Contacts of the strand formed by residues 96 - 101 (chain B) in PDB entry 2ZUQ
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 96 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B CYS 4.0 1.3 - - - -
44B LYS* 1.9 52.6 + - - +
92B GLY* 2.9 20.6 - - - -
93B SER 3.3 10.6 + - - +
94B GLY 3.4 1.6 - - - -
95B THR* 1.3 78.1 + - - +
97B PHE* 1.3 67.9 + - - +
98B THR* 5.0 1.7 + - - -
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Residues in contact with PHE 97 (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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42B SER* 3.2 8.5 + - - -
43B CYS* 2.7 50.8 + - + +
45B SER* 4.8 2.0 - - - -
49B LEU* 3.5 23.8 - - + -
57B ASN* 3.7 36.1 - - + -
59B LEU* 3.4 34.1 - - + -
61B TRP* 4.2 4.3 - - + +
77B ALA* 3.9 17.3 - - + -
91B SER 3.9 3.8 - - - +
92B GLY* 3.7 12.6 - - - -
93B SER 3.7 7.2 - - - -
94B GLY 3.0 31.0 - - - -
95B THR 3.8 3.4 - - - -
96B ASP* 1.3 84.8 - - - +
98B THR* 1.3 60.7 + - - +
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Residues in contact with THR 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B THR* 3.8 28.0 - - + +
41B MET 3.4 12.3 - - - +
42B SER* 4.0 10.7 + - - -
61B TRP* 3.9 4.8 + - - -
89B THR 3.7 1.9 - - - +
90B GLY* 3.8 1.9 - - - -
91B SER* 3.1 48.1 + - - +
92B GLY* 5.7 0.2 - - - -
96B ASP 5.0 2.0 + - - -
97B PHE* 1.3 81.5 + - - +
99B LEU* 1.3 64.1 + - - +
100B THR* 4.4 3.0 - - + +
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Residues in contact with LEU 99 (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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40B THR* 2.9 3.7 - - - -
41B MET* 2.8 58.5 + - + +
61B TRP* 3.5 39.9 - - + -
73B LEU* 4.6 7.4 - - + -
74B ILE* 3.3 34.3 - - + -
88B PHE* 4.5 7.6 - - + -
89B THR 3.5 10.5 - - - +
98B THR* 1.3 74.8 - - - +
100B THR* 1.3 62.6 + - - +
101B ILE* 4.4 10.3 - - + -
112B TYR* 3.9 26.5 - - + -
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Residues in contact with THR 100 (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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38B LYS* 3.8 21.8 - - - +
39B VAL 3.0 3.5 + - - -
40B THR* 3.0 30.0 - - + +
87B ARG 2.6 22.7 - - - +
88B PHE* 3.2 0.3 - - - -
89B THR* 2.7 51.8 + - - +
91B SER* 4.8 8.3 - - - +
98B THR* 4.4 9.4 - - + +
99B LEU* 1.3 75.4 - - - +
101B ILE* 1.3 56.2 + - - +
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Residues in contact with ILE 101 (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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37B GLU 3.2 7.8 - - - +
38B LYS* 4.3 1.3 - - - -
39B VAL* 2.6 43.1 + - + +
41B MET* 4.6 4.7 - - + -
87B ARG* 3.3 23.3 - - + +
88B PHE* 3.3 37.5 - - + -
99B LEU* 4.4 14.1 - - + -
100B THR* 1.3 73.7 - - - +
102B SER* 1.3 60.9 + - - +
104B VAL* 4.5 9.2 - - + -
108B ASP* 4.7 3.6 - - + +
112B TYR* 3.6 36.1 - - + +
129B LEU* 4.0 14.8 - - + -
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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