Contacts of the strand formed by residues 84 - 89 (chain B) in PDB entry 2B4J
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 ILE 84 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B VAL* 4.8 4.3 - - + -
76B ALA 3.3 6.5 - - - +
77B VAL* 3.9 12.3 - - + -
82B GLY 3.6 9.4 - - - +
83B TYR* 1.3 84.2 - - - +
85B GLU* 1.3 71.4 + - - +
86B ALA* 5.1 0.9 - - + -
154B MET* 3.7 34.5 - - + -
158B LEU* 4.0 34.1 - - + -
180B VAL* 3.6 17.7 - - + +
183B HIS* 3.5 28.3 - - + +
184B ASN* 2.8 38.4 + - - +
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Residues in contact with GLU 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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107A ARG* 2.9 23.0 + - + +
61B TRP* 5.0 0.2 - - + -
75B VAL* 3.4 2.4 - - - +
76B ALA* 2.7 38.9 + - + +
83B TYR* 2.6 33.4 + - + +
84B ILE* 1.3 76.0 - - - +
86B ALA* 1.3 63.6 + - - +
100B PHE* 4.1 16.1 - - + -
104B LEU* 3.7 12.7 - - + +
107B ARG* 2.5 31.8 + - - -
108B TRP* 2.8 21.1 + - - -
180B VAL* 4.4 6.7 - - + -
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Residues in contact with ALA 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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103A LYS* 5.5 0.9 - - - +
73B ILE* 4.1 6.5 - - + -
74B LEU 3.1 12.6 - - - +
75B VAL* 4.2 5.2 - - + -
84B ILE* 5.1 1.1 - - + -
85B GLU* 1.3 78.5 - - - +
87B GLU* 1.3 63.7 + - - +
100B PHE* 4.3 4.4 - - - -
158B LEU* 4.0 24.2 - - + -
176B VAL* 4.1 4.1 - - + +
177B GLN* 2.9 24.9 + - - +
180B VAL* 3.7 21.3 - - + +
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Residues in contact with GLU 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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99A TYR* 3.1 27.3 + - - +
103A LYS* 3.1 30.4 + - + +
73B ILE* 4.2 4.9 - - - +
74B LEU* 2.9 31.9 + - - +
86B ALA* 1.3 75.8 - - - +
88B VAL* 1.3 71.9 + - - +
89B ILE* 3.5 8.8 + - + +
100B PHE* 4.0 24.1 - - + -
103B LYS* 3.9 19.2 + - - -
176B VAL* 4.3 1.6 - - - -
177B GLN* 3.7 10.5 - - - +
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A TYR* 4.5 2.9 + - - -
71B LYS* 4.2 24.9 - - + -
72B VAL 3.2 12.1 - - - +
73B ILE* 4.0 9.9 - - + +
87B GLU* 1.3 87.5 - - - +
89B ILE* 1.3 69.2 + - - +
90B PRO* 4.7 2.0 - - + +
172B LEU* 4.1 9.2 - - + -
173B LYS* 3.6 39.6 - - + +
176B VAL* 3.7 22.6 - - + +
177B GLN* 4.9 0.2 - - - +
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Residues in contact with ILE 89 (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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65B CYS* 4.5 5.4 - - - -
71B LYS* 5.6 0.3 - - - +
72B VAL* 3.0 44.8 + - + +
74B LEU* 4.0 34.8 - - + -
87B GLU* 3.9 17.9 - - + +
88B VAL* 1.3 85.5 - - - +
90B PRO* 1.4 73.1 - - + +
91B ALA 3.3 18.2 + - - +
92B GLU* 4.2 5.2 - - - -
96B GLU* 4.1 26.7 - - + +
97B THR* 4.8 4.5 - - - +
100B PHE* 5.3 3.1 - - + -
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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