Contacts of the helix formed by residues 469 - 477 (chain A) in PDB entry 1ONV
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 THR 469 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468A MET* 1.3 77.0 - - - +
470A THR* 1.3 66.6 + - - +
471A LYS* 3.6 9.6 + - - +
472A ASP* 3.1 22.3 + - + +
473A LEU* 2.9 25.9 + - - +
510A LYS* 5.6 2.9 - - + +
511A MET* 3.3 19.1 - - - +
512A HIS* 3.1 35.4 - - + +
513A PHE* 3.8 7.2 - - - -
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Residues in contact with THR 470 (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 THR* 1.3 73.5 - - - +
471A LYS* 1.3 68.9 + - - +
473A LEU* 3.3 5.8 + - + +
474A LEU* 3.0 25.1 + - - +
513A PHE* 3.0 38.9 - - + -
950B ALA* 4.4 3.7 + - - -
953B LEU* 3.6 29.0 - - + +
954B GLU* 3.5 42.9 + - + +
957B LEU* 4.4 7.4 - - + -
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Residues in contact with LYS 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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469A THR* 3.2 8.6 + - - +
470A THR* 1.3 82.6 + - - +
472A ASP* 1.3 57.9 + - - +
474A LEU* 3.5 1.9 + - - +
475A LYS* 3.0 28.2 + - - +
510A LYS* 6.0 4.3 - - - +
947B ASP* 3.4 31.1 + - - +
950B ALA* 3.5 22.5 - - + +
951B LYS* 3.9 24.2 - - - +
954B GLU* 5.0 10.3 - - - +
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Residues in contact with ASP 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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468A MET* 2.9 34.6 - - + +
469A THR* 3.1 24.3 + - + +
471A LYS* 1.3 77.0 - - - +
473A LEU* 1.3 66.7 + - - +
475A LYS* 3.3 27.5 + - - +
476A LYS* 3.3 24.1 + - - +
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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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459A VAL* 4.3 18.4 - - + -
462A TYR* 4.7 11.7 - - + -
463A LEU* 4.4 19.1 - - + -
468A MET* 4.1 28.7 - - + -
469A THR 2.9 25.1 + - - +
470A THR* 3.6 9.6 - - + +
472A ASP* 1.3 78.5 - - - +
474A LEU* 1.3 61.2 + - - +
476A LYS* 3.2 24.1 - - + +
477A PHE* 4.0 5.0 + - - +
493A LEU* 5.7 8.1 - - + +
497A LEU* 4.2 29.6 - - + -
513A PHE* 4.9 6.7 - - + -
953B LEU* 4.7 5.2 - - + -
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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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470A THR 3.0 16.4 + - - +
471A LYS 3.9 4.5 - - - +
473A LEU* 1.3 74.4 - - - +
475A LYS* 1.3 55.9 + - - +
477A PHE* 3.1 4.6 + - - +
478A GLN* 2.6 68.7 + - + +
489A THR* 4.8 8.9 - - + +
490A VAL* 3.6 21.1 - - + -
493A LEU* 5.9 7.0 - - + -
949B MET* 3.1 42.2 - - + +
950B ALA* 3.4 16.2 - - + +
953B LEU* 4.7 10.9 - - + +
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Residues in contact with LYS 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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471A LYS 3.0 20.3 + - - +
472A ASP* 3.5 27.5 + - - +
473A LEU 3.2 0.2 - - - -
474A LEU* 1.3 77.0 - - - +
476A LYS* 1.3 66.9 + - - +
477A PHE 3.2 0.5 + - - -
478A GLN* 3.5 25.9 + - + +
479A THR 5.0 0.5 + - - -
480A LYS* 5.2 4.3 + - - +
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Residues in contact with LYS 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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462A TYR* 4.2 34.2 + - + +
468A MET* 4.2 19.1 - - + -
472A ASP* 3.3 22.0 - - - +
473A LEU* 3.2 17.9 - - + +
474A LEU 3.1 0.4 - - - -
475A LYS* 1.3 81.1 - - + +
477A PHE* 1.3 86.3 + - + +
480A LYS* 4.1 14.4 - - - +
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Residues in contact with PHE 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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452A VAL* 3.3 27.1 - - + -
453A GLN 4.9 7.0 - - - -
454A VAL* 4.4 26.2 - - + -
458A ALA* 6.0 3.8 - - + -
459A VAL* 6.5 1.3 - - + -
462A TYR* 4.8 20.4 - + - -
473A LEU 4.7 3.8 - - - +
474A LEU* 3.1 6.1 + - - +
476A LYS* 1.3 97.0 - - + +
478A GLN* 1.3 64.4 + - - +
479A THR 3.4 2.7 - - - +
480A LYS* 4.7 4.9 - - + +
482A THR* 3.5 35.3 + - + +
489A THR* 3.1 24.7 + - + +
493A LEU* 5.9 5.8 - - + -
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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