Contacts of the helix formed by residues 455 - 466 (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 455 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453A GLN* 5.4 2.7 - - - +
454A VAL* 1.3 77.7 - - - +
456A GLU* 1.3 67.9 + - - +
457A ASP* 3.7 13.4 + - + +
458A ALA* 3.1 37.9 + - + +
459A VAL* 3.3 17.1 + - - +
496A ILE* 3.8 7.4 - - - -
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Residues in contact with GLU 456 (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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455A THR* 1.3 76.1 + - - +
457A ASP* 1.3 58.7 + - - +
459A VAL* 3.2 2.5 + - - +
460A ARG* 2.9 66.1 + - + +
496A ILE* 3.1 53.5 - - + +
499A ARG* 5.6 1.6 - - - +
500A LEU* 4.3 12.2 - - + +
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Residues in contact with ASP 457 (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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455A THR* 3.2 13.6 + - + +
456A GLU* 1.3 79.4 - - - +
458A ALA* 1.3 58.7 + - - +
460A ARG* 3.5 9.1 + - - +
461A ARG* 2.9 46.4 + - - +
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Residues in contact with ALA 458 (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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453A GLN 5.5 3.4 - - - +
454A VAL* 5.6 1.3 - - + -
455A THR* 3.1 29.8 + - + +
457A ASP* 1.3 81.1 + - - +
459A VAL* 1.3 55.5 + - + +
461A ARG* 3.3 14.7 - - - +
462A TYR* 2.7 38.8 - - + +
477A PHE* 6.0 5.4 - - + -
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Residues in contact with VAL 459 (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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454A VAL* 4.6 4.5 - - + -
455A THR 3.4 15.7 - - - +
456A GLU* 3.2 8.4 + - - +
458A ALA* 1.3 77.9 - - + +
460A ARG* 1.3 63.7 + - + +
462A TYR* 3.2 21.1 + - + +
463A LEU* 3.4 16.4 + - + +
473A LEU* 4.3 21.3 - - + +
477A PHE* 6.5 1.3 - - + -
493A LEU* 3.4 29.2 - - + -
496A ILE* 4.6 5.8 - - + -
497A LEU* 3.6 31.2 - - + -
500A LEU* 5.6 0.2 - - + -
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Residues in contact with ARG 460 (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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456A GLU* 2.9 47.5 + - + +
457A ASP* 3.9 6.5 - - - +
459A VAL* 1.3 76.8 - - + +
461A ARG* 1.3 53.9 + - - +
463A LEU* 3.2 2.6 + - - +
464A THR* 2.6 46.7 + - + +
500A LEU* 3.7 31.1 - - + +
515A LEU* 3.9 26.0 - - + +
517A GLU* 5.9 9.1 - - - +
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Residues in contact with ARG 461 (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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457A ASP* 2.9 36.0 + - - +
458A ALA* 3.3 11.9 - - - +
460A ARG* 1.3 78.1 - - - +
462A TYR* 1.3 65.0 + - + +
464A THR* 2.5 35.3 + - - +
465A ARG* 3.1 61.0 + - - +
517A GLU* 5.3 5.9 + - - -
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Residues in contact with TYR 462 (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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458A ALA* 2.7 38.9 - - + +
459A VAL* 3.2 11.4 + - + +
460A ARG 3.2 0.2 - - - -
461A ARG* 1.3 81.8 - - + +
463A LEU* 1.3 51.1 + - - +
465A ARG* 3.2 11.9 + - - +
466A LYS* 2.5 43.5 + - - +
468A MET* 3.7 27.0 - - - +
473A LEU* 4.7 9.0 - - + -
476A LYS* 4.2 30.0 + - + +
477A PHE* 4.8 21.9 - + - -
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Residues in contact with LEU 463 (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* 3.4 20.4 + - + +
460A ARG* 3.2 7.1 + - - +
462A TYR* 1.3 75.7 - - - +
464A THR* 1.3 62.8 + - - +
465A ARG 3.4 0.5 + - - -
466A LYS 3.4 13.8 + - - +
467A PRO* 4.1 2.3 - - - +
468A MET* 3.9 20.6 - - + +
473A LEU* 4.4 12.1 - - + -
497A LEU* 4.9 2.9 - - + -
500A LEU* 3.6 20.4 - - + -
513A PHE* 3.3 40.2 - - + +
514A SER* 4.3 2.6 - - - -
515A LEU* 3.4 50.5 + - + +
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Residues in contact with THR 464 (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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460A ARG* 2.6 23.5 + - + +
461A ARG* 2.5 45.9 + - - +
463A LEU* 1.3 76.1 - - - +
465A ARG* 1.3 60.3 + - - +
515A LEU* 3.8 30.6 - - + +
516A LYS* 5.9 1.0 - - - +
517A GLU* 4.9 19.5 - - + +
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Residues in contact with ARG 465 (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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461A ARG* 3.1 57.0 + - + +
462A TYR* 3.8 11.5 - - - +
463A LEU 4.2 0.2 - - - -
464A THR* 1.3 83.4 - - - +
466A LYS* 1.3 64.8 + - + +
467A PRO* 4.7 0.5 - - - +
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Residues in contact with LYS 466 (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 2.5 33.0 + - - +
463A LEU* 3.4 6.0 - - - -
465A ARG* 1.3 79.3 - - + +
467A PRO* 1.3 90.2 - - + +
468A MET* 3.4 9.8 - - + +
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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