Contacts of the helix formed by residues 51 - 65 (chain J) in PDB entry 2I2X
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 GLU 51 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46J ALA* 3.0 11.1 + - + +
49J GLU* 4.7 17.9 - - + +
50J GLY* 1.3 76.5 - - - +
52J GLU* 1.3 76.0 + - - +
53J ASP* 3.2 10.0 + - + +
54J ASP* 3.1 34.1 + - + +
55J VAL* 3.1 23.0 + - - +
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Residues in contact with GLU 52 (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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50J GLY 3.5 11.5 + - - +
51J GLU* 1.3 84.7 - - - +
53J ASP* 1.3 75.0 + - - +
55J VAL* 3.2 7.2 + - - +
56J VAL* 3.1 27.8 + - - +
100J MET 5.4 0.3 - - - +
103J ASP* 5.1 5.7 - - - +
104J ALA* 3.9 23.3 + - - +
107J GLU* 3.4 39.5 - - + +
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Residues in contact with ASP 53 (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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51J GLU* 3.2 7.3 - - + +
52J GLU* 1.3 88.8 + - - +
54J ASP* 1.3 62.8 + - - +
55J VAL 3.3 0.2 + - - -
56J VAL* 3.3 6.0 + - - +
57J GLU* 3.0 34.3 + - - +
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Residues in contact with ASP 54 (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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42J PRO* 4.7 2.6 - - - +
43J ILE* 5.4 0.2 - - - -
46J ALA* 3.4 24.2 - - + +
49J GLU* 5.0 6.9 - - - +
51J GLU* 3.1 25.7 + - + +
53J ASP* 1.3 79.7 - - - +
55J VAL* 1.3 57.3 + - - +
57J GLU* 3.9 14.6 - - - +
58J GLY* 2.9 26.0 + - - -
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Residues in contact with VAL 55 (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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43J ILE* 4.5 5.8 - - + +
46J ALA* 3.6 27.6 - - + +
47J ILE* 4.0 10.8 - - + +
51J GLU 3.1 17.1 + - - +
52J GLU 3.4 7.9 - - - +
53J ASP 3.2 0.2 - - - -
54J ASP* 1.3 77.8 - - - +
56J VAL* 1.3 57.5 + - + +
58J GLY* 3.4 2.5 + - - -
59J LEU* 2.9 34.5 + - + +
77J LEU* 3.8 27.8 - - + -
104J ALA* 3.6 30.1 - - + +
108J GLY* 3.9 6.5 - - - +
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Residues in contact with VAL 56 (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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52J GLU 3.1 15.9 + - - +
53J ASP* 3.3 5.6 + - - +
55J VAL* 1.3 75.3 - - + +
57J GLU* 1.3 56.4 + - - +
59J LEU* 2.9 10.1 + - - +
60J GLN* 2.8 45.3 + - - +
107J GLU* 4.6 19.1 - - + +
108J GLY* 5.2 0.4 - - - -
111J TYR* 3.7 46.8 - - + -
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Residues in contact with GLU 57 (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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53J ASP* 3.0 19.7 + - - +
54J ASP* 4.1 15.6 - - - +
56J VAL* 1.3 76.3 - - - +
58J GLY* 1.3 58.8 + - - +
60J GLN* 4.0 14.5 - - - +
61J ALA* 3.5 20.8 + - - +
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Residues in contact with GLY 58 (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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39J LEU 4.5 2.9 - - - +
42J PRO* 5.4 8.5 - - - -
43J ILE* 3.6 19.8 - - - +
54J ASP 2.9 20.6 + - - -
55J VAL 3.7 1.8 - - - -
57J GLU* 1.3 76.5 - - - +
59J LEU* 1.3 62.1 + - - +
60J GLN 3.4 0.2 - - - -
61J ALA* 3.9 6.1 + - - +
62J ALA* 3.5 20.3 + - - +
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Residues in contact with LEU 59 (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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43J ILE* 4.2 13.0 - - + -
55J VAL* 2.9 21.1 + - + +
56J VAL* 2.9 10.6 + - - +
58J GLY* 1.3 76.5 - - - +
60J GLN* 1.3 60.8 + - - +
62J ALA* 3.4 4.0 + - - +
63J ILE* 3.1 31.4 + - + +
72J LEU* 3.7 37.8 - - + +
77J LEU* 3.8 21.1 - - + -
108J GLY* 3.7 37.5 - - - +
111J TYR* 4.5 12.8 - - + -
112J CYS* 3.9 12.6 - - - -
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Residues in contact with GLN 60 (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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56J VAL* 2.8 25.2 + - - +
57J GLU* 4.1 14.7 - - - +
59J LEU* 1.3 71.8 - - - +
61J ALA* 1.3 58.8 + - - +
62J ALA 2.9 9.9 + - - -
63J ILE* 3.3 9.4 + - + +
64J GLU* 3.1 38.8 + - + +
111J TYR* 2.7 39.0 + - + +
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Residues in contact with ALA 61 (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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39J LEU* 5.1 2.8 - - - +
57J GLU 3.5 15.8 + - - +
58J GLY* 4.1 6.7 - - - +
59J LEU 3.5 0.2 - - - -
60J GLN* 1.3 77.8 - - - +
62J ALA* 1.3 55.9 + - - +
64J GLU* 4.1 5.1 - - - +
65J ALA* 3.4 28.9 + - - +
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Residues in contact with ALA 62 (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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39J LEU* 4.5 17.8 - - + +
43J ILE* 4.2 9.6 - - + -
58J GLY 3.5 16.7 + - - +
59J LEU* 3.4 7.6 + - - +
60J GLN 2.9 2.4 + - - -
61J ALA* 1.3 77.2 - - - +
63J ILE* 1.3 61.3 + - - +
64J GLU 3.1 4.8 + - - -
65J ALA* 3.6 1.8 + - - +
66J GLY* 3.4 19.6 + - - -
67J LYS 3.9 6.0 + - - +
72J LEU* 3.7 22.2 - - + -
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Residues in contact with ILE 63 (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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59J LEU* 3.1 17.2 + - + +
60J GLN* 3.5 11.2 - - + +
62J ALA* 1.3 75.8 - - - +
64J GLU* 1.3 62.8 + - + +
65J ALA 3.6 0.2 - - - -
66J GLY 3.1 16.3 - - - +
67J LYS* 3.8 10.3 - - - +
68J ASP 3.4 30.7 - - - +
69J PRO* 4.1 9.6 - - + -
72J LEU* 3.5 10.3 - - + -
111J TYR* 4.3 23.3 - - + +
112J CYS* 6.3 4.3 - - - -
115J ASN* 4.4 18.6 - - + +
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Residues in contact with GLU 64 (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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60J GLN* 3.1 28.2 + - + +
61J ALA* 4.5 3.8 - - - +
63J ILE* 1.3 84.6 - - + +
65J ALA* 1.3 57.9 + - - +
66J GLY 3.3 5.9 + - - +
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Residues in contact with ALA 65 (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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39J LEU* 4.5 20.8 - - + +
61J ALA 3.4 19.9 + - - +
62J ALA 3.6 2.7 + - - +
64J GLU* 1.3 77.1 - - + +
66J GLY* 1.3 54.7 + - - +
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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