Contacts of the helix formed by residues 55 - 68 (chain B) in PDB entry 2ODG
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 ASP 55 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B LEU* 2.7 25.4 + - - +
53B LYS* 3.0 4.6 + - + +
54B LYS* 1.3 68.5 - - - +
56B GLU* 1.3 56.7 + - - +
57B ASP* 2.6 13.5 + - - +
58B LEU* 2.3 63.0 + - + +
59B PHE* 2.8 27.2 + - - +
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Residues in contact with GLU 56 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54B LYS 2.8 6.2 + - - +
55B ASP* 1.3 73.3 + - - +
57B ASP* 1.3 63.7 + - - +
59B PHE* 4.3 0.7 - - - -
60B ARG* 2.9 70.7 + - - +
75B ARG* 5.1 6.8 + - - +
78B PHE* 3.5 48.5 - - + +
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Residues in contact with ASP 57 (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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55B ASP* 2.6 13.5 + - - +
56B GLU* 1.3 77.4 - - - +
58B LEU* 1.3 62.7 + - + +
60B ARG* 3.6 24.2 + - - +
61B GLU* 3.1 28.3 + - - +
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Residues in contact with LEU 58 (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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52B LEU* 4.0 25.2 - - + +
55B ASP* 2.3 59.6 + - + +
57B ASP* 1.3 71.7 - - + -
59B PHE* 1.3 57.3 + - - +
61B GLU* 3.8 13.4 - - + +
62B TRP* 2.8 31.5 + - - +
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Residues in contact with PHE 59 (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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45B VAL* 5.3 2.7 - - + -
49B PHE* 3.7 29.4 - + + -
52B LEU* 3.5 16.9 - - + +
55B ASP 2.8 19.9 + - - +
56B GLU* 3.8 4.9 - - - +
58B LEU* 1.3 78.2 - - - +
60B ARG* 1.3 69.1 + - + +
62B TRP* 3.1 27.6 + + - +
63B LEU* 2.8 47.7 + - + +
74B SER* 4.2 5.8 - - - -
77B CYS* 3.9 22.4 - - + -
78B PHE* 4.1 17.9 - + + -
81B LEU* 3.7 31.0 - - + -
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Residues in contact with ARG 60 (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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56B GLU* 2.9 52.8 + - + +
57B ASP* 3.6 20.6 + - - +
59B PHE* 1.3 84.4 - - + +
61B GLU* 1.3 63.1 + - - +
63B LEU* 4.1 0.4 - - - +
64B LYS* 2.9 29.4 + - - +
71B ALA* 5.0 6.4 + - - +
74B SER* 3.3 38.6 - - - +
75B ARG* 4.0 29.7 - - - +
78B PHE* 5.5 1.6 - - + -
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Residues in contact with GLU 61 (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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57B ASP* 3.1 21.2 + - - +
58B LEU* 3.9 14.7 - - + +
60B ARG* 1.3 77.3 - - - +
62B TRP* 1.3 58.0 + - - +
64B LYS* 4.5 4.5 - - + -
65B ASP* 2.7 42.8 + - + +
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Residues in contact with TRP 62 (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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34B LEU* 4.9 4.5 - - + -
39B PHE* 3.8 20.1 - + - -
45B VAL* 4.5 12.3 - - + -
48B GLN* 2.7 57.6 + - + -
52B LEU* 4.2 13.5 - - + -
58B LEU 2.8 20.3 + - - +
59B PHE* 3.5 25.1 - + - +
61B GLU* 1.3 77.6 - - - +
63B LEU* 1.3 87.7 + - + +
65B ASP* 4.7 2.2 - - - -
66B THR* 2.3 68.8 + - + +
27C VAL* 4.6 17.8 - - + +
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Residues in contact with LEU 63 (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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26B ILE* 4.3 22.9 - - + -
34B LEU* 4.3 20.9 - - + -
45B VAL* 5.0 4.7 - - + -
59B PHE* 2.8 40.9 + - + +
60B ARG* 4.1 3.4 - - - +
62B TRP* 1.3 110.9 - - + +
64B LYS* 1.3 59.0 + - - +
66B THR* 3.2 1.3 + - - -
67B CYS* 2.8 63.3 + - - -
69B ALA* 4.2 10.3 - - + -
74B SER* 5.0 5.8 - - - -
77B CYS* 5.5 1.3 - - - -
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Residues in contact with LYS 64 (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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60B ARG 2.9 19.3 + - - +
61B GLU* 4.1 4.3 - - - +
63B LEU* 1.3 79.0 - - - +
65B ASP* 1.3 60.5 + - - +
68B GLY* 2.6 33.6 + - - -
69B ALA* 3.2 31.1 - - + +
70B ASN* 5.2 4.2 - - - +
71B ALA* 5.0 14.6 - - - +
74B SER* 5.8 2.6 - - - -
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Residues in contact with ASP 65 (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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37B ARG* 4.2 7.1 + - - -
61B GLU* 2.7 31.5 + - + +
62B TRP* 4.2 2.7 - - - +
64B LYS* 1.3 75.0 - - - +
66B THR* 1.3 60.9 + - - +
67B CYS 5.2 0.2 - - - -
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Residues in contact with THR 66 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B LYS* 4.8 3.1 - - - +
34B LEU* 4.0 20.0 - - + -
37B ARG* 3.4 52.9 + - + +
39B PHE* 5.4 1.6 - - + -
62B TRP* 2.3 56.1 + - + +
63B LEU* 3.7 5.2 - - - -
64B LYS 3.1 0.2 - - - -
65B ASP* 1.3 80.8 - - - +
67B CYS* 1.3 57.8 + - - +
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Residues in contact with CYS 67 (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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30B LEU* 3.7 20.8 - - + +
33B LYS* 3.4 47.7 + - + +
34B LEU* 4.8 5.6 - - + -
63B LEU* 2.8 50.0 + - + -
64B LYS 3.6 0.2 - - - -
65B ASP 5.1 0.2 - - - -
66B THR* 1.3 75.2 - - - +
68B GLY* 1.3 62.4 + - - +
69B ALA* 3.1 19.1 - - - -
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Residues in contact with GLY 68 (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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30B LEU* 4.8 3.1 - - - -
64B LYS* 2.6 29.3 + - - +
67B CYS* 1.3 74.7 - - - +
69B ALA* 1.3 71.9 + - - +
70B ASN* 3.5 9.2 + - - +
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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