Contacts of the helix formed by residues 470 - 477 (chain A) in PDB entry 1NK0
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 GLN 470 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400A LEU* 3.2 30.4 + - + +
401A LEU* 3.8 0.5 - - - +
465A LEU* 2.7 29.0 + - + +
468A ASN* 3.0 40.7 + - + +
469A GLU* 1.3 76.8 - - - +
471A ASP* 1.3 64.7 + - - +
472A ARG 3.3 2.5 - - - -
473A LEU* 3.2 19.7 + - + +
474A LEU* 3.1 22.0 + - - +
768A HIS 3.2 28.5 + - - +
769A ARG* 4.1 3.0 - - - +
770A ARG* 3.7 19.6 - - - +
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Residues in contact with ASP 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A LEU* 5.2 6.5 - - + +
465A LEU* 3.5 11.1 + - + -
466A ARG* 2.8 57.2 + - + +
469A GLU* 3.9 7.3 - - - -
470A GLN* 1.3 80.0 + - - +
472A ARG* 1.3 71.2 + - - +
474A LEU* 3.4 3.8 + - - +
475A VAL* 3.1 34.6 + - + +
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Residues in contact with ARG 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A ARG* 6.2 0.2 - - - +
469A GLU 5.3 1.7 + - - +
470A GLN 3.3 0.4 - - - -
471A ASP* 1.3 87.7 + - - +
473A LEU* 1.3 59.9 + - - +
475A VAL* 4.8 1.8 - - - -
476A GLU* 2.7 78.2 + - + +
477A LEU* 3.4 1.4 + - - +
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Residues in contact with LEU 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A LEU* 3.7 27.8 - - + -
469A GLU 5.3 0.8 + - - +
470A GLN* 3.2 21.5 + - + +
472A ARG* 1.3 79.0 - - - +
474A LEU* 1.3 57.3 + - - +
477A LEU* 3.2 41.7 - - + +
478A GLU* 2.9 27.4 + - + +
767A LEU* 3.6 33.7 - - + +
768A HIS 3.8 5.2 - - - +
769A ARG* 3.6 39.7 - - + +
802A ASP* 4.8 0.7 - - - +
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Residues in contact with LEU 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A SER 5.6 0.2 - - - +
392A PHE* 4.1 11.4 - - + -
393A ASP 4.4 0.4 - - - +
396A LEU* 3.8 29.8 - - + -
397A ALA* 3.9 11.7 - - + +
400A LEU* 3.7 14.8 - - + +
462A LEU* 4.0 18.6 - - + -
465A LEU* 3.5 25.8 - - + -
470A GLN 3.1 10.3 + - - +
471A ASP* 3.7 6.1 - - - +
472A ARG 3.1 0.2 - - - -
473A LEU* 1.3 79.4 - - - +
475A VAL* 1.3 64.9 + - + +
478A GLU* 3.6 3.1 + - + -
479A GLN* 2.9 62.7 + - + +
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Residues in contact with VAL 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A SER 4.8 6.1 - - - +
462A LEU* 5.2 8.7 - - + -
471A ASP* 3.1 18.6 + - + +
472A ARG* 4.8 1.8 - - - -
474A LEU* 1.3 85.8 - - + +
476A GLU* 1.3 66.1 + - + +
479A GLN* 4.0 19.4 + - - +
480A PRO* 3.3 18.6 - - - +
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Residues in contact with GLU 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472A ARG* 2.7 72.6 + - + +
475A VAL* 1.3 83.3 - - + +
477A LEU* 1.3 57.3 + - + +
480A PRO* 3.6 12.2 - - - +
809A ILE* 3.7 12.6 - - - +
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Residues in contact with LEU 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472A ARG 3.4 1.0 + - - +
473A LEU* 3.2 40.2 + - + +
475A VAL 3.6 0.4 - - - -
476A GLU* 1.3 81.2 - - + +
478A GLU* 1.3 73.0 + - - +
479A GLN 3.5 0.9 - - - -
480A PRO* 3.3 2.1 - - - +
481A LEU* 3.0 24.9 + - - +
767A LEU* 4.2 17.7 - - + -
769A ARG* 3.8 17.9 - - - +
802A ASP* 4.2 3.6 - - - +
805A LYS* 4.0 14.1 - - + -
806A LYS* 3.7 42.2 - - + +
809A ILE* 3.3 12.7 - - + +
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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