Contacts of the helix formed by residues 63 - 72 (chain E) in PDB entry 2ODY
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 THR 63 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E PHE* 3.5 8.2 - - - -
61E PHE* 3.6 8.8 - - - +
62E GLU* 1.3 86.2 - - + +
64E ILE* 1.3 63.3 + - - +
65E GLU* 3.4 21.0 + - - +
66E GLU* 3.3 36.8 + - - +
67E CYS* 3.3 15.8 + - - +
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Residues in contact with ILE 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E PHE* 3.6 31.8 - - + -
46E CYS* 3.7 34.3 - - + +
63E THR* 1.3 71.9 - - - +
65E GLU* 1.3 78.8 + - + +
67E CYS* 3.4 3.7 + - - +
68E GLN* 2.9 52.3 + - - +
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Residues in contact with GLU 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E THR* 3.2 18.1 + - - +
64E ILE* 1.3 95.9 + - + +
66E GLU* 1.3 61.3 + - + +
68E GLN* 3.3 14.0 + - - +
69E LYS* 2.9 32.8 + - - +
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Residues in contact with GLU 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E PHE* 3.9 15.4 - - + +
62E GLU* 3.4 33.5 + - - +
63E THR* 3.3 31.1 + - - +
65E GLU* 1.3 77.7 - - + +
67E CYS* 1.3 62.0 + - - +
69E LYS* 3.6 7.7 + - - +
70E ALA* 3.1 25.1 + - - +
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Residues in contact with CYS 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E PHE* 4.1 5.4 - - + -
38E TYR* 3.8 5.2 - - - -
39E PHE* 3.8 26.9 - - - -
46E CYS* 2.1 48.0 - - + -
61E PHE* 3.5 32.0 - - + -
63E THR 3.3 6.3 + - - +
64E ILE 3.5 6.1 - - - +
65E GLU 3.3 0.4 - - - -
66E GLU* 1.3 78.5 - - - +
68E GLN* 1.3 50.6 + - - +
70E ALA* 3.2 1.2 + - - +
71E CYS* 2.7 40.4 + - - +
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Residues in contact with GLN 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E CYS* 3.9 17.4 - - + +
64E ILE* 2.9 42.2 + - - +
65E GLU* 3.3 14.3 + - - +
67E CYS* 1.3 76.6 - - - +
69E LYS* 1.3 60.0 + - - +
72E GLY* 2.8 35.5 + - - +
73E ALA 4.9 2.1 - - - +
74E PRO* 5.9 0.3 - - - +
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Residues in contact with LYS 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B THR* 6.0 4.6 - - + +
148B TRP* 3.6 59.7 + - + +
149B THR* 5.5 2.4 + - - +
18E ASN* 5.4 0.3 + - - -
65E GLU 2.9 16.9 + - - +
66E GLU* 3.8 7.6 - - - +
68E GLN* 1.3 78.3 - - - +
70E ALA* 1.3 59.2 + - - +
72E GLY 4.9 2.9 - - - +
74E PRO* 5.8 4.5 - - - +
75E GLU* 5.9 6.3 - - - +
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Residues in contact with ALA 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B TRP* 5.8 0.9 - - - -
18E ASN* 2.8 29.0 + - - +
20E PHE* 4.2 12.1 - - + -
21E CYS* 3.5 5.4 - - - -
61E PHE* 3.6 28.9 - - + -
66E GLU 3.1 18.0 + - - +
67E CYS 3.9 0.2 - - - +
69E LYS* 1.3 79.9 - - - +
71E CYS* 1.3 56.7 + - - +
72E GLY 5.0 0.9 - - - -
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Residues in contact with CYS 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B TRP* 2.8 25.6 + - - +
16E GLN 5.3 0.3 + - - -
20E PHE* 4.1 0.9 - - - -
21E CYS* 2.1 53.9 - - - +
39E PHE* 3.5 37.3 - - + -
59E ASN* 4.5 0.2 - - - -
61E PHE* 4.0 25.1 - - - -
67E CYS 2.7 16.2 + - - +
69E LYS 3.5 0.2 - - - -
70E ALA* 1.3 76.8 - - - +
72E GLY* 1.3 60.3 + - - +
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Residues in contact with GLY 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B TRP* 3.2 17.3 - - - -
39E PHE* 4.6 8.0 - - - -
46E CYS* 5.8 0.9 - - - -
67E CYS 3.8 0.4 + - - -
68E GLN* 2.8 32.1 + - - +
69E LYS 4.9 2.8 - - - +
70E ALA 5.0 0.3 - - - -
71E CYS* 1.3 76.6 + - - +
73E ALA* 1.3 68.2 - - - -
74E PRO* 3.3 4.7 - - - +
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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