Contacts of the helix formed by residues 83 - 88 (chain B) in PDB entry 4WYV
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 GLN 83 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ILE* 5.7 2.2 - - - +
79B PHE* 4.6 1.3 - - - -
80B PRO* 2.7 46.5 + - + +
82B GLU* 1.3 89.0 - - + +
84B TYR* 1.3 53.1 + - - +
85B TYR 3.2 2.7 - - - -
86B ARG* 2.8 67.2 + - + +
87B PHE* 3.8 16.8 + - + -
85F TYR* 4.7 10.7 - - + -
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Residues in contact with TYR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 4.0 14.1 - + + -
80B PRO 4.1 0.6 + - - -
81B ALA 3.6 11.9 + - - +
82B GLU 3.3 4.7 + - - +
83B GLN* 1.3 75.6 - - - +
85B TYR* 1.3 93.2 + + + +
86B ARG 3.2 0.5 + - - -
87B PHE 3.3 1.7 + - - -
88B HIS* 3.0 45.9 + + - -
91B TRP* 3.2 38.8 + + - -
95B LEU* 3.6 13.2 - - - +
133B PHE* 3.7 30.4 - + - -
134B HIS* 2.8 42.2 + + + -
136B ASP* 4.7 3.8 + - + -
139B ASP* 4.5 1.2 + - - -
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Residues in contact with TYR 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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83B GLN 3.2 1.0 - - - -
84B TYR* 1.3 105.9 - + + +
86B ARG* 1.3 63.2 + - - +
87B PHE 3.6 0.2 + - - -
88B HIS* 3.9 24.7 + + + +
89B GLU* 4.1 4.5 - - - +
134B HIS* 5.7 8.1 - + + +
136B ASP* 3.1 42.4 + - - +
83F GLN* 4.1 18.2 - - + -
85F TYR* 3.8 32.7 - - + +
86F ARG* 3.5 47.8 + - + +
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Residues in contact with ARG 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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17B GLU* 2.7 39.4 + - - +
21B ARG* 3.7 18.5 + - - +
83B GLN* 2.8 51.2 + - + +
85B TYR* 1.3 71.8 - - - +
87B PHE* 1.3 74.6 + - + +
89B GLU* 3.4 17.7 - - - +
85F TYR* 3.5 51.8 + - + +
136F ASP* 3.6 11.1 + - - -
137F VAL 5.8 0.2 - - - +
138F GLU* 3.1 24.5 + - - -
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Residues in contact with PHE 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLU* 4.3 13.2 - - + -
20B ILE* 3.8 20.4 - - + -
21B ARG* 3.8 37.9 - - + -
24B ILE* 3.5 21.5 - - + -
79B PHE* 3.9 33.2 - + + -
80B PRO* 4.3 0.9 - - + -
83B GLN* 3.9 30.3 - - + -
84B TYR 3.3 2.2 + - - -
86B ARG* 1.3 106.9 - - + +
88B HIS* 1.3 63.9 + - - +
89B GLU* 3.2 4.5 + - - -
90B HIS* 3.3 22.1 + - + +
91B TRP* 3.1 20.7 - - + -
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Residues in contact with HIS 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B TYR* 3.0 42.1 + + + +
85B TYR* 3.9 25.2 - + + +
86B ARG 3.6 2.0 - - - -
87B PHE* 1.3 77.2 - - - +
89B GLU* 1.3 61.0 + - - +
91B TRP* 3.1 27.6 + + - -
92B ARG* 3.0 55.9 + - + +
136B ASP* 4.0 12.6 + - - -
139B ASP* 2.8 30.8 + - - -
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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