Contacts of the helix formed by residues 477 - 486 (chain B) in PDB entry 2JDQ
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 GLY 477 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A GLN* 5.4 4.5 - - - -
473B GLU* 3.0 17.8 + - - +
474B GLU 4.6 1.5 + - - -
475B ALA 3.8 0.4 - - - -
476B TYR* 1.3 80.3 - - - +
478B LEU* 1.3 64.8 + - - -
479B ASP 3.3 2.9 - - - -
480B LYS* 3.4 4.4 + - - -
481B ILE* 3.1 25.2 + - - +
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Residues in contact with LEU 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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329A ILE* 3.3 35.9 - - + -
473B GLU* 3.8 29.7 + - + +
477B GLY* 1.3 69.8 - - - -
479B ASP* 1.3 66.0 + - - +
481B ILE* 4.5 4.5 - - + -
482B GLU* 2.8 56.6 + - + +
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Residues in contact with ASP 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 GLY* 3.3 1.4 - - - -
478B LEU* 1.3 81.0 - - - +
480B LYS* 1.3 64.3 + - + +
482B GLU* 4.3 10.8 - - - +
483B PHE* 3.3 21.8 + - - +
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Residues in contact with LYS 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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433B THR* 4.4 21.9 - - - +
476B TYR* 3.5 56.2 + - + +
477B GLY* 3.4 8.3 + - - +
478B LEU 3.2 0.6 - - - -
479B ASP* 1.3 79.9 - - + +
481B ILE* 1.3 64.0 + - - +
483B PHE* 3.5 7.1 + - - +
484B LEU* 3.2 27.5 + - - +
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Residues in contact with ILE 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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472B ILE* 4.2 17.9 - - + -
473B GLU* 4.1 34.5 - - + +
476B TYR* 3.6 25.6 - - + -
477B GLY 3.1 18.3 + - - +
478B LEU* 3.9 6.5 - - + +
480B LYS* 1.3 78.2 - - - +
482B GLU* 1.3 56.7 + - + +
484B LEU* 3.2 9.9 + - + +
485B GLN* 2.9 46.6 + - + +
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Residues in contact with GLU 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 LEU* 2.8 48.8 + - + +
479B ASP* 4.3 10.3 - - - +
481B ILE* 1.3 70.2 - - + +
483B PHE* 1.3 67.6 + - - +
485B GLN* 3.2 29.0 + - - +
486B SER* 3.5 11.3 + - - -
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Residues in contact with PHE 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 ASP 3.3 18.1 + - - +
480B LYS* 3.6 7.4 - - - +
482B GLU* 1.3 79.6 - - - +
484B LEU* 1.3 81.5 + - + +
486B SER* 3.5 5.7 + - - +
489B ASN* 3.0 53.4 + - + +
493B TYR* 3.5 40.6 - + - -
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Residues in contact with LEU 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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432B LEU* 6.3 0.4 - - + -
444B LEU* 6.4 2.0 - - + -
476B TYR* 4.0 28.3 - - + +
480B LYS* 3.2 15.9 + - + +
481B ILE* 3.2 11.2 + - + +
483B PHE* 1.3 94.7 - - + +
485B GLN* 1.3 61.0 + - - +
486B SER 3.3 4.9 - - - +
490B GLN* 5.9 2.6 + - - +
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Residues in contact with GLN 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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473B GLU* 5.5 1.3 - - - +
481B ILE* 2.9 35.6 + - + +
482B GLU* 3.2 25.3 + - - +
484B LEU* 1.3 77.1 - - - +
486B SER* 1.3 60.9 + - - +
487B HIS* 3.4 4.2 + - - +
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Residues in contact with SER 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 GLU 3.5 6.8 + - - -
483B PHE 3.7 2.5 - - - +
484B LEU 3.3 4.9 - - - +
485B GLN* 1.3 76.9 - - - +
487B HIS* 1.3 58.3 + - - +
488B GLU* 3.3 15.7 + - - +
489B ASN* 2.9 44.8 + - - +
490B GLN* 3.2 20.6 + - - +
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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