Contacts of the helix formed by residues 46 - 54 (chain B) in PDB entry 1OZ7
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 LYS 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A ARG* 5.0 2.3 - - - +
9B TYR* 3.3 21.8 + - - +
44B ASN* 2.5 44.4 + - - +
45B SER* 1.3 84.2 - - - +
47B GLU* 1.3 62.4 + - - +
48B VAL* 3.2 7.4 - - - +
49B ASP* 3.4 35.4 + - + +
50B PHE* 3.4 12.3 + - - +
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Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B TYR* 3.8 13.2 - - + -
12B TYR* 4.3 4.7 - - + -
14B TYR* 2.8 28.8 + - - +
41B SER 3.2 8.1 - - - +
42B PHE* 3.0 20.2 - - + -
43B ARG* 2.6 36.3 + - - +
44B ASN 4.2 1.7 - - - +
45B SER* 3.1 27.8 - - - +
46B LYS* 1.3 76.6 - - - +
48B VAL* 1.3 58.8 + - - +
50B PHE 3.1 0.7 + - - -
51B VAL* 2.4 45.1 + - + +
120B LYS* 3.1 18.4 + - - -
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Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ARG* 3.8 26.2 - - - +
91A TYR* 6.1 2.2 - - + -
42B PHE* 4.1 30.1 - - + -
44B ASN* 4.4 11.0 - - - +
46B LYS* 4.3 6.5 - - - +
47B GLU* 1.3 78.8 - - - +
49B ASP* 1.3 57.7 + - - +
51B VAL 3.5 0.3 - - - -
52B ILE* 2.7 42.3 + - + +
99B TYR* 3.3 42.0 - - + +
106B TRP* 5.0 1.6 - - - +
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Residues in contact with ASP 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LYS* 3.4 36.0 + - + +
47B GLU 3.4 0.2 - - - -
48B VAL* 1.3 79.9 - - - +
50B PHE* 1.3 52.3 + - - +
52B ILE* 3.0 14.3 - - - +
53B SER* 2.3 49.4 + - - +
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Residues in contact with PHE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B SER* 3.5 28.3 - - - -
8B VAL 3.6 14.8 - - - -
9B TYR* 3.4 55.0 - + + -
14B TYR* 3.6 22.9 - + - -
46B LYS 3.4 3.2 + - - +
47B GLU 3.1 6.1 + - - +
49B ASP* 1.3 77.6 - - - +
51B VAL* 1.3 73.0 + - + +
53B SER* 3.0 5.8 + - - -
54B LEU* 2.5 70.6 + - + -
55B ALA* 3.0 10.5 + - + -
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B TYR* 3.9 28.3 - - + -
40B VAL* 4.5 0.2 - - + -
42B PHE* 3.2 39.0 - - + -
47B GLU* 2.4 36.6 + - + +
48B VAL 3.6 0.7 - - - +
50B PHE* 1.3 76.2 - - + +
52B ILE* 1.3 60.0 + - + +
55B ALA* 2.6 44.1 - - + +
56B PHE* 2.8 2.9 + - + +
64B VAL* 5.8 3.8 - - + -
118B VAL* 4.1 28.9 - - + -
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Residues in contact with ILE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B PHE* 5.6 0.7 - - + -
48B VAL* 2.7 36.1 + - + +
49B ASP* 3.0 23.3 - - - +
51B VAL* 1.3 77.6 - - + +
53B SER* 1.3 58.8 + - - +
56B PHE* 2.9 24.4 - - + +
57B PRO* 3.5 4.7 - - - +
61B ASN* 4.3 7.1 - - - +
64B VAL* 6.1 3.1 - - + -
99B TYR* 3.4 37.7 - - + +
101B ASN* 3.3 26.2 - - - +
104B ASN* 4.7 9.6 - - - +
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Residues in contact with SER 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ASP* 2.3 48.5 + - - +
50B PHE* 3.3 0.2 - - - -
52B ILE* 1.3 69.8 - - - +
54B LEU* 1.3 87.4 + - - +
57B PRO* 2.8 22.8 - - - +
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B SER* 5.1 1.6 - - - +
50B PHE* 2.5 47.6 + - + -
53B SER* 1.3 112.4 - - - +
55B ALA* 1.3 56.9 + - - +
56B PHE 3.0 9.1 + - - -
57B PRO* 3.2 11.0 - - + +
58B MET* 3.2 25.6 - - + +
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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