Contacts of the helix formed by residues 484 - 492 (chain A) in PDB entry 2ZNS
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 484 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471A ASP* 3.5 11.9 - - - +
473A LYS* 3.7 17.4 - - - +
475A GLY* 3.3 16.3 - - - -
476A ALA 2.9 34.3 + - - -
482A GLU 5.7 0.2 - - - -
483A TRP* 1.3 73.7 - - - +
485A GLY* 1.3 69.7 + - - +
487A VAL* 3.6 2.3 + - - +
488A LYS* 3.1 21.2 + - - -
672A ASP* 2.8 28.8 + - - +
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Residues in contact with GLY 485 (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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469A VAL* 3.5 6.4 - - - +
471A ASP* 3.1 21.4 + - - -
473A LYS* 3.0 22.9 - - - -
474A TYR 3.9 2.7 - - - -
484A ASN* 1.3 81.4 - - - +
486A MET* 1.3 66.7 + - - -
488A LYS* 3.3 7.2 + - - +
489A GLU* 3.3 14.7 + - - +
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Residues in contact with MET 486 (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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422A THR* 3.9 18.3 - - + +
423A THR* 3.9 18.4 - - - -
424A ILE* 3.5 16.6 - - + -
469A VAL* 3.6 25.4 - - + -
473A LYS 3.0 5.5 + - - -
474A TYR* 2.9 51.0 + - + +
485A GLY* 1.3 71.3 - - - -
487A VAL* 1.3 62.9 + - - +
489A GLU* 3.2 8.9 + - - +
490A LEU* 3.2 26.1 + - - +
498A ALA* 4.4 10.5 - - + -
500A ALA* 3.5 26.5 - - + -
502A LEU* 4.1 11.2 - - + -
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Residues in contact with VAL 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A TYR 3.6 12.8 - - - +
475A GLY* 4.1 4.3 - - - -
483A TRP* 3.6 28.5 - - + -
484A ASN 3.8 6.7 - - - +
485A GLY 3.1 0.8 - - - -
486A MET* 1.3 76.3 - - - +
488A LYS* 1.3 58.3 - - - +
490A LEU* 3.2 7.0 + - - +
491A ILE* 3.0 29.1 + - + +
502A LEU* 4.5 5.2 - - + -
508A ARG* 3.8 33.0 - - + +
511A VAL* 3.8 20.6 - - + -
512A ILE* 3.7 23.5 - - + +
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Residues in contact with LYS 488 (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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482A GLU* 6.0 3.1 - - - +
483A TRP* 3.7 21.9 - - + +
484A ASN* 3.1 31.2 + - - -
485A GLY 3.7 2.0 - - - +
487A VAL* 1.3 74.3 - - - +
489A GLU* 1.3 61.6 + - - +
491A ILE* 4.1 20.4 - - + -
492A ASP* 2.7 63.9 + - - +
494A ARG* 4.2 7.6 - - - +
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Residues in contact with GLU 489 (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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422A THR* 4.2 20.0 - - + +
469A VAL* 4.2 7.0 - - + +
470A PRO* 3.8 35.4 - - + +
485A GLY 3.3 13.9 + - - +
486A MET* 3.2 11.2 + - - +
488A LYS* 1.3 78.3 - - - +
490A LEU* 1.3 59.7 + - - +
492A ASP 3.7 0.2 + - - -
493A HIS 3.4 2.1 + - - -
494A ARG* 2.8 79.4 + - + +
495A ALA* 3.4 7.8 + - + -
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Residues in contact with LEU 490 (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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422A THR* 4.7 0.9 - - + -
486A MET 3.2 12.0 + - - +
487A VAL* 3.2 6.8 + - - +
489A GLU* 1.3 74.4 - - - +
491A ILE* 1.3 68.6 + - - +
493A HIS* 2.9 17.3 + - - -
495A ALA* 3.8 25.1 - - + +
497A LEU 4.0 5.2 - - - +
498A ALA* 3.9 25.1 - - + +
502A LEU* 4.9 1.1 - - + -
512A ILE* 3.7 33.2 - - + -
752A GLY* 3.6 32.1 - - - +
753A THR 3.8 1.6 - - - +
754A PRO* 3.5 31.4 - - + +
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Residues in contact with ILE 491 (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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483A TRP* 3.8 41.3 - - + -
487A VAL* 3.0 26.5 + - + +
488A LYS* 3.7 15.0 - - + +
490A LEU* 1.3 77.6 - - - +
492A ASP* 1.3 66.2 + - - +
493A HIS* 3.3 15.9 - - - -
511A VAL* 3.8 30.1 - - + +
512A ILE* 3.9 5.4 - - + +
754A PRO* 5.6 1.3 - - - -
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Residues in contact with ASP 492 (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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488A LYS* 2.7 53.2 + - - +
489A GLU 4.3 0.9 - - - +
491A ILE* 1.3 80.9 - - - +
493A HIS* 1.3 69.6 + - - +
494A ARG* 2.8 43.2 + - - +
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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