Contacts of the strand formed by residues 82 - 88 (chain B) in PDB entry 1ZN8
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 GLY 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A LEU 3.6 5.6 - - - -
34A LYS 3.3 24.0 + - - -
36A PRO* 3.9 9.8 - - - +
59B ASP 4.5 0.4 + - - -
60B TYR* 3.6 18.3 - - - -
61B ILE 3.1 22.3 + - - -
76B ALA* 3.5 4.2 - - - +
81B LEU* 1.3 78.0 - - - +
83B CYS* 1.3 61.4 + - - -
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Residues in contact with CYS 83 (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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30A SER 4.6 0.9 - - - +
33A LEU* 2.9 40.3 + - + +
34A LYS* 3.4 7.4 + - - +
61B ILE* 3.2 10.5 - - - -
63B GLY* 4.1 7.9 - - - -
72B GLY* 3.7 29.4 - - - -
73B PRO* 3.8 16.2 - - + -
76B ALA* 3.9 12.1 - - + -
82B GLY* 1.3 74.5 - - - +
84B VAL* 1.3 76.4 + - - +
85B LEU* 4.6 7.9 - - - +
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Residues in contact with VAL 84 (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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34A LYS* 4.1 20.4 - - + -
60B TYR* 4.4 8.3 - - + -
61B ILE 2.8 16.0 + - - +
62B ALA* 3.3 19.0 - - + -
63B GLY 3.0 24.9 + - - -
82B GLY 4.3 0.2 - - - -
83B CYS* 1.3 81.7 - - - +
85B LEU* 1.3 64.1 + - - +
112B ILE* 5.1 6.1 - - + -
116B ALA* 3.6 36.1 - - + +
117B LEU* 4.3 27.8 - - + -
123B VAL* 4.9 0.4 - - + -
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Residues in contact with LEU 85 (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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29A ILE* 4.9 3.1 - - + -
30A SER* 3.8 31.4 - - - +
33A LEU* 4.8 8.5 - - + -
67A ARG* 6.0 2.0 - - + -
70A LEU* 3.5 44.2 - - + -
63B GLY 3.9 2.0 - - - +
69B PHE* 3.8 19.3 - - + -
83B CYS* 4.6 11.2 - - - +
84B VAL* 1.3 84.2 - - - +
86B ILE* 1.3 66.3 - - - +
87B ARG* 4.0 18.3 + - + -
92B LEU* 4.3 12.5 - - + +
112B ILE* 3.8 16.3 - - - +
113B GLN 5.0 0.3 + - - -
116B ALA* 5.2 1.6 - - - +
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Residues in contact with ILE 86 (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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62B ALA* 4.2 12.6 - - + -
63B GLY 3.1 6.9 + - - +
64B LEU* 3.7 17.0 - - + -
65B ASP* 3.0 27.9 + - - +
69B PHE* 4.0 0.8 - - - -
84B VAL* 5.7 0.2 - - + -
85B LEU* 1.3 75.9 - - - +
87B ARG* 1.3 62.0 + - - +
110B LEU* 3.9 34.0 - - + +
111B GLU 3.6 11.2 - - - +
112B ILE* 3.8 16.2 - - + -
125B VAL* 5.1 0.2 - - + -
139B ALA* 3.7 24.5 - - + +
142B LEU* 4.1 8.3 - - + -
143B LEU* 3.8 31.4 - - + -
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Residues in contact with ARG 87 (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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66A SER* 2.7 29.1 + - - -
67A ARG* 3.4 34.5 - - - +
88A LYS* 6.1 1.2 - - - +
65B ASP* 2.9 30.3 + - - -
69B PHE* 3.7 19.1 - - + -
85B LEU* 4.4 11.2 - - + -
86B ILE* 1.3 77.4 - - - +
88B LYS* 1.3 67.1 + - - +
91B LYS* 3.8 30.1 + - + +
92B LEU* 3.8 41.7 - - + +
110B LEU* 3.2 9.5 - - - -
111B GLU* 2.7 39.2 + - - +
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Residues in contact with LYS 88 (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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87A ARG* 6.0 1.8 - - - +
65B ASP* 3.1 46.0 + - + +
66B SER* 4.3 5.1 - - - +
87B ARG* 1.3 79.0 - - - +
89B ARG* 1.3 69.8 + - - +
90B GLY 3.4 0.2 + - - -
91B LYS* 3.5 15.7 + - + +
101B TYR* 5.3 6.5 + - - -
109B GLU 3.6 8.7 - - - +
110B LEU* 4.1 9.2 - - + +
111B GLU* 3.3 9.5 - - - +
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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