Contacts of the helix formed by residues 436 - 446 (chain A) in PDB entry 4KM9
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 THR 436 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411A THR* 4.3 16.6 - - + -
420A GLU* 4.3 24.9 - - + +
434A LEU* 3.6 2.9 - - + +
435A LEU* 1.3 76.5 - - - +
437A GLU* 1.3 64.7 + - - +
438A GLU* 4.2 6.4 + - - +
439A PHE* 3.1 32.5 + - - +
440A VAL* 3.1 13.4 + - - +
467A LYS* 5.0 6.9 + - - +
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Residues in contact with GLU 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A LEU 5.5 2.9 - - - +
390A LEU* 3.9 34.9 - - + +
411A THR* 5.3 6.0 + - - +
435A LEU 3.9 0.8 + - - -
436A THR* 1.3 74.1 - - - +
438A GLU* 1.3 62.7 + - - +
440A VAL* 3.2 14.3 - - - +
441A GLU* 3.2 28.4 - - + +
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Residues in contact with GLU 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A THR* 3.2 6.4 + - - +
437A GLU* 1.3 78.4 - - - +
439A PHE* 1.3 61.6 + - - +
440A VAL 3.6 0.3 + - - -
441A GLU* 3.6 7.7 + - - +
442A LYS* 3.6 17.5 + - - +
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Residues in contact with PHE 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A TYR* 5.0 1.3 - - - -
435A LEU* 4.2 20.4 - - + -
436A THR* 3.1 21.4 + - - +
438A GLU* 1.3 80.2 - - - +
440A VAL* 1.3 57.6 + - - +
442A LYS* 3.4 19.9 + - + +
443A MET* 3.0 50.6 + - + +
464A TRP* 3.8 35.0 - + - -
467A LYS* 3.5 53.2 - - + +
469A LEU* 3.7 17.9 - - + -
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Residues in contact with VAL 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A LEU* 4.7 11.4 - - + +
389A LEU* 4.2 19.3 - - + -
390A LEU* 3.6 25.8 - - + +
435A LEU* 3.5 43.1 - - + +
436A THR 3.1 8.0 + - - +
437A GLU* 3.2 22.0 - - - +
439A PHE* 1.3 76.2 - - - +
441A GLU* 1.3 60.2 + - - +
443A MET* 3.4 10.7 + - + +
444A LEU* 3.1 34.9 + - + +
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Residues in contact with GLU 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A LEU* 3.9 28.0 - - + +
437A GLU* 3.2 24.0 - - + +
438A GLU* 3.8 9.2 - - - +
439A PHE 3.3 0.6 - - - -
440A VAL* 1.3 76.4 - - - +
442A LYS* 1.3 61.7 + - - +
444A LEU* 3.6 10.5 + - - +
445A GLU* 3.4 28.3 + - - +
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Residues in contact with LYS 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438A GLU 3.6 9.6 + - - +
439A PHE* 3.4 24.3 + - + +
440A VAL 3.3 0.2 - - - -
441A GLU* 1.3 77.1 - - - +
443A MET* 1.3 64.9 + - - +
445A GLU* 3.2 19.5 + - - +
446A ASP* 3.3 22.1 + - - +
464A TRP* 4.1 18.3 - - - +
466A GLU* 3.1 40.4 + - - +
467A LYS* 5.7 0.8 - - - +
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Residues in contact with MET 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A ILE* 5.5 2.7 - - + -
385A LEU* 4.0 22.9 - - + -
408A PHE* 5.7 3.6 - - + -
435A LEU* 3.9 22.9 - - + -
439A PHE* 3.0 49.0 + - + +
440A VAL* 3.5 11.9 - - - +
442A LYS* 1.3 75.8 - - - +
444A LEU* 1.3 60.9 + - - +
446A ASP* 3.2 9.9 + - - +
447A LEU* 3.1 29.4 - - + +
464A TRP* 3.7 42.6 - - + -
469A LEU* 4.4 8.5 - - + -
471A VAL* 4.8 9.0 - - + -
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Residues in contact with LEU 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A PRO* 4.2 11.7 - - + +
385A LEU* 4.0 27.6 - - + -
386A ARG* 3.9 36.8 - - + +
390A LEU* 3.7 29.4 - - + -
440A VAL 3.1 21.9 + - - +
441A GLU* 3.8 15.3 - - - +
442A LYS 3.2 0.4 - - - -
443A MET* 1.3 76.4 - - - +
445A GLU* 1.3 60.6 + - + +
447A LEU* 3.2 27.5 + - + +
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Residues in contact with GLU 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A GLU* 3.4 15.4 + - - +
442A LYS* 3.2 12.2 + - - +
444A LEU* 1.3 77.5 - - + +
446A ASP* 1.3 62.8 + - - +
447A LEU 3.3 2.9 + - - -
448A GLU 5.3 0.7 + - - -
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Residues in contact with ASP 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A LYS* 3.3 20.8 + - - +
443A MET 3.2 11.8 + - - +
445A GLU* 1.3 80.8 - - - +
447A LEU* 1.3 58.3 + - - +
448A GLU 4.0 1.7 + - - -
462A TYR* 3.2 28.6 - - + -
464A TRP* 3.7 29.4 + - + -
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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