Contacts of the helix formed by residues 45 - 54 (chain A) in PDB entry 1OJ7
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 GLY 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A VAL 3.5 5.3 + - - -
42A LYS 3.7 6.2 + - - -
43A LYS 3.4 3.6 + - - -
44A THR* 1.3 77.8 + - - +
46A VAL* 1.3 64.6 + - - +
47A LEU 3.4 2.7 - - - -
48A ASP* 3.3 17.1 + - - +
49A GLN* 3.1 29.8 + - - +
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Residues in contact with VAL 46 (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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41A VAL* 3.4 7.0 + - + +
44A THR* 3.3 23.5 - - - +
45A GLY* 1.3 75.6 - - - +
47A LEU* 1.3 66.9 + - - +
49A GLN* 3.1 11.8 + - - +
50A VAL* 3.1 23.9 + - + +
92A VAL* 4.0 23.3 - - + -
136A VAL* 4.6 0.9 - - + -
138A THR* 4.4 11.4 - - + -
179A TYR* 3.8 55.0 - - + +
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Residues in contact with LEU 47 (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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34A ILE* 3.8 28.3 - - + -
36A TYR* 3.9 36.1 - - + -
41A VAL* 3.2 29.9 + - + +
42A LYS* 4.2 21.3 - - + +
46A VAL* 1.3 78.0 - - - +
48A ASP* 1.3 61.2 + - - +
50A VAL* 3.2 8.9 + - + +
51A LEU* 3.0 46.4 + - + +
61A GLU* 4.0 12.8 - - - +
92A VAL* 5.1 5.2 - - + -
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Residues in contact with ASP 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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42A LYS* 5.1 6.5 - - - +
45A GLY* 3.3 17.9 + - - +
46A VAL 3.2 0.8 - - - -
47A LEU* 1.3 79.6 - - - +
49A GLN* 1.3 59.2 + - - +
51A LEU* 3.5 16.7 + - - +
52A ASP* 3.0 30.0 + - - +
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Residues in contact with GLN 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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19A ILE* 4.0 17.9 - - + +
44A THR 5.1 2.6 + - - -
45A GLY 3.1 23.9 + - - +
46A VAL* 3.1 11.0 + - - +
48A ASP* 1.3 77.2 - - + +
50A VAL* 1.3 56.4 + - + +
52A ASP* 3.4 7.2 + - - +
53A ALA* 3.0 28.8 + - - +
179A TYR* 2.6 45.9 + - - +
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Residues in contact with VAL 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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19A ILE* 4.1 19.3 - - + -
22A LEU* 4.2 5.2 - - + -
34A ILE* 3.8 18.8 - - + -
46A VAL* 3.1 15.0 + - + +
47A LEU* 3.2 8.9 + - + +
49A GLN* 1.3 77.3 - - + +
51A LEU* 1.3 62.8 + - - +
53A ALA* 3.1 9.6 + - - +
54A LEU* 3.1 22.8 + - + +
90A LEU* 3.7 28.7 - - + -
92A VAL* 4.1 27.6 - - + -
136A VAL* 4.2 9.9 - - + -
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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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34A ILE* 3.5 26.9 - - + -
47A LEU* 3.0 36.5 + - + +
48A ASP* 3.9 17.3 - - - +
49A GLN 3.4 0.2 - - - -
50A VAL* 1.3 76.5 - - - +
52A ASP* 1.3 56.4 + - - +
54A LEU* 3.5 5.5 + - - -
55A LYS* 3.1 27.2 + - - +
59A VAL* 4.0 12.3 - - + -
61A GLU* 3.9 29.6 - - + +
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Residues in contact with ASP 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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23A ARG* 4.7 0.5 + - - -
48A ASP 3.0 19.2 + - - +
49A GLN* 3.6 6.9 - - - +
51A LEU* 1.3 75.4 - - - +
53A ALA* 1.3 65.9 + - - +
55A LYS* 2.7 51.1 + - - +
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Residues in contact with ALA 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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19A ILE* 4.3 17.7 - - + +
22A LEU* 4.0 23.6 - - + -
23A ARG* 2.9 35.5 + - + +
49A GLN 3.0 14.2 + - - +
50A VAL 3.1 9.4 + - - +
52A ASP* 1.3 77.7 + - - +
54A LEU* 1.3 60.4 + - + +
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Residues in contact with LEU 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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22A LEU* 4.1 10.3 - - + -
23A ARG* 3.4 21.3 - - - +
26A ILE* 3.6 25.8 - - + -
32A VAL* 4.3 9.0 - - + -
34A ILE* 4.2 17.7 - - + -
50A VAL 3.1 14.3 + - - +
51A LEU* 3.5 6.9 + - - +
52A ASP 3.2 0.2 - - - -
53A ALA* 1.3 81.1 - - - +
55A LYS* 1.3 65.4 + - - +
56A GLY 3.3 0.3 + - - -
57A MET* 3.0 33.4 + - - +
59A VAL* 4.1 22.2 - - + +
90A LEU* 3.8 25.4 - - + -
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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