Contacts of the helix formed by residues 82 - 93 (chain N) 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 SER 82 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6590 A 3.3 31.0 - - - -
6600 A 2.6 28.1 + - - -
63N LYS* 3.8 1.6 - - - +
64N VAL 3.1 8.1 + - - -
65N LEU* 4.0 12.3 - - - -
66N GLY 3.5 0.5 + - - -
81N PHE* 1.3 80.2 - - - +
83N GLY* 1.3 65.2 + - - +
84N THR 3.8 2.1 + - - -
85N ALA* 3.2 19.9 + - - +
86N GLU* 3.2 18.2 + - - +
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Residues in contact with GLY 83 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6590 A 2.9 18.0 + - - -
81N PHE 3.9 0.2 + - - -
82N SER* 1.3 72.6 - - - +
84N THR* 1.3 59.9 + - - +
86N GLU* 3.7 7.3 + - - +
87N THR* 3.1 26.6 + - - -
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Residues in contact with THR 84 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6590 A 4.8 0.8 + - - -
6600 A 3.4 25.6 + - - +
66N GLY 4.3 4.9 - - - +
82N SER* 3.3 1.4 + - - -
83N GLY* 1.3 73.4 - - - +
85N ALA* 1.3 67.4 + - - +
87N THR* 3.1 6.4 + - - -
88N LYS* 3.0 49.8 + - + +
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Residues in contact with ALA 85 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45N LEU* 4.6 6.1 - - + -
64N VAL* 3.3 37.2 - - + +
65N LEU 3.6 14.6 - - - +
66N GLY* 4.0 8.2 - - - -
81N PHE* 4.2 2.5 - - + -
82N SER* 3.2 15.7 + - - +
84N THR* 1.3 79.3 - - - +
86N GLU* 1.3 58.6 + - - +
87N THR 3.1 0.3 + - - -
88N LYS* 3.2 1.2 + - - +
89N ILE* 2.9 36.2 + - + +
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Residues in contact with GLU 86 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81N PHE* 3.9 25.9 - - + +
82N SER 3.2 13.6 + - - +
83N GLY* 4.0 7.0 - - - +
85N ALA* 1.3 79.1 - - - +
87N THR* 1.3 61.3 + - - +
89N ILE* 4.0 0.7 - - - -
90N ASP* 3.2 37.1 + - - +
95N ALA* 3.9 24.8 - - + +
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Residues in contact with THR 87 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83N GLY 3.1 13.8 + - - -
84N THR* 3.1 11.1 + - - -
85N ALA 3.1 0.8 - - - -
86N GLU* 1.3 77.8 - - - +
88N LYS* 1.3 64.2 + - + +
89N ILE 3.5 0.3 + - - -
90N ASP* 3.5 4.7 + - - +
91N GLN* 2.9 44.4 + - + +
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Residues in contact with LYS 88 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71K GLU 5.4 1.6 + - - -
72K ASN* 4.5 12.9 + - - -
75K LEU* 4.4 19.1 - - + +
45N LEU* 3.4 29.6 - - + -
66N GLY 2.9 23.9 + - - +
68N GLY 3.1 20.4 + - - +
69N VAL* 5.6 1.5 - - - +
70N LEU* 5.1 4.8 - - + +
84N THR* 3.0 32.9 + - + +
85N ALA 3.8 0.2 - - - +
87N THR* 1.3 78.5 - - + +
89N ILE* 1.3 63.5 + - - +
91N GLN* 3.3 31.9 + - - +
92N VAL* 3.8 10.3 + - - +
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Residues in contact with ILE 89 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45N LEU* 3.6 30.7 - - + -
48N ILE* 4.6 0.9 - - + -
64N VAL* 3.9 16.4 - - + -
70N LEU* 3.7 20.2 - - + -
74N VAL 4.8 1.6 - - - +
76N VAL* 4.3 20.9 - - + -
81N PHE* 4.3 14.8 - - + -
85N ALA 2.9 19.5 + - - +
86N GLU 4.3 2.9 - - - +
88N LYS* 1.3 77.9 - - - +
90N ASP* 1.3 52.1 + - - +
91N GLN 3.2 0.5 + - - -
92N VAL* 3.3 2.4 + - - +
93N GLY* 2.7 33.3 + - - -
94N GLU 3.7 30.7 - - - +
95N ALA* 3.7 6.5 - - + +
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Residues in contact with ASP 90 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86N GLU* 3.2 32.9 + - - +
87N THR* 4.1 4.5 - - - +
88N LYS 3.4 0.4 - - - -
89N ILE* 1.3 76.6 - - - +
91N GLN* 1.3 61.2 + - - +
92N VAL 3.3 0.2 - - - -
93N GLY 3.6 13.4 - - - +
94N GLU* 3.4 6.8 - - - +
95N ALA* 2.7 35.2 + - - +
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Residues in contact with GLN 91 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75K LEU* 5.8 6.1 - - - +
87N THR* 2.9 39.2 + - + +
88N LYS* 3.5 23.7 - - - +
89N ILE 3.1 0.6 - - - -
90N ASP* 1.3 78.0 - - - +
92N VAL* 1.3 67.2 + - + +
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Residues in contact with VAL 92 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70N LEU* 3.6 37.2 - - + +
71N GLN* 3.6 17.2 - - + +
72N LYS 3.6 14.8 - - - +
73N ASP* 3.0 27.8 - - - +
88N LYS 4.0 7.6 - - - +
89N ILE 3.7 7.0 - - - +
90N ASP 4.9 0.2 - - - -
91N GLN* 1.3 88.3 - - + +
93N GLY* 1.3 59.2 + - - +
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Residues in contact with GLY 93 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70N LEU* 6.2 0.4 - - - -
73N ASP* 3.6 11.4 - - - -
74N VAL 3.6 14.1 - - - -
89N ILE 2.7 19.4 + - - +
90N ASP* 3.6 14.4 - - - +
91N GLN 3.7 0.2 - - - -
92N VAL* 1.3 78.5 - - - +
94N GLU* 1.3 63.4 + - - +
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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