Contacts of the helix formed by residues 463 - 473 (chain B) in PDB entry 1DQ8
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 SER 463 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462B LEU* 1.3 75.1 - - - +
464B ASP* 1.3 67.1 + - - +
465B ALA* 3.6 8.8 + - - +
466B GLU* 3.0 47.5 + - - +
467B ILE* 3.2 13.2 + - - +
490B ARG* 3.7 2.2 - - - -
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Residues in contact with ASP 464 (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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463B SER* 1.3 72.7 - - - +
465B ALA* 1.3 61.7 + - - +
467B ILE* 3.4 3.6 + - - +
468B ILE* 3.1 28.7 + - - +
490B ARG* 3.0 33.9 + - - +
493B SER* 4.1 6.9 + - - -
494B ILE* 4.1 15.5 - - + +
497B GLN* 3.1 35.4 + - - +
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Residues in contact with ALA 465 (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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463B SER* 3.8 8.7 - - - +
464B ASP* 1.3 80.4 - - - +
466B GLU* 1.3 58.2 + - + +
468B ILE* 3.2 14.5 + - - +
469B GLN* 2.9 27.1 + - - +
497B GLN* 5.3 0.2 + - - -
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Residues in contact with GLU 466 (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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462B LEU* 3.3 33.3 - - + +
463B SER* 3.0 35.0 + - - +
465B ALA* 1.3 74.1 - - + +
467B ILE* 1.3 61.9 + - - +
469B GLN* 3.2 8.5 + - - +
470B LEU* 2.9 34.3 + - + +
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Residues in contact with ILE 467 (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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462B LEU* 4.1 22.9 - - + -
463B SER 3.2 8.4 + - - +
464B ASP 3.7 5.4 - - - +
466B GLU* 1.3 75.4 - - - +
468B ILE* 1.3 57.8 + - - +
470B LEU* 3.1 12.9 + - + +
471B VAL* 2.9 44.5 + - + +
476B ILE* 5.7 3.1 - - + -
481B LEU* 4.5 1.3 - - + -
485B ILE* 4.1 25.4 - - + -
490B ARG* 3.2 31.6 - - - +
494B ILE* 3.5 30.7 - - + -
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Residues in contact with ILE 468 (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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464B ASP 3.1 16.6 + - - +
465B ALA* 3.3 11.7 - - - +
466B GLU 3.1 0.2 - - - -
467B ILE* 1.3 77.6 - - - +
469B GLN* 1.3 56.5 + - - +
471B VAL* 3.1 4.1 + - - +
472B ASN* 2.9 51.4 + - - +
494B ILE* 4.1 6.5 - - + -
497B GLN* 3.6 44.0 - - + +
498B LEU* 3.4 30.7 - - + -
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Residues in contact with GLN 469 (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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465B ALA 2.9 13.5 + - - +
466B GLU* 3.2 11.2 + - - +
468B ILE* 1.3 77.1 - - - +
470B LEU* 1.3 64.2 + - + +
472B ASN* 3.8 16.4 + - - +
473B ALA* 3.5 22.4 + - - +
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Residues in contact with LEU 470 (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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462B LEU* 4.3 23.8 - - + -
466B GLU* 2.9 15.2 + - + +
467B ILE* 3.2 13.7 - - + +
469B GLN* 1.3 81.3 - - + +
471B VAL* 1.3 54.4 + - - +
473B ALA* 2.7 24.7 - - - +
475B HIS* 3.1 28.3 + - + +
476B ILE* 4.3 16.8 - - + -
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Residues in contact with VAL 471 (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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467B ILE* 2.9 22.4 + - + +
468B ILE* 3.1 7.6 + - - +
470B LEU* 1.3 74.1 - - - +
472B ASN* 1.3 67.9 + - - +
473B ALA 3.1 12.4 + - - +
474B LYS* 3.5 8.0 + - - +
475B HIS 3.8 1.4 + - - -
476B ILE* 3.7 27.3 + - + +
477B PRO* 4.4 7.3 - - + +
478B ALA* 4.1 19.7 - - + +
481B LEU* 4.0 20.0 - - + -
494B ILE* 5.6 0.4 - - + -
498B LEU* 3.8 27.6 - - + -
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Residues in contact with ASN 472 (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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468B ILE* 2.9 43.1 + - - +
469B GLN* 4.0 19.0 - - - +
471B VAL* 1.3 78.5 - - - +
473B ALA* 1.3 57.1 + - - +
474B LYS* 3.1 22.0 + - - +
498B LEU* 5.3 7.0 - - - +
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Residues in contact with ALA 473 (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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469B GLN* 3.5 15.9 + - - +
470B LEU* 2.7 9.2 - - - +
471B VAL 3.1 0.8 - - - +
472B ASN* 1.3 77.6 - - - +
474B LYS* 1.3 52.1 + - - +
475B HIS* 2.5 54.1 + - + +
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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