Contacts of the helix formed by residues 424 - 432 (chain F) in PDB entry 3KHU
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 424 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402F TYR* 2.9 20.7 + - + +
422F GLU 3.7 1.0 + - - -
423F LEU* 1.3 68.0 - - - +
425F TYR* 1.3 58.3 + - - +
426F GLU* 3.6 10.0 + - - +
427F ARG* 3.4 35.5 + - + +
428F ILE* 3.1 27.9 + - - +
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Residues in contact with TYR 425 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334F LEU* 5.1 0.9 - - - +
411F VAL* 5.3 9.4 - - + -
413F ILE* 4.0 9.0 - - - +
420F PHE* 2.7 29.9 + - - -
421F LYS 4.4 6.5 - - - -
423F LEU* 3.1 42.7 + - + +
424F ASP* 1.3 69.8 + - - +
426F GLU* 1.3 61.0 + - - +
428F ILE* 3.8 21.3 - - + -
429F HIS* 2.9 30.0 + - - +
438F ILE* 4.0 27.8 - - + -
445F LEU* 3.7 26.6 - - + +
448F LEU* 5.2 4.7 - - + -
452F LEU* 3.6 26.2 - - + -
455F ILE* 4.3 5.2 - - + -
457F PHE* 3.4 13.6 - + + -
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Residues in contact with GLU 426 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424F ASP* 3.3 9.5 + - - +
425F TYR* 1.3 76.1 - - - +
427F ARG* 1.3 63.4 + - - +
429F HIS* 3.4 4.2 + - - +
430F LYS* 3.3 42.4 + - - +
455F ILE* 4.0 34.4 - - + +
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Residues in contact with ARG 427 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400F ASP* 5.3 0.2 + - - -
402F TYR* 3.6 59.0 - - + +
424F ASP* 3.3 29.3 + - - +
425F TYR 3.3 0.2 - - - -
426F GLU* 1.3 77.0 - - - +
428F ILE* 1.3 68.8 + - - +
430F LYS* 3.3 24.6 + - - +
431F LYS* 3.7 9.3 + - + +
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Residues in contact with ILE 428 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401F PRO 5.5 0.4 - - - +
402F TYR* 3.8 26.9 - - + -
405F CYS* 3.7 36.4 - - + +
411F VAL* 4.4 4.0 - - + -
423F LEU* 4.2 15.9 - - + -
424F ASP 3.1 14.4 + - - +
425F TYR* 3.3 31.8 + - + +
427F ARG* 1.3 76.6 - - - +
429F HIS* 1.3 65.7 + - - +
431F LYS* 3.2 12.7 + - - +
432F MET* 3.2 33.2 + - - +
457F PHE* 4.2 6.5 - - + -
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Residues in contact with HIS 429 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425F TYR 2.9 17.0 + - - +
426F GLU 3.5 3.8 - - - +
428F ILE* 1.3 76.2 - - - +
430F LYS* 1.3 65.3 + - + +
432F MET* 3.1 15.1 + - - +
434F LYS* 2.9 39.2 + - + +
436F ALA* 4.8 4.3 - - + +
455F ILE* 2.8 52.0 + - + -
456F GLY* 3.3 23.4 + - - -
457F PHE* 3.7 18.4 - + + -
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Residues in contact with LYS 430 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426F GLU* 3.3 32.4 + - - +
427F ARG* 3.3 14.4 + - - +
428F ILE 3.2 0.6 - - - -
429F HIS* 1.3 80.4 - - - +
431F LYS* 1.3 64.1 + - + +
432F MET 4.3 0.2 - - - +
434F LYS* 3.4 15.3 + - - +
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Residues in contact with LYS 431 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405F CYS 4.6 0.7 - - - -
406F ASP* 3.6 25.0 - - - +
407F GLY* 2.8 30.1 + - - +
427F ARG* 3.7 6.9 + - + +
428F ILE* 3.2 8.7 + - - +
430F LYS* 1.3 82.4 - - + +
432F MET* 1.3 60.6 + - - +
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Residues in contact with MET 432 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405F CYS 3.5 15.7 - - - +
408F ALA* 3.3 23.8 - - + +
409F HIS 3.4 24.5 - - - +
410F ALA* 3.6 5.6 - - - +
411F VAL* 3.8 12.3 - - + -
428F ILE* 3.2 24.7 + - + +
429F HIS 3.1 10.9 + - - +
431F LYS* 1.3 80.6 - - - +
433F LEU* 1.3 64.1 + - - +
434F LYS* 2.6 30.5 + - - -
436F ALA* 3.8 11.7 - - + -
437F PHE 3.8 15.5 - - - +
457F PHE* 3.6 27.8 - - - -
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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