Contacts of the helix formed by residues 8 - 13 (chain J) in PDB entry 3KDO
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 8 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7J THR* 1.3 84.7 + - - +
9J TYR* 1.3 64.1 + - + +
11J TYR* 3.2 19.3 + - - +
12J TYR* 3.4 14.4 - - + -
54J THR 4.0 21.1 - - - +
55J TRP 5.2 2.0 - - - +
56J THR* 4.3 20.4 - - - +
57J THR* 4.6 8.9 - - + +
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Residues in contact with TYR 9 (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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322D LYS* 4.4 4.0 - - - +
444D VAL 5.0 4.0 - - - -
7J THR 3.2 2.3 - - - +
8J ILE* 1.3 81.2 - - + +
10J ASP* 1.3 61.6 + - - +
12J TYR* 2.9 30.0 + - - +
41J GLN 4.7 0.4 - - - +
44J GLY* 3.5 20.4 - - - -
45J ALA* 3.7 22.7 - - + +
48J ALA* 3.4 26.7 - - + -
49J GLU* 2.8 28.4 + - + +
54J THR 3.2 22.0 - - - -
55J TRP* 3.2 26.3 - - + +
115J MET* 5.3 1.0 - - - -
117J ARG* 3.4 44.0 - - - +
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Residues in contact with ASP 10 (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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7J THR* 3.1 32.1 + - - +
9J TYR* 1.3 82.9 - - - +
11J TYR* 1.3 61.1 + - - +
12J TYR 3.1 0.7 + - - -
13J VAL* 3.3 27.0 + - - +
40J GLU 5.1 1.6 - - - +
41J GLN* 4.7 20.0 - - - +
117J ARG* 5.2 1.6 + - - -
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Residues in contact with TYR 11 (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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7J THR 3.6 4.8 + - - +
8J ILE* 3.2 14.5 + - - +
9J TYR 3.1 0.6 + - - -
10J ASP* 1.3 77.5 - - - +
12J TYR* 1.3 72.9 + + + +
13J VAL 3.2 7.8 + - - +
14J ASP* 5.5 1.9 - - - +
67J TRP* 3.6 33.2 - + + -
68J ALA* 3.4 32.9 + - - +
71J SER* 4.1 18.3 - - - -
72J ALA 5.5 1.3 - - - -
73J LYS* 5.9 3.1 - - + +
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Residues in contact with TYR 12 (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 ILE* 3.4 25.1 - - + -
9J TYR 2.9 10.9 + - - +
11J TYR* 1.3 85.3 - + - +
13J VAL* 1.3 61.3 + - - +
14J ASP* 4.0 0.4 - - - -
44J GLY 3.8 3.8 - - - +
47J ALA* 3.7 15.8 - - + +
48J ALA* 3.4 31.0 - - + -
51J SER* 3.6 13.7 - - - -
52J THR* 2.9 29.8 + - - -
53J GLY* 3.1 23.3 + - - -
67J TRP* 3.5 20.3 + + - -
71J SER* 3.7 12.1 - - - -
72J ALA 3.5 20.2 - - - -
73J LYS* 3.5 5.5 - - - -
74J ALA* 2.9 27.7 + - - +
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Residues in contact with VAL 13 (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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9J TYR 4.4 1.3 - - - +
10J ASP* 3.3 19.3 + - - +
11J TYR 3.2 4.7 - - - +
12J TYR* 1.3 77.9 - - - +
14J ASP* 1.3 65.1 + - - +
15J LYS* 4.5 15.0 - - + -
40J GLU* 3.5 35.2 - - + +
44J GLY* 3.7 18.8 - - - +
74J ALA* 3.8 6.5 - - + +
77J PHE* 4.0 24.5 - - + -
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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