Contacts of the helix formed by residues 444 - 455 (chain A) in PDB entry 4WMJ
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 444 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A LEU* 6.3 2.9 - - + -
441A LYS 5.7 3.4 - - - +
443A LYS* 1.3 77.2 - - - +
445A ASP* 1.3 65.9 + - - +
446A ALA* 3.5 9.9 + - - +
447A GLU* 3.0 37.9 + - - +
448A ALA* 2.9 22.9 + - - +
470A VAL* 4.3 4.5 - - - -
471A PHE 5.1 0.9 - - - -
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Residues in contact with ASP 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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444A THR* 1.3 72.2 - - - +
446A ALA* 1.3 58.9 + - - +
448A ALA 3.3 0.2 + - - -
449A LYS* 2.8 33.3 + - - +
466A LEU* 3.8 19.9 - - + +
467A PRO* 5.5 2.3 - - - +
470A VAL* 3.8 32.5 - - - +
472A LYS* 5.4 3.3 + - - -
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Residues in contact with ALA 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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444A THR* 3.3 8.4 + - - +
445A ASP* 1.3 79.7 - - - +
447A GLU* 1.3 59.2 + - + +
449A LYS* 3.7 5.6 - - - +
450A ALA* 2.9 30.9 + - - +
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Residues in contact with GLU 447 (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 LYS* 3.6 26.4 + - - +
442A GLY 4.3 2.1 - - - +
443A LYS* 3.4 21.3 + - + +
444A THR* 3.0 46.5 + - - +
446A ALA* 1.3 77.6 - - + +
448A ALA* 1.3 64.3 + - - +
450A ALA* 3.4 5.8 + - - +
451A GLU* 3.1 27.6 + - - +
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Residues in contact with ALA 448 (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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443A LYS* 3.9 21.5 - - + +
444A THR 2.9 16.1 + - - +
447A GLU* 1.3 78.0 - - - +
449A LYS* 1.3 62.8 + - - +
451A GLU* 3.4 6.9 + - - +
452A LEU* 3.0 27.9 + - + +
466A LEU* 3.7 18.4 - - + -
469A LYS* 4.0 25.5 - - + +
470A VAL* 4.5 1.8 - - + -
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Residues in contact with LYS 449 (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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445A ASP 2.8 19.2 + - - +
446A ALA* 3.7 5.6 - - - +
448A ALA* 1.3 78.4 - - - +
450A ALA* 1.3 64.3 + - - +
452A LEU* 3.1 6.8 + - - +
453A GLU* 2.9 51.3 + - - +
462A ILE* 4.3 20.4 - - + -
466A LEU* 3.7 20.4 - - + +
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Residues in contact with ALA 450 (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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446A ALA 2.9 17.2 + - - +
447A GLU* 3.9 5.8 - - - +
449A LYS* 1.3 76.7 - - - +
451A GLU* 1.3 55.3 + - + +
453A GLU* 3.4 11.9 + - - +
454A LYS* 3.0 56.8 + - - +
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Residues in contact with GLU 451 (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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443A LYS* 2.8 37.4 + - - +
447A GLU* 3.1 19.5 + - - +
448A ALA* 3.6 7.4 - - - +
449A LYS 3.2 0.2 - - - -
450A ALA* 1.3 73.1 - - - +
452A LEU* 1.3 67.2 + - + +
454A LYS* 3.4 7.0 + - - +
455A SER* 3.0 24.4 + - - -
469A LYS* 5.8 3.3 - - - +
523B GLN* 3.3 22.8 + - - -
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Residues in contact with LEU 452 (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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448A ALA 3.0 20.7 + - - +
449A LYS 3.6 5.4 - - - +
451A GLU* 1.3 78.1 - - + +
453A GLU* 1.3 59.6 + - - +
455A SER* 2.7 21.9 + - - +
457A MET* 3.2 40.4 + - + +
462A ILE* 3.8 31.9 - - + -
465A ILE* 3.8 24.7 - - + -
466A LEU* 4.1 18.8 - - + -
469A LYS* 4.2 25.8 - - + +
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Residues in contact with GLU 453 (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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449A LYS* 2.9 44.6 + - - +
450A ALA* 3.7 14.0 - - - +
452A LEU* 1.3 75.4 - - - +
454A LYS* 1.3 56.5 + - + +
456A GLY* 2.6 28.8 + - - -
457A MET 4.8 2.4 - - - +
462A ILE* 3.7 19.4 - - + +
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Residues in contact with LYS 454 (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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450A ALA* 3.0 39.4 + - - +
451A GLU* 4.0 5.8 - - - +
453A GLU* 1.3 76.8 - - + +
455A SER* 1.3 59.7 + - - +
456A GLY 3.5 0.7 + - - -
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Residues in contact with SER 455 (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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451A GLU 3.0 13.5 + - - -
452A LEU* 2.7 25.7 + - - +
454A LYS* 1.3 77.6 - - - +
456A GLY* 1.3 56.6 + - - +
457A MET* 3.7 10.4 + - - +
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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