Contacts of the strand formed by residues 1482 - 1485 (chain B) in PDB entry 4BHW
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 ASP1482 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1475B VAL* 4.6 3.8 - - - -
1480B VAL* 3.4 8.3 - - - +
1481B HIS* 1.3 84.8 + - + +
1483B TYR* 1.3 57.5 + - - +
1484B LYS* 3.8 20.2 + - - +
1599B ARG* 2.7 81.1 + - - +
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Residues in contact with TYR1483 (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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1468B LYS* 3.7 21.6 - - + +
1471B LEU* 3.6 46.7 - - + -
1472B ASP* 2.7 35.2 + - - -
1475B VAL* 4.3 13.5 - - + -
1480B VAL* 4.5 3.4 - - + -
1482B ASP* 1.3 77.7 - - - +
1484B LYS* 1.3 73.3 + - - +
1596B PHE* 4.0 21.3 - + - -
1597B VAL 3.1 14.1 - - - +
1598B ILE* 3.9 11.0 - - + -
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Residues in contact with LYS1484 (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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1482B ASP* 3.8 29.2 + - - +
1483B TYR* 1.3 85.9 - - - +
1485B ASP* 1.3 66.6 + - - +
1488B LYS* 4.3 23.7 - - + +
1489B GLN* 3.3 27.8 - - + +
1492B GLU* 2.8 42.2 + - - +
1596B PHE* 3.7 3.9 - - - +
1597B VAL* 2.7 36.2 + - - +
1599B ARG* 3.8 8.3 - - - +
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Residues in contact with ASP1485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1484B LYS* 1.3 76.1 - - - +
1486B ILE* 1.3 63.8 + - - +
1487B PHE* 3.0 7.3 + - - +
1488B LYS* 2.8 42.5 + - - +
1489B GLN* 3.0 19.3 + - - +
1592B LYS* 3.1 49.3 + - + +
1593B GLU* 4.9 2.7 - - - -
1595B PHE 3.3 6.7 - - - -
1596B PHE* 4.8 1.8 - - - +
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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