Contacts of the helix formed by residues 477 - 488 (chain B) in PDB entry 4WGK
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 477 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454B TYR* 3.4 13.3 + - - -
473B LYS* 5.0 8.7 + - - -
476B GLY* 1.3 74.2 - - - +
478B PRO* 1.3 74.3 - - + +
479B PHE* 4.3 6.1 - - + +
480B TRP* 2.9 42.3 + - - +
481B ASP* 2.9 23.7 + - - +
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Residues in contact with PRO 478 (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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476B GLY 4.8 0.2 - - - +
477B ASP* 1.3 89.3 - - + +
479B PHE* 1.3 56.4 + - + +
481B ASP* 4.1 6.1 - - + +
482B THR* 2.4 36.7 + - - +
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Residues in contact with PHE 479 (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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477B ASP* 3.1 8.0 - - + +
478B PRO* 1.3 80.5 - - - +
480B TRP* 1.3 90.7 + + - +
482B THR* 3.2 8.6 + - - -
483B ILE* 3.2 50.2 + - + +
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Residues in contact with TRP 480 (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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454B TYR* 3.6 15.0 - - + +
467B LEU* 4.1 28.2 + - + -
469B PHE* 3.3 38.0 - + - -
473B LYS* 6.2 0.4 - - - -
477B ASP* 2.9 30.7 + - - +
479B PHE* 1.3 97.3 - + - +
481B ASP* 1.3 65.5 + - - +
482B THR 3.1 0.4 - - - -
483B ILE* 3.8 31.3 - - + +
484B ARG* 3.0 26.3 + - + +
505B LEU* 4.2 19.2 - - + +
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Residues in contact with ASP 481 (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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454B TYR* 2.7 27.1 + - - -
476B GLY* 3.9 6.5 - - - -
477B ASP 2.9 29.3 + - - +
478B PRO* 4.1 5.9 - - + +
480B TRP* 1.3 75.7 - - - +
482B THR* 1.3 58.4 + - - +
484B ARG* 2.4 39.6 + - - +
485B ASP* 3.0 39.7 + - - +
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Residues in contact with THR 482 (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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478B PRO* 2.4 26.8 + - - +
479B PHE* 3.3 7.6 - - - -
480B TRP 3.1 0.4 - - - -
481B ASP* 1.3 74.2 - - - +
483B ILE* 1.3 57.2 + - + +
485B ASP* 3.0 8.5 + - - +
486B GLN* 2.6 62.8 + - + +
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Residues in contact with ILE 483 (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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479B PHE* 3.2 50.1 + - + +
480B TRP* 3.5 36.8 + - + +
482B THR* 1.3 76.9 - - + +
484B ARG* 1.3 58.8 - - - +
486B GLN* 4.3 6.3 - - - -
487B ILE* 2.9 54.6 + - + +
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Residues in contact with ARG 484 (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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454B TYR* 4.7 0.6 - - - -
480B TRP* 3.0 16.8 + - + +
481B ASP* 2.4 37.9 + - - +
483B ILE* 1.3 76.6 - - - +
485B ASP* 1.3 100.3 + - - +
487B ILE* 5.3 0.2 - - - -
488B LEU* 3.0 35.2 + - + +
489B GLY 3.1 8.3 + - - +
490B LYS* 4.8 2.6 - - - +
491B PRO* 3.3 34.5 - - - +
496B LYS* 5.5 12.7 - - - +
504B ILE* 3.0 28.4 + - - +
505B LEU* 3.2 27.8 - - + +
506B LEU* 6.1 0.2 - - + -
507B HIS* 4.1 10.8 - - + -
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Residues in contact with ASP 485 (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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481B ASP* 3.0 26.3 + - - +
482B THR* 3.3 10.1 - - - +
484B ARG* 1.3 104.5 + - - +
486B GLN* 1.3 68.7 + - + +
489B GLY* 3.1 25.8 + - - -
490B LYS* 3.2 40.0 + - + +
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Residues in contact with GLN 486 (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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482B THR* 2.6 43.9 + - + +
483B ILE* 3.8 6.5 - - - +
485B ASP* 1.3 77.7 - - - +
487B ILE* 1.3 64.7 + - + +
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Residues in contact with ILE 487 (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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483B ILE* 2.9 39.0 + - + +
484B ARG* 5.3 0.2 - - - -
486B GLN* 1.3 85.4 - - + +
488B LEU* 1.3 79.9 + - + +
489B GLY 3.6 0.2 - - - -
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Residues in contact with LEU 488 (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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484B ARG* 3.0 18.2 + - + +
487B ILE* 1.3 94.2 - - + +
489B GLY* 1.3 60.1 + - - +
505B LEU 4.7 5.4 - - - +
506B LEU* 3.6 33.2 - - + -
507B HIS* 3.8 6.6 - - - +
511B LEU* 3.3 43.7 - - + +
517B TRP* 3.6 31.2 - - + -
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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