Contacts of the strand formed by residues 2085 - 2092 (chain A) 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 TYR2085 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A GLU* 4.0 15.9 - - - -
2062A LEU* 5.2 7.6 - - + -
2064A CYS* 2.3 52.9 + - + +
2083A ASP 3.4 2.4 - - - -
2084A LEU* 1.3 80.9 - - - +
2086A PHE* 1.3 69.5 + - - +
2087A SER* 3.4 30.3 - - - -
2122A THR 4.9 6.4 + - - -
2124A PRO* 4.1 20.5 - - + +
2126A TYR* 3.2 32.8 - + - -
2127A LEU* 3.6 29.6 - - + -
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Residues in contact with PHE2086 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A GLU* 5.2 2.7 + - - +
240A SER* 5.6 11.4 - - - +
242A THR* 5.8 2.5 - - - -
2061A THR* 4.3 7.4 - - - -
2062A LEU 3.8 7.6 - - - -
2063A THR* 3.3 32.5 - - + -
2064A CYS 4.2 0.2 - - - +
2083A ASP* 4.9 12.1 - - + +
2085A TYR* 1.3 89.1 - - - +
2087A SER* 1.3 66.3 + - - +
2088A ARG* 3.5 46.2 - - + -
2162A GLU* 3.3 47.8 - - + -
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Residues in contact with SER2087 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2062A LEU* 2.5 62.9 + - - +
2085A TYR* 3.4 28.3 - - - -
2086A PHE* 1.3 78.9 - - - +
2088A ARG* 1.3 58.5 + - - +
2089A VAL* 5.6 1.1 - - - -
2121A LEU* 4.1 6.4 - - - +
2122A THR 5.0 1.9 + - - -
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Residues in contact with ARG2088 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2059A TYR* 5.2 6.1 - - + -
2061A THR* 3.7 21.5 - - + +
2086A PHE* 3.5 38.2 - - + -
2087A SER* 1.3 72.3 - - - +
2089A VAL* 1.3 72.2 + - - +
2153A PHE* 5.8 0.2 - - + -
2159A ASP* 2.6 58.9 + - - +
2160A PRO* 5.0 6.6 - - - +
2162A GLU* 4.3 10.5 - - + -
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Residues in contact with VAL2089 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2059A TYR* 3.3 7.8 - - - +
2060A VAL* 2.4 58.4 + - + +
2087A SER* 4.7 2.5 - - - +
2088A ARG* 1.3 84.9 - - - +
2090A GLN* 1.3 72.6 + - + +
2119A PHE* 5.6 4.3 - - + -
2120A LEU 5.4 5.4 - - - +
2121A LEU* 3.3 28.5 - - + -
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Residues in contact with GLN2090 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2057A LYS* 2.9 36.9 + - - +
2058A VAL 4.0 0.2 - - - -
2059A TYR* 3.6 19.6 - - + -
2060A VAL* 4.1 0.2 - - - +
2089A VAL* 1.3 91.4 - - + +
2091A VAL* 1.3 70.0 + - - +
2093A PRO 4.3 0.2 - - - +
2094A PRO* 5.0 3.1 - - + +
2095A VAL* 3.2 41.2 - - + +
2119A PHE* 5.5 0.7 - - - +
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Residues in contact with VAL2091 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2046A VAL* 3.5 22.2 - - + -
2048A VAL* 5.5 0.4 - - + -
2058A VAL* 3.0 18.6 + - + +
2059A TYR 4.3 0.7 - - - -
2060A VAL* 3.4 37.9 - - + +
2090A GLN* 1.3 82.1 - - - +
2092A TYR* 1.3 64.4 + - + +
2093A PRO 3.8 0.7 - - - -
2094A PRO* 2.9 37.0 - - - +
2117A TYR* 3.4 35.3 - - + +
2118A PRO 4.8 4.3 - - - +
2119A PHE* 4.7 5.8 - - + -
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Residues in contact with TYR2092 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2048A VAL* 4.3 9.6 - - + -
2049A ASP 5.7 0.2 - - - -
2050A PRO* 4.9 10.0 + - + +
2053A VAL* 3.7 44.5 + - + -
2054A LYS* 5.6 1.1 - - - -
2055A GLY 6.2 0.4 - - - -
2056A LYS 3.8 6.5 - - - +
2057A LYS* 3.5 9.2 - - - +
2058A VAL* 3.2 40.1 + - + -
2091A VAL* 1.3 84.9 - - + +
2093A PRO* 1.4 76.3 - - + +
2094A PRO* 5.5 0.2 - - + -
2117A TYR* 3.4 45.5 - + + -
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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