Contacts of the helix formed by residues 47 - 58 (chain A) in PDB entry 1OZJ
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 GLN 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A LEU* 2.7 26.8 + - + +
45A THR* 2.7 38.6 + - - +
46A GLY* 1.3 73.7 - - - +
48A LEU* 1.3 64.9 - - - +
49A ASP 3.5 1.3 - - - -
50A GLU* 3.1 23.5 + - + +
51A LEU* 3.1 10.2 + - - +
64A CYS 3.8 6.4 - - - +
65A ILE* 3.7 9.5 - - + +
66A THR* 2.9 54.7 + - - +
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 4.1 28.3 - - + -
15A LEU* 4.8 1.6 - - + -
39A VAL* 4.0 39.9 - - + +
42A LEU* 3.5 9.6 + - + +
43A LYS* 3.7 42.0 - - + +
46A GLY* 3.5 2.7 - - - -
47A GLN* 1.3 75.9 - - - +
49A ASP* 1.3 60.5 + - - +
51A LEU* 2.6 38.7 + - + +
52A GLU* 2.9 10.9 + - - +
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Residues in contact with ASP 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLY 5.4 3.4 + - - +
47A GLN 3.5 0.6 - - - -
48A LEU* 1.3 81.8 - - - +
50A GLU* 1.3 57.0 + - - +
52A GLU* 3.2 21.2 + - - +
53A LYS* 2.8 30.8 + - - +
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Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLY 5.7 0.2 - - - +
47A GLN* 3.1 19.8 + - + +
48A LEU 3.0 0.4 - - - -
49A ASP* 1.3 79.0 - - - +
51A LEU* 1.3 59.9 + - - +
53A LYS* 3.5 14.6 + - + +
54A ALA* 3.2 18.7 + - - +
62A THR* 3.8 13.9 - - - +
63A LYS* 3.2 54.1 + - + +
64A CYS 5.8 1.1 - - - +
65A ILE* 3.9 15.8 - - + +
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Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 4.0 23.1 - - + -
38A LEU* 4.0 17.0 - - + -
39A VAL* 5.0 4.0 - - + -
42A LEU* 3.4 34.5 - - + -
47A GLN 3.1 4.0 + - - +
48A LEU* 2.6 22.7 + - + +
50A GLU* 1.3 69.6 - - - +
52A GLU* 1.3 66.5 + - - +
54A ALA* 3.3 1.6 + - + -
55A ILE* 3.0 48.5 + - + +
65A ILE* 4.1 20.8 - - + +
92A TRP* 4.5 12.6 - - + -
124A PRO* 5.2 4.3 - - + -
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 4.0 9.9 - - + +
14A ARG* 2.7 45.7 + - - +
15A LEU* 4.1 19.1 - - + +
48A LEU 2.9 9.2 + - - +
49A ASP* 3.4 24.1 - - - +
51A LEU* 1.3 78.0 - - - +
53A LYS* 1.3 61.5 + - - +
55A ILE* 3.9 0.5 - - - +
56A THR* 2.9 42.6 + - + +
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Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ASP 2.8 17.1 + - - +
50A GLU* 3.5 19.2 + - + +
51A LEU 3.1 0.2 - - - -
52A GLU* 1.3 76.1 - - - +
54A ALA* 1.3 55.1 + - - +
56A THR* 3.0 6.2 + - - -
57A THR* 2.7 53.5 + - + +
59A ASN* 4.1 16.2 - - - +
61A ASN 5.5 0.4 + - - -
62A THR* 3.6 24.1 - - + +
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Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLU 3.2 11.7 + - - +
51A LEU* 3.9 2.9 - - + +
53A LYS* 1.3 79.5 - - - +
55A ILE* 1.3 59.9 + - + +
57A THR* 4.0 2.0 - - - -
58A GLN* 2.7 29.9 + - - +
59A ASN 4.7 1.8 - - - +
62A THR* 3.4 35.0 - - + +
65A ILE* 4.1 4.9 - - + -
123A ASN* 3.9 19.1 - - - +
124A PRO* 5.6 0.4 - - + -
125A TYR* 3.5 9.9 - - + -
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Residues in contact with ILE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 4.4 13.5 - - + -
18A TRP* 3.7 42.3 - - + -
51A LEU* 3.0 35.4 + - + +
52A GLU 3.9 2.2 - - - +
54A ALA* 1.3 76.3 - - + +
56A THR* 1.3 62.7 + - - +
58A GLN* 3.4 15.9 - - - +
92A TRP* 3.6 34.8 - - + +
124A PRO* 3.5 33.9 - - + -
125A TYR* 4.4 6.7 + - + -
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Residues in contact with THR 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ARG* 5.4 4.9 - - - +
15A LEU* 5.4 3.4 - - + -
18A TRP* 3.6 49.0 - - + +
52A GLU* 2.9 38.3 + - + +
53A LYS* 3.0 7.4 + - - -
55A ILE* 1.3 78.7 - - + +
57A THR* 1.3 69.5 + - - +
58A GLN* 3.7 8.1 + - - -
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Residues in contact with THR 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LYS* 2.7 45.8 + - + +
54A ALA* 4.0 0.5 - - - -
56A THR* 1.3 78.5 - - - +
58A GLN* 1.3 74.0 + - - +
59A ASN* 3.0 24.7 + - - +
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Residues in contact with GLN 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TRP* 3.9 17.5 - - + -
54A ALA 2.7 19.6 + - - -
55A ILE 3.4 15.9 - - - +
56A THR 3.7 12.7 + - - +
57A THR* 1.3 79.3 + - - +
59A ASN* 1.3 62.2 + - - +
60A VAL* 3.4 6.8 + - - +
125A TYR* 3.5 43.6 + - + +
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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