Contacts of the helix formed by residues 87 - 93 (chain B) in PDB entry 4AU8
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 LEU 87 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ASP* 1.3 72.3 - - - +
88B LYS* 1.3 61.0 + - - +
90B TYR* 3.3 10.0 + - + +
91B PHE* 3.0 60.0 + - + -
106B PHE* 4.0 27.4 - - + -
129B PRO* 3.3 19.2 + - + +
132B LEU* 2.7 40.5 + - + +
134B ILE* 4.0 15.6 - - + +
140B LEU* 5.0 5.2 - - + -
191B ILE* 4.1 10.5 - - + -
195B LEU* 4.0 9.9 - - + -
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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
----------------------------------------------------------
86B ASP* 2.9 12.9 + - - +
87B LEU* 1.3 75.6 - - - +
89B LYS* 1.4 77.0 + - + +
91B PHE* 3.2 19.1 + - + +
92B ASP* 3.2 23.0 + - - +
129B PRO* 3.8 16.6 + - + +
130B GLN* 3.3 40.6 - - + +
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Residues in contact with LYS 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B GLN* 3.3 21.0 + - + +
86B ASP* 2.9 14.2 + - - +
88B LYS* 1.4 91.2 - - + +
90B TYR* 1.3 65.2 + - - +
92B ASP* 3.5 20.4 + - + +
93B SER* 3.4 16.6 + - - -
1293B Z3R 3.4 42.0 + - - +
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Residues in contact with TYR 90 (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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85B GLN* 3.5 25.3 - - - +
86B ASP 3.0 12.7 + - - +
87B LEU* 3.3 20.6 + - + +
89B LYS* 1.3 77.6 - - - +
91B PHE* 1.3 65.6 + + - +
93B SER* 3.4 13.2 + - - -
94B CYS* 3.4 31.6 + - - -
98B LEU* 3.7 16.0 - - + +
102B ILE* 3.4 26.7 - - - +
106B PHE* 3.7 32.7 - + - -
134B ILE* 3.8 18.6 - - + -
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Residues in contact with PHE 91 (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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87B LEU* 3.0 44.0 + - + -
88B LYS* 3.2 11.9 + - + +
90B TYR* 1.3 80.2 - + - +
92B ASP* 1.4 60.4 + - - +
94B CYS* 2.9 31.3 + - - +
98B LEU* 4.2 9.2 - - + -
129B PRO* 4.4 3.8 - - + -
191B ILE 5.2 0.2 - - - -
194B GLU* 3.7 30.5 - - + -
195B LEU* 3.8 44.9 - - + -
198B ALA* 3.7 11.1 - - - +
199B GLY* 3.4 33.0 - - - -
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Residues in contact with ASP 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LYS* 3.2 21.6 + - - +
89B LYS* 3.5 28.4 + - + +
91B PHE* 1.4 78.3 - - - +
93B SER* 1.3 57.6 + - - +
94B CYS 3.4 9.7 + - - +
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Residues in contact with SER 93 (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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85B GLN* 4.2 11.7 - - - -
89B LYS 3.4 9.3 + - - -
90B TYR* 3.7 10.1 - - - -
91B PHE 3.2 1.0 - - - -
92B ASP* 1.3 75.0 - - - +
94B CYS* 1.4 60.1 + - - +
95B ASN 3.9 1.0 + - - -
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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