Contacts of the helix formed by residues 460 - 467 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458B LYS 3.6 2.4 + - - +
459B VAL* 1.3 82.9 - - - +
461B VAL* 1.3 64.0 + - - +
462B LEU* 3.3 6.1 + - - +
463B THR* 3.2 26.2 + - - -
464B LEU* 3.1 18.7 + - - +
502B ASN 3.4 12.4 + - - +
503B HIS* 3.7 23.1 - - - +
504B LYS 3.5 7.0 - - - -
505B LYS* 4.1 20.6 - - + +
506B LEU* 4.0 2.9 - - - +
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Residues in contact with VAL 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B THR* 1.3 74.9 - - - +
462B LEU* 1.3 57.6 + - - +
464B LEU* 3.3 4.3 + - + +
465B GLN* 2.8 28.1 + - + +
490B LEU* 3.7 21.8 - - + +
491B ILE* 3.7 26.7 - - + -
498B THR 5.6 0.2 - - - +
501B ASN* 3.2 30.3 - - + +
502B ASN* 3.6 6.8 + - - +
504B LYS 3.2 11.5 + - - +
506B LEU* 4.1 16.8 - - + -
509B PHE* 3.7 21.5 - - + -
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Residues in contact with LEU 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B THR* 3.1 4.9 - - - +
461B VAL* 1.3 75.5 - - - +
463B THR* 1.3 70.8 + - - +
465B GLN* 3.6 4.0 - - - +
466B ASP* 2.8 48.3 + - + +
502B ASN* 3.2 48.8 + - + +
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Residues in contact with THR 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459B VAL* 4.0 17.0 - - + -
460B THR* 3.2 22.8 + - - -
462B LEU* 1.3 85.7 - - - +
464B LEU* 1.3 59.7 + - - +
466B ASP* 5.1 0.4 - - - -
467B LYS* 2.8 46.5 + - + +
468B ILE* 3.2 11.4 + - + -
543B GLU* 3.3 32.0 + - + +
544B PHE* 5.5 0.9 - - + -
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Residues in contact with LEU 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B LEU* 5.6 2.2 - - + -
459B VAL* 4.3 3.5 - - + +
460B THR 3.1 14.1 + - - +
461B VAL* 3.5 10.1 - - - +
463B THR* 1.3 78.2 - - - +
465B GLN* 1.3 56.8 + - - +
468B ILE* 3.6 27.5 - - + +
469B VAL* 2.9 51.1 + - + +
480B VAL* 4.7 4.3 - - + -
490B LEU* 4.0 22.0 - - + -
491B ILE* 4.3 12.1 - - + -
506B LEU* 3.9 26.0 - - + -
517B LEU* 4.2 19.3 - - + -
530B ILE* 5.2 6.1 - - + -
532B ILE* 5.9 2.9 - - + -
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Residues in contact with GLN 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461B VAL* 2.8 17.6 + - + +
462B LEU* 3.6 3.8 - - - +
464B LEU* 1.3 78.3 - - - +
466B ASP* 1.3 79.1 + - - +
469B VAL* 3.7 3.7 - - - +
470B LYS* 3.0 49.2 + - + +
478B PRO* 4.6 4.7 - - + -
491B ILE* 2.9 46.3 - - + +
492B SER 4.9 1.7 - - - +
498B THR* 4.7 4.5 + - - -
502B ASN* 4.2 22.2 + - - +
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Residues in contact with ASP 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462B LEU* 2.8 42.4 + - + +
463B THR* 5.1 0.2 - - - -
465B GLN* 1.3 89.7 + - - +
467B LYS* 1.3 63.8 + - + +
470B LYS* 3.3 31.3 + - - +
471B GLU* 3.0 31.4 + - - +
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Residues in contact with LYS 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B ASP* 4.6 13.2 - - - +
463B THR* 2.8 29.9 + - + +
466B ASP* 1.3 79.4 - - + +
468B ILE* 1.3 58.4 + - - +
471B GLU* 3.5 23.8 + - - +
472B LYS* 3.1 23.0 + - - +
543B GLU* 3.7 29.4 + - - +
544B PHE* 3.4 32.2 - - + -
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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