Contacts of the strand formed by residues 2023 - 2027 (chain B) in PDB entry 4ZWJ
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 VAL2023 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2017B VAL* 4.4 0.2 - - - +
2018B SER* 3.2 34.7 + - - -
2020B ASP* 4.6 0.9 + - - +
2022B SER* 1.3 84.5 + - - +
2024B THR* 1.3 72.1 + - - +
2025B ILE* 4.8 2.7 - - + +
2046B VAL* 4.8 12.8 - - + -
2047B LEU 3.6 7.6 - - - +
2048B VAL* 4.9 3.1 - - + +
2053B VAL* 4.7 11.9 - - + -
2058B VAL* 4.5 28.5 - - + -
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Residues in contact with THR2024 (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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2015B LYS* 4.0 13.2 - - + +
2016B LYS 3.6 15.7 - - - +
2017B VAL* 3.6 30.8 - - + +
2021B LYS 5.3 1.0 - - - -
2022B SER 4.6 3.6 + - - -
2023B VAL* 1.3 80.3 + - - +
2025B ILE* 1.3 60.1 + - - +
2026B TYR* 3.3 29.4 - - + +
2046B VAL* 3.5 1.6 - - - -
2047B LEU* 2.9 49.5 + - + +
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Residues in contact with ILE2025 (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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2015B LYS* 3.2 7.2 - - - +
2016B LYS* 3.0 55.0 + - + +
2023B VAL* 4.3 4.0 - - + +
2024B THR* 1.3 73.0 - - - +
2026B TYR* 1.3 70.0 + - - +
2027B LEU* 4.8 18.4 - - + -
2045B VAL 4.1 1.6 - - - +
2046B VAL* 3.8 24.5 - - + -
2060B VAL* 4.8 14.1 - - + -
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Residues in contact with TYR2026 (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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2013B ILE* 5.1 2.2 - - + -
2014B PHE 3.7 7.9 - - - +
2015B LYS* 3.6 39.6 + - + +
2024B THR* 3.3 32.7 - - + +
2025B ILE* 1.3 76.8 - - - +
2027B LEU* 1.3 73.9 + - - +
2044B GLY* 3.8 0.6 - - - -
2045B VAL* 2.8 53.1 + - + +
2047B LEU* 3.8 25.0 - - + +
2108B LEU* 4.2 22.2 - - + -
2112B LEU* 3.5 31.0 - - + +
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Residues in contact with LEU2027 (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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2013B ILE* 3.5 5.1 - - - +
2014B PHE* 3.0 42.4 + - + +
2015B LYS* 4.9 0.4 - - - +
2025B ILE* 4.8 20.4 - - + -
2026B TYR* 1.3 81.8 - - - +
2028B GLY* 1.3 64.2 + - - +
2029B LYS 3.4 13.7 - - - +
2030B ARG* 6.3 0.9 - - + -
2032B TYR* 3.8 8.3 - - + +
2042B VAL* 3.6 25.1 - - + -
2043B ASP 3.4 22.9 - - - +
2044B GLY* 4.2 2.0 - - - -
2104B LEU* 4.7 0.2 - - - -
2108B LEU* 5.9 0.2 - - - -
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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