Contacts of the strand formed by residues 83 - 89 (chain J) in PDB entry 1OZT
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 ASP 83 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46J ARG* 3.1 24.5 + - - +
63J HIS* 3.0 27.8 + - - -
79J ARG* 2.7 32.4 + - + +
80J HIS* 2.8 41.3 + - - +
82J GLY* 1.3 68.6 - - - +
84J LEU* 1.3 57.4 + - - +
85J GLY* 3.3 5.6 + - - +
124J ASP* 4.9 7.9 - - - +
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Residues in contact with LEU 84 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J PHE* 5.0 7.2 - - + -
31J VAL* 5.2 5.6 - - + -
45J PHE* 3.1 44.1 + - + +
47J VAL* 4.1 22.0 - - + +
79J ARG* 3.9 9.4 - - - +
82J GLY 3.2 8.2 + - - +
83J ASP* 1.3 74.3 - - - +
85J GLY* 1.3 60.7 + - - +
86J ASN 3.8 2.3 + - - +
99J ILE* 3.9 23.8 - - + +
101J ASP* 3.6 33.0 - - + +
104J ILE* 4.0 22.0 - - + -
117J LEU* 4.3 7.4 - - + -
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Residues in contact with GLY 85 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44J GLY* 3.6 2.8 - - - -
45J PHE* 2.9 22.0 + - - +
46J ARG* 5.1 0.9 - - - +
83J ASP* 3.3 5.7 + - - +
84J LEU* 1.3 78.6 - - - +
86J ASN* 1.3 70.1 + - - -
124J ASP* 3.8 17.7 + - - +
126J LEU* 5.7 8.3 - - - -
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Residues in contact with ASN 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42J LEU* 3.9 32.1 - - + +
43J HIS 3.0 9.5 - - - +
44J GLY 3.3 10.4 + - - -
45J PHE* 4.2 2.2 - - - +
84J LEU 3.8 4.2 + - - +
85J GLY* 1.3 75.1 - - - -
87J VAL* 1.3 66.7 + - - +
88J THR* 5.3 0.7 - - - -
99J ILE* 4.6 7.6 - - - +
123J ALA* 3.4 1.4 - - - -
124J ASP* 2.5 57.2 + - - +
126J LEU* 4.3 10.7 - - - +
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Residues in contact with VAL 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35J ILE* 4.4 7.6 - - + -
38J LEU* 4.8 2.2 - - + -
41J GLY 3.5 1.4 - - - +
42J LEU* 3.5 2.8 - - - -
43J HIS* 2.8 51.7 + - + +
45J PHE* 3.5 34.5 - - + -
86J ASN* 1.3 75.9 - - - +
88J THR* 1.3 62.3 + - - +
95J ALA* 4.4 9.9 - - + -
96J ASP 6.1 0.2 - - - -
97J VAL* 3.6 33.9 - - + -
99J ILE* 5.0 1.6 - - + -
119J VAL* 4.1 15.9 - - + -
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Residues in contact with THR 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41J GLY* 3.3 11.0 - - - +
42J LEU* 3.1 25.9 - - + +
86J ASN 5.3 0.5 - - - -
87J VAL* 1.3 75.5 - - - +
89J ALA* 1.3 71.2 + - - +
90J ASP* 3.9 1.6 + - - -
94J VAL 3.8 0.7 - - - +
95J ALA* 3.2 20.6 - - - +
96J ASP 4.1 7.1 + - - +
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Residues in contact with ALA 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38J LEU* 3.6 26.0 - - + -
39J THR 3.4 24.0 - - - +
40J GLU* 3.4 3.0 - - - +
41J GLY* 2.7 36.1 + - - +
43J HIS* 4.4 0.4 - - + -
87J VAL 4.2 0.4 + - - -
88J THR* 1.3 78.2 - - - +
90J ASP* 1.3 63.2 + - - +
93J GLY 4.0 8.1 - - - -
94J VAL 3.3 11.2 - - - +
95J ALA* 4.1 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