Contacts of the helix formed by residues 460 - 467 (chain D) in PDB entry 1Y8Q
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 460 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458D LYS 3.8 2.9 + - - +
459D VAL* 1.3 82.6 - - - +
461D VAL* 1.3 64.8 + - - +
462D LEU* 3.3 10.0 + - - +
463D THR* 3.2 25.2 + - - +
464D LEU* 3.3 17.2 + - - +
502D ASN 3.5 10.1 - - - -
503D HIS* 3.4 33.9 - - + +
504D LYS 3.7 12.6 - - - +
505D LYS* 4.2 18.2 - - + +
506D LEU* 4.0 3.2 - - - +
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Residues in contact with VAL 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460D THR* 1.3 72.9 - - - +
462D LEU* 1.3 64.2 + - - +
464D LEU* 3.4 2.9 + - + +
465D GLN* 3.1 21.3 + - - +
490D LEU* 3.4 31.9 - - + +
491D ILE* 3.4 17.9 - - + +
498D THR 5.9 0.2 - - - +
501D ASN* 3.3 22.0 - - + +
502D ASN* 3.3 3.4 + - - +
504D LYS 3.3 17.4 + - - +
506D LEU* 3.9 19.3 - - + -
509D PHE* 3.5 24.5 - - + -
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Residues in contact with LEU 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460D THR* 3.1 7.4 - - - +
461D VAL* 1.3 75.2 - - - +
463D THR* 1.3 60.0 + - - +
465D GLN* 2.9 9.2 + - - +
466D ASP* 2.8 69.1 + - + +
502D ASN* 2.8 49.1 + - + +
503D HIS* 4.7 6.1 - - + +
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Residues in contact with THR 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459D VAL* 3.7 19.5 - - + -
460D THR* 3.2 17.0 + - - +
462D LEU* 1.3 80.2 - - - +
464D LEU* 1.3 63.5 + - - +
466D ASP* 5.0 0.7 - - - -
467D LYS* 2.9 53.0 + - + +
468D ILE* 3.2 12.5 + - + +
543D GLU* 3.4 31.2 + - + +
544D PHE* 5.2 1.1 - - + -
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Residues in contact with LEU 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454D LEU* 5.8 1.6 - - + -
459D VAL* 4.4 0.6 - - - +
460D THR 3.3 10.4 + - - +
461D VAL* 3.5 9.9 - - + +
462D LEU 3.2 0.4 - - - -
463D THR* 1.3 78.5 - - - +
465D GLN* 1.3 57.5 + - - +
468D ILE* 3.2 29.9 - - + +
469D VAL* 2.8 48.8 + - + +
480D VAL* 4.7 5.6 - - + -
490D LEU* 4.3 11.0 - - + -
491D ILE* 4.1 16.6 - - + -
506D LEU* 3.8 27.8 - - + -
517D LEU* 4.0 27.1 - - + -
530D ILE* 5.3 7.0 - - + -
532D ILE* 6.1 1.8 - - + -
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Residues in contact with GLN 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461D VAL* 3.1 7.6 + - - +
462D LEU* 2.9 14.3 + - - +
464D LEU* 1.3 79.1 - - - +
466D ASP* 1.3 71.7 + - - +
469D VAL* 3.8 4.2 - - - +
470D LYS* 2.9 60.8 + - + +
478D PRO* 4.3 6.5 - - + -
491D ILE* 3.1 45.9 - - + +
492D SER 5.2 1.5 - - - +
498D THR* 5.4 2.9 + - - -
502D ASN* 4.8 9.9 + - - +
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Residues in contact with ASP 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462D LEU* 2.8 47.4 + - + +
463D THR* 5.0 0.2 - - - -
465D GLN* 1.3 92.0 + - - +
467D LYS* 1.3 64.8 + - + +
470D LYS* 3.8 12.0 + - - +
471D GLU* 2.9 34.2 + - - +
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Residues in contact with LYS 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D ASP* 2.8 30.8 + - - +
463D THR* 2.9 33.8 + - + +
466D ASP* 1.3 82.2 - - + +
468D ILE* 1.3 63.7 + - - +
471D GLU* 3.5 21.8 + - - +
472D LYS* 3.1 25.8 + - - +
543D GLU* 3.7 18.6 - - - +
544D PHE* 3.7 25.4 - - + -
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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