Contacts of the helix formed by residues 465 - 477 (chain B) in PDB entry 3NAU
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 465 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463B PHE 3.3 4.5 + - - +
464B PRO* 1.3 76.4 - - - +
466B ASP* 1.3 61.6 + - - +
467B ALA* 3.3 13.0 + - - +
468B GLU* 2.7 40.4 + - - +
469B VAL* 3.1 6.6 + - - +
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Residues in contact with ASP 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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465B ASP* 1.3 70.6 - - - +
467B ALA* 1.3 61.2 + - - +
468B GLU 3.3 0.2 - - - -
469B VAL* 3.9 9.8 - - - +
470B TYR* 3.1 25.6 + - - +
480B ARG* 3.6 30.7 + - - +
484B LYS* 6.1 0.4 - - - +
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Residues in contact with ALA 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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465B ASP* 3.1 12.8 + - - +
466B ASP* 1.3 78.7 + - - +
468B GLU* 1.3 61.5 + - - +
470B TYR* 3.4 11.3 - - + +
471B ARG* 3.0 26.5 + - - +
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Residues in contact with GLU 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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457A SER* 2.4 29.3 + - - +
460A GLN* 3.9 14.2 + - - +
464B PRO* 3.6 19.3 - - + -
465B ASP* 2.7 29.4 + - - +
467B ALA* 1.3 72.7 - - - +
469B VAL* 1.3 56.8 + - - +
471B ARG* 3.1 42.8 + - - +
472B LEU* 3.0 27.9 + - - +
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Residues in contact with VAL 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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464B PRO* 3.8 28.5 - - + +
465B ASP 3.1 13.3 + - - +
466B ASP* 4.2 10.1 - - - +
468B GLU* 1.3 73.6 - - - +
470B TYR* 1.3 61.0 + - - +
472B LEU* 3.1 7.8 + - - +
473B ILE* 2.9 37.9 + - + +
480B ARG* 4.3 22.4 - - + +
483B ILE* 4.1 28.3 - - + -
484B LYS* 4.5 19.3 - - + +
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Residues in contact with TYR 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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466B ASP 3.1 21.0 + - - +
467B ALA* 3.4 10.3 - - - +
469B VAL* 1.3 75.8 - - - +
471B ARG* 1.3 60.7 + - - +
473B ILE* 3.3 18.6 + - + +
474B GLU* 3.1 57.0 + - + +
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Residues in contact with ARG 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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453A HIS* 4.2 16.2 + - - -
456A ALA* 5.7 4.4 - - - +
457A SER* 4.2 6.5 + - - +
460A GLN* 4.8 3.2 - - - +
467B ALA 3.0 14.2 + - - +
468B GLU* 3.1 46.1 + - - +
470B TYR* 1.3 76.2 - - + +
472B LEU* 1.3 70.3 + - - +
474B GLU* 3.4 20.7 - - + +
475B VAL* 3.1 52.3 + - + +
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Residues in contact with LEU 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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453A HIS* 3.6 37.7 - - + +
454A LEU* 4.3 10.5 - - + -
457A SER* 3.7 14.6 - - - +
464B PRO* 4.8 3.8 - - + -
468B GLU* 3.0 34.3 + - - +
469B VAL* 3.1 13.4 + - - +
471B ARG* 1.3 82.2 - - - +
473B ILE* 1.3 54.5 + - - +
475B VAL* 3.8 3.4 - - + -
476B THR* 2.7 45.7 + - + +
483B ILE* 4.0 18.2 - - + -
487B PHE* 4.0 21.5 - - + -
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Residues in contact with ILE 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 VAL* 2.9 29.9 + - + +
470B TYR* 3.3 20.8 + - + +
472B LEU* 1.3 74.8 - - - +
474B GLU* 1.3 62.4 + - + +
476B THR* 4.1 0.2 - - - -
477B GLY* 2.6 35.4 + - - -
478B LEU 3.5 24.9 - - - +
479B ALA* 5.1 0.2 - - - -
480B ARG* 4.4 19.7 - - + +
483B ILE* 3.6 8.9 - - + +
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Residues in contact with GLU 474 (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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470B TYR* 3.1 52.0 + - + +
471B ARG* 3.4 25.4 - - + +
473B ILE* 1.3 81.8 - - + +
475B VAL* 1.3 58.1 + - + +
477B GLY 4.7 0.4 - - - -
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Residues in contact with VAL 475 (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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449A GLU* 4.5 7.3 - - - +
453A HIS* 3.3 48.9 + - + +
471B ARG* 3.1 34.2 + - + +
472B LEU* 3.4 13.0 - - - +
474B GLU* 1.3 78.5 - - + +
476B THR* 1.3 71.2 + - + +
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Residues in contact with THR 476 (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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449A GLU* 6.5 0.2 - - - -
450A GLN* 2.8 52.5 + - + +
453A HIS* 3.5 21.1 - - + -
454A LEU* 4.8 1.1 - - + -
472B LEU* 2.7 38.3 + - + +
475B VAL* 1.3 90.0 - - + +
477B GLY* 1.3 56.8 + - - +
478B LEU* 3.0 28.6 + - + +
483B ILE* 4.4 1.0 - - - +
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Residues in contact with GLY 477 (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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450A GLN* 5.0 0.4 - - - -
473B ILE* 2.6 24.7 + - - -
474B GLU 4.7 0.6 - - - -
475B VAL 3.9 0.2 - - - -
476B THR* 1.3 72.7 + - - +
478B LEU* 1.3 62.8 + - - +
479B ALA 4.0 0.5 + - - -
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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