Contacts of the strand formed by residues 81 - 87 (chain B) in PDB entry 4ZCH
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 ARG 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A ILE* 4.3 13.1 - - - +
167A GLN 2.8 39.2 + - - +
168A LYS* 3.6 25.4 - - + +
169A GLY 5.3 5.4 - - - +
76B ARG* 3.6 26.9 - - - +
77B GLU* 3.6 6.8 - - - +
78B GLY* 2.8 45.9 + - - +
79B GLN* 3.6 25.7 + - - +
80B GLY* 1.3 79.1 - - - +
82B GLN* 1.3 60.5 + - - +
83B GLU* 2.8 35.6 + - - +
112B HIS* 5.3 2.2 + - - -
115B ASP* 5.4 1.0 + - - -
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Residues in contact with GLN 82 (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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75B SER* 3.4 37.3 + - - +
76B ARG 3.5 1.3 - - - -
77B GLU* 2.9 51.6 + - + +
81B ARG* 1.3 73.4 - - - +
83B GLU* 1.3 58.8 + - - +
84B THR* 4.1 1.4 + - - -
116B ILE 4.3 1.2 + - - -
118B SER* 4.2 9.0 + - - -
120B ILE* 5.0 8.3 - - + -
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Residues in contact with GLU 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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167A GLN* 3.6 29.2 + - + +
75B SER* 3.4 3.6 - - - -
76B ARG* 2.8 69.6 + - + +
81B ARG* 2.8 41.9 + - - +
82B GLN* 1.3 73.6 - - - +
84B THR* 1.3 73.4 + - - +
85B LEU* 3.7 5.5 + - - +
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Residues in contact with THR 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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73B VAL* 3.6 30.7 - - + +
74B VAL 3.7 5.6 - - - +
75B SER* 4.1 5.3 + - - -
82B GLN 4.1 1.7 + - - -
83B GLU* 1.3 85.2 - - - +
85B LEU* 1.3 60.8 + - - +
86B PHE 4.1 9.2 - - - +
87B ARG* 4.7 10.7 + - + +
283B ASP* 3.4 46.3 - - + +
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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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57B LEU* 3.7 26.9 - - + -
74B VAL* 2.7 21.2 + - + +
76B ARG* 4.0 45.8 - - + +
83B GLU* 4.5 5.8 - - - +
84B THR* 1.3 77.7 - - - +
86B PHE* 1.3 67.6 + - + +
109B PHE* 3.6 42.3 - - + -
111B LEU* 4.0 11.0 - - + -
117B LEU* 3.8 17.7 - - + -
156B GLN* 5.6 0.2 + - - -
282B GLY 5.0 1.7 - - - +
283B ASP* 4.2 10.9 - - - +
286B PHE* 5.8 0.3 - - - -
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Residues in contact with PHE 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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57B LEU* 3.6 40.2 - - + -
59B SER* 4.1 9.9 - - - -
72B GLN* 5.7 1.3 - - + -
74B VAL* 2.9 51.7 + - + +
84B THR* 3.8 3.0 - - - +
85B LEU* 1.3 81.9 - - + +
87B ARG* 1.3 62.1 + - - +
105B SER* 3.3 46.2 - - - -
106B ALA* 3.8 4.7 - - - -
107B GLY 4.0 2.7 - - - -
109B PHE* 3.3 37.2 - + + -
283B ASP* 3.2 14.8 - - - +
286B PHE* 3.9 15.9 - - + -
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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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72B GLN* 3.3 15.7 - - - +
73B VAL* 4.1 23.3 - - + +
84B THR* 4.7 8.1 + - + +
86B PHE* 1.3 78.0 - - - +
88B CYS* 1.3 61.6 + - - +
89B ILE* 4.2 18.5 - - + +
105B SER* 3.9 5.1 + - - -
122B PRO* 6.2 0.6 - - - +
206B GLN* 3.0 24.4 + - - -
208B LEU* 6.2 0.4 - - - +
281B ASP* 2.8 28.9 + - - -
283B ASP* 2.8 29.2 + - + +
284B VAL* 3.6 20.8 - - + +
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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