Contacts of the helix formed by residues 428 - 439 (chain J) in PDB entry 3KDO
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 428 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410J GLN* 3.3 29.8 - - + +
424J TYR* 2.9 71.5 + + + +
425J ALA 3.2 13.8 - - - +
426J LYS 3.5 2.8 + - - -
427J THR* 1.3 100.8 + - - +
429J LYS* 1.3 67.7 + - - +
430J GLU* 3.5 3.1 - - - -
431J LEU* 3.3 7.0 + - + +
432J ALA 3.3 8.8 + - - -
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Residues in contact with LYS 429 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399J ASP* 6.0 1.1 - - - +
425J ALA 4.9 0.2 - - - -
427J THR 4.3 0.6 - - - -
428J HIS* 1.3 69.7 - - - +
430J GLU* 1.3 77.3 + - - +
432J ALA* 2.9 20.2 + - - +
433J ARG* 3.1 20.6 + - + +
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Residues in contact with GLU 430 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397J HIS* 2.8 30.7 + - - -
399J ASP* 5.3 3.4 - - - +
403J ALA* 3.6 34.3 - - + +
406J ARG* 3.5 29.5 + - + +
407J ALA* 3.4 11.0 - - + +
410J GLN* 2.8 28.7 + - - +
428J HIS* 4.5 0.2 - - - -
429J LYS* 1.3 80.6 + - - +
431J LEU* 1.3 60.0 + - - +
433J ARG* 4.8 1.1 - - - -
434J ALA 3.3 4.7 + - - -
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Residues in contact with LEU 431 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372J PRO* 4.2 23.8 - - + +
407J ALA* 3.8 6.5 - - + +
410J GLN* 3.0 23.0 + - + +
411J ALA* 4.3 22.0 - - + +
414J ALA* 5.1 0.7 - - + -
421J LEU* 3.6 27.1 - - + +
424J TYR* 3.9 22.2 - - + -
425J ALA* 3.6 18.2 - - + +
428J HIS* 3.5 7.4 - - + +
429J LYS 3.0 0.4 - - - -
430J GLU* 1.3 74.6 - - - +
432J ALA* 1.3 65.6 + - - +
434J ALA* 3.1 2.9 + - - +
435J LEU* 3.1 35.7 + - + +
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Residues in contact with ALA 432 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425J ALA* 3.5 31.4 - - + +
428J HIS 3.3 2.2 + - - +
429J LYS* 2.9 12.1 + - - +
431J LEU* 1.3 79.3 - - - +
433J ARG* 1.3 64.4 + - + +
435J LEU* 3.4 6.5 + - - +
436J GLU* 3.1 22.2 + - - +
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Residues in contact with ARG 433 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397J HIS* 3.5 19.7 - - + +
398J PRO* 3.5 35.5 + - + +
399J ASP* 3.1 34.3 + - - +
429J LYS* 3.1 20.6 + - + +
430J GLU 4.6 0.2 - - - -
432J ALA* 1.3 76.9 - - + +
434J ALA* 1.3 64.2 + - - +
436J GLU* 3.3 21.3 + - - +
437J LYS 3.5 7.6 + - - -
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Residues in contact with ALA 434 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372J PRO* 4.1 21.1 - - + -
373J GLY 6.3 0.7 - - - -
397J HIS* 3.5 26.0 + - + -
398J PRO* 4.4 2.5 - - - -
407J ALA* 4.6 0.9 - - + -
430J GLU 3.3 6.0 + - - +
431J LEU* 3.1 10.4 + - - +
433J ARG* 1.3 78.3 - - - +
435J LEU* 1.3 62.6 + - - +
437J LYS* 3.3 2.8 + - - +
438J TRP* 3.1 47.3 + - + +
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Residues in contact with LEU 435 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372J PRO* 4.4 2.0 - - + +
373J GLY* 3.8 20.0 - - - +
421J LEU* 4.0 11.2 - - + +
422J ASP* 3.1 26.2 - - - +
425J ALA* 3.8 26.9 - - + -
431J LEU* 3.1 22.4 + - + +
432J ALA* 3.7 6.7 - - - +
433J ARG 3.3 0.2 - - - -
434J ALA* 1.3 76.7 - - - +
436J GLU* 1.3 60.3 + - - +
438J TRP* 5.4 0.2 - - - -
439J GLY* 2.4 54.0 + - - +
440J HIS* 4.0 11.4 - - + +
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Residues in contact with GLU 436 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432J ALA 3.1 13.8 + - - +
433J ARG* 3.5 20.6 - - - +
434J ALA 3.3 0.2 - - - -
435J LEU* 1.3 77.9 - - - +
437J LYS* 1.3 59.0 + - - +
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Residues in contact with LYS 437 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D THR* 3.7 21.7 + - - -
57D THR* 3.8 17.8 + - - -
396J GLY 2.5 37.4 + - - +
397J HIS 4.9 0.2 - - - -
398J PRO* 4.4 18.5 - - + +
433J ARG 3.5 6.9 + - - +
434J ALA 3.3 7.5 + - - +
435J LEU 3.1 0.4 - - - -
436J GLU* 1.3 81.9 - - - +
438J TRP* 1.3 78.5 + - + +
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Residues in contact with TRP 438 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D TRP* 3.5 31.3 - + - -
56D THR* 3.5 14.4 + - - -
371J HIS* 3.7 36.2 + + + +
372J PRO* 4.0 3.4 - - + -
373J GLY 5.7 0.2 - - - -
392J GLY 3.7 11.9 - - - -
393J GLY* 3.6 24.0 - - - -
396J GLY* 3.4 23.1 - - - -
397J HIS* 3.4 29.2 - + + -
398J PRO* 4.9 0.7 - - + -
434J ALA* 3.1 46.7 + - + +
437J LYS* 1.3 94.7 - - + +
439J GLY* 1.3 66.1 + - - +
440J HIS 3.1 3.8 + - - -
441J VAL* 3.4 19.9 + - - +
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Residues in contact with GLY 439 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371J HIS* 3.5 0.4 - - - -
373J GLY* 3.2 24.3 - - - -
435J LEU* 2.4 40.3 + - - +
438J TRP* 1.3 66.9 - - - +
440J HIS* 1.3 74.0 + - - -
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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