.0 - - + +
392B LEU* 3.1 33.0 - - + +
393B GLU* 3.8 37.9 - - + +
428B GLY 3.2 21.3 - - - +
429B CYS* 3.0 13.2 - - - +
431B LYS* 1.3 94.8 - - + +
433B LEU* 1.3 60.7 + - - -
435B ASP* 3.8 8.8 + - + +
436B LEU* 3.4 17.7 + - - +
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Residues in contact with LEU 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU* 3.8 24.8 - - + +
404B CYS* 5.0 12.1 - - - +
407B ILE* 4.7 16.8 - - + -
408B SER 6.1 0.2 - - - +
429B CYS* 2.9 31.4 + - + +
430B ILE* 3.1 5.1 + - - +
432B PRO* 1.3 76.0 - - - +
434B CYS* 1.3 64.6 + - - +
436B LEU* 3.0 20.1 + - + +
437B LEU 3.7 0.3 + - - -
448B THR* 3.5 27.9 - - + +
451B ALA* 4.2 19.1 - - + -
452B LEU* 4.3 12.3 - - + -
455B ILE* 3.9 27.8 - - + -
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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
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430B ILE* 2.9 26.8 + - - +
431B LYS 3.8 4.0 - - - +
433B LEU* 1.3 77.2 - - - +
435B ASP* 1.3 67.3 + - - +
436B LEU 3.2 0.9 + - - -
437B LEU* 3.2 22.2 + - - +
452B LEU* 4.0 18.8 - - - -
477B ILE* 3.9 16.6 - - - -
480B ALA* 4.4 7.6 - - + -
481B GLY 4.9 0.4 - - - -
482B GLY* 3.4 36.1 - - - +
485B LYS* 3.3 17.3 - - - +
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Residues in contact with ASP 435 (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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431B LYS* 3.1 40.7 + - - +
432B PRO* 4.1 8.1 - - + +
433B LEU 3.3 0.2 - - - -
434B CYS* 1.3 78.0 - - - +
436B LEU* 1.3 61.9 + - - +
437B LEU 3.2 0.2 - - - -
438B GLU* 3.3 19.5 + - - +
439B ILE* 4.2 6.1 + - - +
480B ALA 3.7 18.4 - - - +
485B LYS* 4.4 14.3 + - - +
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Residues in contact with LEU 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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392B LEU* 4.3 15.3 - - + +
397B TYR* 4.3 18.2 - - + -
400B LYS* 4.4 22.0 - - + +
404B CYS* 3.9 20.2 - - + -
432B PRO 3.4 10.9 + - - +
433B LEU* 3.0 15.1 + - + +
435B ASP* 1.3 75.8 - - - +
437B LEU* 1.3 64.1 + - - +
438B GLU 3.0 2.9 + - - -
439B ILE* 3.2 21.6 + - + -
440B ALA* 2.9 35.0 + - + +
444B ILE* 3.8 13.9 - - + -
448B THR* 3.8 18.8 - - + +
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Residues in contact with LEU 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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398A LYS* 5.4 1.4 + - - -
434B CYS* 3.2 17.2 + - - +
436B LEU* 1.3 78.3 - - - +
438B GLU* 1.3 60.6 + - - +
439B ILE 3.4 0.9 + - - -
440B ALA* 3.9 8.6 + - - +
445B ILE* 3.8 41.7 - - + +
448B THR* 3.6 32.5 - - + -
449B LEU* 4.1 11.9 - - + -
452B LEU* 4.1 13.5 - - + -
482B GLY 4.8 0.4 - - - +
485B LYS* 4.2 19.5 - - + +
486B ILE* 4.0 30.1 - - + +
489B CYS* 4.6 9.2 - - - -
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Residues in contact with GLU 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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355A GLU* 5.6 5.4 - - - +
356A ASN* 5.5 2.8 + - - -
398A LYS* 3.3 28.6 + - - -
434B CYS 4.2 0.4 + - - -
435B ASP 3.3 13.8 + - - +
436B LEU 3.0 0.6 - - - -
437B LEU* 1.3 80.5 - - - +
439B ILE* 1.3 65.9 + - + +
485B LYS* 3.3 36.8 - - - +
488B ASN* 5.2 4.2 - - - +
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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
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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