Contacts of the strand formed by residues 464 - 468 (chain B) in PDB entry 1OH7
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 LYS 464 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451B GLU* 3.5 20.4 - - - +
455B ARG* 5.2 1.1 - - - +
462B THR* 3.1 27.3 + - - +
463B LEU* 1.3 75.7 - - - +
465B VAL* 1.3 69.4 + - - +
466B GLY 5.3 0.2 - - - +
475B ILE* 3.4 5.9 - - - +
476B GLN* 2.8 55.9 + - + +
18F G 3.5 9.3 + - - -
19F T 2.5 38.8 + - - -
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Residues in contact with VAL 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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447B LEU* 4.0 17.3 - - + +
450B LEU* 4.1 15.5 - - + -
451B GLU* 3.5 39.2 + - + +
463B LEU* 5.2 0.2 - - + -
464B LYS* 1.3 83.8 - - - +
466B GLY* 1.3 68.2 + - - +
473B TYR* 3.9 19.7 - - + -
474B TYR 3.4 10.3 - - - +
475B ILE* 4.3 10.5 - - + -
506B LEU* 4.4 11.2 - - + -
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Residues in contact with GLY 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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464B LYS* 4.2 0.8 - - - +
465B VAL* 1.3 73.7 - - - +
467B PHE* 1.3 61.1 + - - +
473B TYR* 3.1 29.8 - - - -
474B TYR* 3.1 36.4 + - - -
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Residues in contact with PHE 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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466B GLY* 1.3 73.9 - - - +
468B ASN* 1.3 79.4 + - - +
469B ALA* 4.5 4.7 - - - -
472B GLY* 3.3 36.8 - - - -
473B TYR* 3.5 33.4 - + + -
474B TYR* 3.7 9.7 + - - -
510B GLU* 4.7 2.5 - - + -
514B LEU* 3.9 35.4 - - + -
5E G 4.9 1.5 + - - -
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Residues in contact with ASN 468 (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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467B PHE* 1.3 84.2 - - - +
469B ALA* 1.3 56.7 + - - +
470B VAL* 3.4 12.4 + - - +
471B HIS* 3.2 22.3 + - - +
472B GLY* 2.8 37.2 + - - -
474B TYR* 3.7 13.3 + - - -
500B ARG* 2.9 32.1 - - - +
5E G 3.4 35.1 + - - +
6E C 3.7 7.5 + - - -
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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