Contacts of the helix formed by residues 56 - 68 (chain F) in PDB entry 1DUX
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 ASN 56 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F GLU* 3.5 13.9 - - - +
43F ALA* 3.2 14.2 - - - +
54F ASN 4.5 3.6 + - - +
55F MET* 1.3 77.4 - - - +
57F TYR* 1.3 60.6 + - - +
58F ASP* 3.2 12.0 + - - +
59F LYS* 3.0 40.6 + - - +
60F LEU* 3.0 20.4 + - - +
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Residues in contact with TYR 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D A 4.8 7.9 - - + -
4D C 2.6 29.7 + - - -
36F LEU* 3.6 26.0 - - + -
39F ALA* 3.6 26.9 - - + +
40F GLU* 3.0 27.7 + - - +
43F ALA* 3.5 5.7 - - - +
56F ASN* 1.3 73.4 - - - +
58F ASP* 1.3 60.1 + - - +
60F LEU* 4.3 6.7 - - + -
61F SER* 2.7 59.7 + - - -
81F PHE* 3.6 22.9 - + - -
83F TYR* 2.6 29.0 + + - -
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Residues in contact with ASP 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D C 5.4 3.6 + - - -
5D C 4.4 7.4 + - - -
7E C 4.2 4.7 - - - -
8E C 2.9 38.4 + - - -
40F GLU* 4.8 1.4 + - - -
56F ASN* 3.2 12.9 + - - +
57F TYR* 1.3 78.7 - - - +
59F LYS* 1.3 71.3 + - - +
61F SER* 2.9 18.0 + - - -
62F ARG* 3.4 10.7 + - - +
65F ARG* 4.0 3.1 + - - -
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Residues in contact with LYS 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E T 4.4 2.6 + - + +
6E T 2.6 84.6 + - + +
7E C 5.0 5.2 + - + +
54F ASN* 2.9 39.5 + - - +
55F MET* 3.6 14.8 - - + +
56F ASN* 3.0 30.1 + - - +
58F ASP* 1.3 87.1 - - - +
60F LEU* 1.3 64.2 + - - +
61F SER 3.3 0.2 - - - -
62F ARG* 3.2 4.3 + - - +
63F ALA* 3.1 20.3 + - - +
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Residues in contact with LEU 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E T 5.0 0.4 - - - -
7F LEU* 4.3 14.6 - - + -
11F LEU* 5.1 1.8 - - + -
36F LEU* 4.1 16.8 - - + -
39F ALA 5.3 0.2 - - - +
42F VAL* 4.1 12.3 - - + -
43F ALA* 3.7 32.1 - - + +
46F TRP* 3.9 27.1 - - + -
55F MET* 3.7 9.1 - - - -
56F ASN 3.0 17.3 + - - +
57F TYR* 4.1 6.3 - - + +
59F LYS* 1.3 74.4 - - - +
61F SER* 1.3 69.0 + - - +
63F ALA* 3.0 9.8 + - - +
64F LEU* 3.0 42.7 + - + +
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Residues in contact with SER 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D C 5.6 1.8 - - - -
57F TYR* 2.7 52.3 + - - -
58F ASP* 2.9 14.2 + - - -
60F LEU* 1.3 79.0 - - - +
62F ARG* 1.3 55.3 + - - +
64F LEU* 3.1 8.9 + - - +
65F ARG* 2.9 51.9 + - - +
83F TYR* 4.0 7.8 + - - -
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Residues in contact with ARG 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D G 3.3 41.6 + - - +
7D G 2.8 46.4 + - - -
8D A 3.9 10.2 + - - +
5E T 4.3 5.6 - - + -
6E T 3.3 27.4 - - + +
7E C 4.0 2.5 - - - +
58F ASP 3.4 7.1 + - - +
59F LYS 3.2 9.8 + - - +
60F LEU 3.1 0.4 - - - -
61F SER* 1.3 77.5 + - - +
63F ALA* 1.3 66.4 + - - +
65F ARG* 3.1 22.3 + - - +
66F TYR* 2.9 40.7 + - - +
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Residues in contact with ALA 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E C 4.0 15.9 - - - -
5E T 3.9 29.8 - - + +
7F LEU* 3.5 19.7 - - + -
59F LYS 3.1 11.5 + - - +
60F LEU 3.0 10.6 + - - +
62F ARG* 1.3 76.9 - - - +
64F LEU* 1.3 61.9 + - - +
66F TYR* 3.1 24.8 + - - +
67F TYR* 3.4 8.3 + - - -
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Residues in contact with LEU 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F LEU* 3.4 21.5 - - + -
11F LEU* 3.8 21.1 - - + -
34F PHE* 5.4 0.9 - - + -
36F LEU* 4.5 5.6 - - + -
57F TYR* 5.1 0.2 - - + -
60F LEU* 3.0 34.0 + - + +
61F SER* 3.1 7.8 + - - +
63F ALA* 1.3 77.3 - - - +
65F ARG* 1.3 56.4 + - - +
67F TYR* 3.0 38.2 + - + +
68F TYR* 3.3 13.0 - - - -
73F ILE* 3.9 13.0 - - + +
83F TYR* 3.6 49.6 - - + +
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Residues in contact with ARG 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D C 4.3 10.7 - - - +
5D C 3.3 62.4 + - - +
6D G 2.9 44.0 + - + +
8E C 4.8 1.0 - - - +
58F ASP* 4.0 4.8 + - - -
61F SER* 2.9 40.2 + - - +
62F ARG* 3.1 38.7 + - - +
64F LEU* 1.3 76.5 - - - +
66F TYR* 1.3 60.4 + - - +
68F TYR* 3.0 46.3 + - + +
69F ASP* 4.4 1.4 + - - -
83F TYR* 5.2 1.2 + - - +
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Residues in contact with TYR 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E C 5.3 0.3 - - - +
3E A 3.4 41.0 + + + +
4E C 3.7 47.8 - + - -
5E T 5.0 4.7 - - + -
62F ARG* 2.9 22.4 + - - +
63F ALA* 3.1 17.3 - - - +
65F ARG* 1.3 76.2 - - - +
67F TYR* 1.3 77.7 + + - +
68F TYR 3.3 0.4 + - - -
69F ASP* 4.1 6.9 + - - +
70F LYS* 3.5 44.7 + - + +
72F ILE* 6.1 0.2 - - + -
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Residues in contact with TYR 67 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E C 2.6 34.1 + - - -
7F LEU* 3.3 22.2 - - + +
8F TRP* 3.1 50.1 + + + -
63F ALA 3.9 1.6 - - - -
64F LEU* 3.0 34.4 + - + +
66F TYR* 1.3 97.9 - + - +
68F TYR* 1.3 62.3 + - - +
69F ASP 3.3 0.2 - - - -
70F LYS* 3.0 13.5 + - + -
71F ASN 3.2 8.8 + - - -
72F ILE* 3.4 29.8 + - + -
73F ILE* 3.5 25.4 - - + +
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Residues in contact with TYR 68 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D C 2.7 33.0 + - - -
6D G 3.9 19.3 - - - -
64F LEU 3.3 17.9 - - - -
65F ARG* 3.0 35.4 + - + +
67F TYR* 1.3 76.4 - - - +
69F ASP* 1.3 67.9 + - - +
71F ASN 3.2 5.0 + - - -
73F ILE* 3.3 18.2 - - + -
74F ARG* 2.9 39.0 + - - +
75F LYS* 3.4 30.7 - - + +
83F TYR* 3.5 18.0 - + - -
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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
------------------------------------------------------------
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