Contacts of the helix formed by residues 80 - 88 (chain V) in PDB entry 1JJ2
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 ASP 80 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67V ALA* 5.6 0.7 - - - +
78V ASP* 3.3 19.0 + - + +
79V VAL* 1.3 73.9 - - - +
81V ASP* 1.3 66.0 + - - +
82V GLU* 3.1 13.8 + - - +
83V TRP* 2.7 34.1 + - - +
84V VAL* 2.9 26.1 + - - +
93V ILE* 3.9 7.2 - - - -
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Residues in contact with ASP 81 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80V ASP* 1.3 73.8 - - - +
82V GLU* 1.3 59.1 + - - +
84V VAL* 3.2 4.0 + - - +
85V ALA* 2.8 29.9 + - - +
91V ASP 4.0 3.6 - - - +
92V ASP* 2.9 18.4 - - + +
93V ILE* 2.8 45.9 + - - +
94V SER 4.6 0.2 + - - -
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Residues in contact with GLU 82 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80V ASP* 3.1 11.9 + - - +
81V ASP* 1.3 77.3 - - - +
83V TRP* 1.3 55.1 + - - +
85V ALA* 3.1 6.5 + - - -
86V GLU* 2.7 71.9 + - + +
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Residues in contact with TRP 83 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72V PRO* 3.9 24.1 - - + +
77V ALA* 3.9 23.1 - - + +
78V ASP 3.5 22.4 - - - +
79V VAL* 3.9 14.1 - - + -
80V ASP* 2.7 26.5 + - - +
82V GLU* 1.3 73.7 - - - +
84V VAL* 1.3 65.7 + - + +
86V GLU* 3.2 1.7 + - - -
87V HIS* 2.8 84.7 + + + +
88V THR* 3.8 13.7 - - - -
110V GLN 3.9 6.1 - - - -
111V GLY* 3.9 11.2 - - - -
112V LEU* 3.3 30.7 - - + -
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Residues in contact with VAL 84 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79V VAL* 3.9 17.7 - - + -
80V ASP 2.9 20.4 + - - +
81V ASP 3.4 6.5 - - - +
83V TRP* 1.3 84.8 - - + +
85V ALA* 1.3 57.0 + - - +
88V THR* 2.8 44.2 + - - +
90V TYR* 3.4 7.2 - - + +
92V ASP* 3.5 30.1 - - - +
93V ILE* 3.7 22.9 - - + +
96V LEU* 4.2 22.0 - - + -
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Residues in contact with ALA 85 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81V ASP 2.8 12.5 + - - +
82V GLU* 3.5 7.0 - - - +
84V VAL* 1.3 78.3 - - - +
86V GLU* 1.3 64.5 + - + +
87V HIS 3.2 1.1 + - - -
88V THR 3.9 9.9 - - - +
90V TYR 3.5 11.4 - - - +
91V ASP* 3.3 24.5 - - - +
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Residues in contact with GLU 86 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82V GLU* 2.7 54.7 + - + +
83V TRP* 4.1 2.7 - - - +
85V ALA* 1.3 75.2 - - + +
87V HIS* 1.3 75.3 + - + +
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Residues in contact with HIS 87 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83V TRP* 2.8 77.6 + + + +
85V ALA 3.2 0.2 - - - -
86V GLU* 1.3 89.7 + - + +
88V THR* 1.3 62.2 + - - +
110V GLN* 4.5 7.3 + - - +
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Residues in contact with THR 88 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83V TRP* 3.8 11.4 - - - -
84V VAL* 2.8 24.0 + - + +
85V ALA 3.9 7.4 - - - +
87V HIS* 1.3 82.4 + - - +
89V ASP* 1.3 78.1 + - - +
90V TYR* 3.2 31.0 + - + +
96V LEU* 4.6 6.0 - - + +
110V GLN* 2.7 47.6 + - + +
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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