Contacts of the helix formed by residues 79 - 90 (chain Z) in PDB entry 3J7Y
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 PRO 79 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2120A G 3.7 7.2 - - - +
2121A G 3.5 11.4 - - - +
228N LYS* 4.7 7.6 - - + -
36Z PHE* 3.3 35.9 - - + -
78Z ARG* 1.3 96.5 - - + +
80Z TYR* 1.3 66.0 + - - +
81Z TRP* 3.5 35.0 - - + +
82Z GLU* 3.0 29.4 + - - +
83Z LYS* 3.1 9.2 + - - +
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Residues in contact with TYR 80 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2058A C 5.7 4.7 - - - -
2120A G 3.8 27.4 + - - -
2121A G 2.6 23.6 + - - +
38Z ARG* 3.6 20.0 + - - -
79Z PRO* 1.3 72.9 - - - +
81Z TRP* 1.3 86.9 + + + +
83Z LYS* 3.1 16.6 + - + +
84Z ASP* 2.9 44.8 + - - +
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Residues in contact with TRP 81 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2059A C 6.1 0.2 - - - -
2119A U 5.4 0.9 - - - -
2120A G 3.8 24.7 - - - -
36Z PHE* 3.5 31.9 - + - -
37Z THR* 3.9 3.6 - - - -
38Z ARG* 3.5 81.8 - - + +
39Z SER 5.0 1.0 - - - +
79Z PRO* 3.5 18.4 - - + -
80Z TYR* 1.3 111.0 - + + +
82Z GLU* 1.3 90.5 + - + +
84Z ASP* 3.2 9.1 + - - +
85Z ILE* 2.9 34.6 + - + +
112Z VAL* 4.2 12.6 - - + +
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Residues in contact with GLU 82 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222N ASN* 5.9 0.3 + - - -
36Z PHE* 5.1 2.8 - - - -
75Z THR* 5.0 1.1 - - - -
78Z ARG* 3.4 24.6 - - + +
79Z PRO* 3.0 26.0 + - - +
81Z TRP* 1.3 103.6 + - + +
83Z LYS* 1.3 62.7 + - - +
85Z ILE* 3.2 10.4 + - - -
86Z ILE* 3.2 20.2 + - - +
112Z VAL* 4.1 10.7 - - + +
113Z VAL* 3.6 23.0 - - + +
115Z HIS* 2.7 33.7 + - - -
116Z LEU* 4.3 3.9 - - + +
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Residues in contact with LYS 83 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2121A G 5.0 2.4 + - - -
2122A A 3.1 27.7 + - - -
2140A G 5.5 6.5 - - - -
75Z THR* 3.6 42.8 + - - +
76Z ARG* 4.2 7.9 - - - +
78Z ARG 3.0 26.3 + - - -
79Z PRO 3.1 13.7 + - - +
80Z TYR* 3.1 15.2 + - + +
82Z GLU* 1.3 76.6 - - - +
84Z ASP* 1.3 63.7 + - - +
86Z ILE* 3.5 3.6 + - - +
87Z LYS* 3.3 31.9 + - + +
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Residues in contact with ASP 84 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2057A C 4.6 8.3 + - - -
2058A C 6.2 0.4 - - - -
80Z TYR* 2.9 35.7 + - - +
81Z TRP* 3.3 11.4 - - - +
83Z LYS* 1.3 75.7 - - - +
85Z ILE* 1.3 60.1 + - + +
87Z LYS* 3.2 12.5 + - - +
88Z MET* 2.9 54.6 + - + +
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Residues in contact with ILE 85 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2058A C 3.3 39.3 - - - +
2059A C 4.8 1.6 - - - +
81Z TRP* 2.9 21.0 + - + +
82Z GLU 3.2 7.4 + - - +
84Z ASP* 1.3 78.2 - - + +
86Z ILE* 1.3 58.0 + - - +
88Z MET* 3.2 10.6 + - + +
89Z LEU* 2.9 36.3 + - + +
109Z LYS* 3.5 34.5 - - + +
112Z VAL* 3.8 24.7 - - + -
113Z VAL* 3.6 20.4 - - + -
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Residues in contact with ILE 86 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71Z ARG* 4.0 15.9 - - + +
75Z THR* 3.6 25.8 - - + -
82Z GLU 3.2 12.3 + - - +
83Z LYS 3.6 8.1 - - - +
84Z ASP 3.3 0.2 - - - -
85Z ILE* 1.3 77.7 - - - +
87Z LYS* 1.3 61.1 + - + +
89Z LEU* 3.2 5.3 + - - +
90Z GLY 2.8 23.4 + - - -
91Z LEU* 2.9 63.4 + - + +
92Z GLU* 4.9 1.8 - - - -
113Z VAL* 4.0 18.2 - - + -
116Z LEU* 4.0 7.2 - - + -
117Z ILE* 3.9 15.3 - - + -
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Residues in contact with LYS 87 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2083A U 4.7 6.9 + - - +
75Z THR* 6.4 0.2 - - + -
83Z LYS* 3.3 21.5 + - + +
84Z ASP* 3.2 12.2 + - - +
86Z ILE* 1.3 80.3 - - + +
88Z MET* 1.3 59.4 + - + +
90Z GLY* 3.0 19.5 + - - +
92Z GLU* 4.8 19.9 - - + +
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Residues in contact with MET 88 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2056A G 5.5 0.9 - - - +
2057A C 3.5 27.1 - - + +
2058A C 3.3 45.5 - - - +
2082A G 2.6 52.6 + - - +
2083A U 3.4 26.7 - - - +
84Z ASP* 2.9 41.0 + - + +
85Z ILE* 3.4 11.2 - - + +
87Z LYS* 1.3 75.8 - - + +
89Z LEU* 1.3 55.6 + - - +
90Z GLY 3.5 0.3 + - - -
109Z LYS* 4.9 6.1 - - + -
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Residues in contact with LEU 89 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2082A G 3.7 5.6 - - - +
2083A U 5.5 2.0 + - - -
85Z ILE* 2.9 38.0 + - + +
86Z ILE* 3.2 6.3 + - - +
88Z MET* 1.3 78.0 - - - +
90Z GLY* 1.3 60.6 + - - +
91Z LEU* 3.6 19.3 + - + +
98Z GLN* 4.1 10.9 - - - +
100Z HIS* 3.1 43.1 + - + +
106Z VAL* 4.6 6.1 - - + -
109Z LYS* 4.2 19.7 - - + -
110Z LEU* 3.4 33.9 - - + -
113Z VAL* 4.0 12.3 - - + -
76j ARG* 5.1 1.4 + - - -
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Residues in contact with GLY 90 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2083A U 6.2 1.6 - - - -
86Z ILE 2.8 4.6 + - - -
87Z LYS 3.0 14.4 + - - -
88Z MET 3.2 1.0 + - - -
89Z LEU* 1.3 79.7 - - - +
91Z LEU* 1.3 57.5 + - - +
92Z GLU* 3.3 25.9 + - - +
98Z GLN* 4.0 18.2 + - - +
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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