Contacts of the helix formed by residues 85 - 93 (chain J) in PDB entry 6O81
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 85 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10J VAL* 4.8 10.2 - - - +
84J MET* 1.3 76.5 - - - +
86J THR* 1.3 64.1 + - - -
87J ALA 3.5 1.3 - - - -
88J ASP* 3.9 9.2 - - - +
89J SER* 3.1 21.8 + - - -
222J THR* 3.7 14.5 - - - -
223J SER* 5.5 0.2 - - - -
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Residues in contact with THR 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J MET* 4.7 13.2 - - + -
10J VAL* 4.3 22.4 - - + +
85J GLY* 1.3 71.9 - - - -
87J ALA* 1.3 58.9 + - - +
89J SER* 2.6 20.5 + - - -
90J LEU* 2.9 23.2 + - - +
203J HIS* 4.4 20.0 - - + +
222J THR 3.2 2.0 + - - -
223J SER* 3.3 6.1 - - - +
224J ILE* 2.5 40.8 + - - +
225J ARG* 4.0 4.8 + - + +
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Residues in contact with ALA 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86J THR* 1.3 75.7 + - - +
88J ASP* 1.3 61.3 + - - +
90J LEU* 3.3 5.6 + - - -
91J ARG* 2.9 25.8 + - - +
215J LEU* 3.5 19.7 - - + +
221J ILE* 3.4 33.2 - - + +
222J THR 2.9 18.8 + - - +
224J ILE* 3.8 16.1 - - + +
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Residues in contact with ASP 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81J ASP* 5.6 2.8 - - - +
83J ASP 5.4 1.6 - - - -
84J MET* 3.4 21.3 - - + +
85J GLY* 3.9 19.7 + - - +
86J THR 3.3 0.4 - - - -
87J ALA* 1.3 79.7 - - - +
89J SER* 1.3 57.9 + - - +
91J ARG* 3.5 7.1 + - - +
92J TYR* 2.9 34.0 + - - +
221J ILE 4.8 2.0 + - - -
222J THR* 4.0 4.8 + - - +
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Residues in contact with SER 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J MET* 3.2 31.1 - - - +
10J VAL* 5.7 0.7 - - - +
54J VAL* 5.0 10.6 - - - +
84J MET* 6.1 1.1 - - - -
85J GLY 3.1 14.3 + - - -
86J THR* 2.6 21.3 + - - -
88J ASP* 1.3 75.8 + - - +
90J LEU* 1.3 62.9 + - - +
92J TYR* 3.5 12.5 + - - +
93J ILE* 3.4 24.6 + - - +
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Residues in contact with LEU 90 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J VAL* 6.1 0.2 - - + -
8J MET* 3.7 20.2 - - + -
86J THR* 2.9 27.9 + - - +
87J ALA* 3.6 9.4 - - - +
89J SER* 1.3 79.3 + - - +
91J ARG* 1.3 61.7 + - - +
92J TYR 3.4 0.3 + - - -
93J ILE* 3.6 15.6 + - + +
94J TYR* 3.6 11.4 + - - +
97J LEU* 4.4 7.7 - - + +
101J VAL* 4.2 23.1 - - + -
103J VAL* 4.9 16.2 - - + -
207J LEU* 5.5 3.8 - - + -
212J VAL* 4.0 25.5 - - + +
215J LEU* 3.8 23.1 - - + -
224J ILE* 4.6 11.0 - - + -
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Residues in contact with ARG 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87J ALA 2.9 18.0 + - - +
88J ASP* 3.7 7.9 - - - +
90J LEU* 1.3 75.0 - - - +
92J TYR* 1.3 61.6 + - - +
93J ILE 3.4 0.2 - - - -
94J TYR* 3.6 19.2 + - + +
95J PRO* 4.8 2.3 - - - +
215J LEU* 3.9 16.8 - - + +
216J MET* 5.1 9.6 - - + -
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Residues in contact with TYR 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78J ILE* 3.8 27.8 - - + -
79J PRO* 3.5 29.0 + - - +
80J ASP* 5.2 7.6 - - + -
88J ASP* 2.9 23.6 + - - +
89J SER* 3.8 10.8 - - - +
90J LEU 3.2 0.8 - - - -
91J ARG* 1.3 79.5 - - - +
93J ILE* 1.3 60.8 + - + +
94J TYR 3.3 1.5 + - - -
95J PRO* 4.2 7.6 - - - +
96J LYS* 5.4 0.9 - - - +
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Residues in contact with ILE 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J VAL* 3.8 41.1 - - + -
8J MET* 5.0 1.8 - - + -
52J ILE* 5.0 10.8 - - + -
54J VAL* 4.8 4.0 - - + -
78J ILE* 3.7 29.8 - - + -
89J SER 3.4 18.2 - - - +
90J LEU* 3.7 13.2 - - + +
92J TYR* 1.3 80.3 - - + +
94J TYR* 1.3 63.1 + - - +
95J PRO* 3.5 2.7 - - - -
96J LYS* 3.3 37.8 + - + +
97J LEU* 3.3 24.3 + - + +
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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