Contacts of the helix formed by residues 459 - 470 (chain N) in PDB entry 6AH0
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 ASN 459 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450N ARG* 6.3 3.4 - - - +
456N ALA* 3.4 13.8 + - - +
457N ARG 3.3 0.4 - - - -
458N GLU* 1.3 71.4 - - - +
460N ILE* 1.3 60.1 + - - +
461N PRO 3.1 1.6 - - - -
462N THR* 3.0 19.6 + - - +
463N ASP* 3.3 8.5 + - - -
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Residues in contact with ILE 460 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456N ALA 3.5 7.0 + - - -
457N ARG* 3.3 12.5 + - - +
459N ASN* 1.3 79.1 - - - +
461N PRO* 1.3 55.0 - - - +
463N ASP* 3.4 3.1 + - - +
464N ARG* 2.9 23.4 + - - -
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Residues in contact with PRO 461 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457N ARG 4.1 2.8 - - - -
458N GLU 3.4 10.6 - - - +
459N ASN 3.1 1.2 - - - -
460N ILE* 1.3 73.6 - - - +
462N THR* 1.3 54.4 + - - +
464N ARG* 3.2 3.0 + - - +
465N HIS* 2.5 32.2 + - - -
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Residues in contact with THR 462 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458N GLU 4.0 3.8 + - - -
459N ASN* 3.0 13.0 + - - +
461N PRO* 1.3 77.0 - - - +
463N ASP* 1.3 51.5 + - - +
465N HIS* 3.1 2.7 + - - +
466N ILE* 2.4 35.0 + - - -
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Residues in contact with ASP 463 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459N ASN 3.3 10.5 + - - -
460N ILE* 3.4 4.0 + - - +
462N THR* 1.3 74.6 - - - +
464N ARG* 1.3 54.4 + - - +
466N ILE* 4.0 2.5 - - - +
467N TRP* 2.5 34.3 + - - -
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Residues in contact with ARG 464 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460N ILE 2.9 16.2 + - - -
461N PRO* 3.2 6.5 + - - -
463N ASP* 1.3 75.6 - - - +
465N HIS* 1.3 59.1 + - - +
467N TRP* 4.3 1.1 - - - +
468N ILE* 3.3 16.1 + - - -
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Residues in contact with HIS 465 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461N PRO 2.5 18.9 + - - -
462N THR* 3.3 3.8 - - - +
464N ARG* 1.3 71.9 - - - +
466N ILE* 1.3 52.8 + - - +
468N ILE* 3.4 2.0 + - - +
469N THR* 2.7 32.2 + - - -
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Residues in contact with ILE 466 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462N THR 2.4 25.5 + - - -
463N ASP* 3.4 3.4 - - - +
465N HIS* 1.3 64.4 - - - +
467N TRP* 1.3 56.2 + - - +
469N THR* 2.7 9.1 + - - +
470N ALA* 2.4 40.5 + - - +
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Residues in contact with TRP 467 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463N ASP 2.5 19.6 + - - -
464N ARG* 4.3 1.6 - - - +
466N ILE* 1.3 68.9 - - - +
468N ILE* 1.3 56.1 + - - +
471N ALA* 3.1 27.5 - - - +
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Residues in contact with ILE 468 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464N ARG 3.3 14.3 + - - -
465N HIS* 3.6 4.3 - - - +
466N ILE 2.9 1.2 + - - -
467N TRP* 1.3 79.1 - - - +
469N THR* 1.3 61.1 + - - +
471N ALA* 3.5 7.3 + - - -
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Residues in contact with THR 469 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465N HIS 2.7 12.3 + - - -
466N ILE* 2.7 8.0 + - - +
468N ILE* 1.3 70.2 - - - +
470N ALA* 1.3 65.3 + - - +
471N ALA* 3.4 0.9 + - - -
474N GLU* 5.7 0.2 - - - -
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Residues in contact with ALA 470 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466N ILE* 2.4 26.1 + - - +
469N THR* 1.3 67.9 - - - +
471N ALA* 1.3 65.8 + - - +
472N LYS 3.4 0.2 + - - -
473N LEU 4.3 0.2 + - - -
474N GLU* 3.2 32.8 + - - +
475N GLU* 3.3 6.4 + - - +
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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