Contacts of the strand formed by residues 34 - 40 (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 ILE 34 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32E ALA* 3.9 15.0 - - + -
33E LEU* 1.3 74.8 - - - +
35E PRO* 1.4 71.3 - - + +
36E ARG* 3.3 32.6 + - - +
49E PHE 3.6 0.9 - - - +
50E SER* 4.4 1.1 - - - -
51E TYR* 2.8 47.9 + - + +
53E GLY* 3.6 31.0 - - - +
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Residues in contact with PRO 35 (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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33E LEU 3.4 10.1 - - - +
34E ILE* 1.4 87.5 - - + +
36E ARG* 1.3 68.4 + - - +
37E PHE* 5.4 6.0 - - + -
48E MET* 5.6 12.6 - - + -
49E PHE 3.7 7.0 - - - +
50E SER* 5.0 2.0 - - - +
62E GLU* 4.4 7.1 - - - +
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Residues in contact with ARG 36 (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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34E ILE* 3.8 22.2 - - + +
35E PRO* 1.3 78.6 + - - +
37E PHE* 1.3 65.9 + - - +
48E MET* 3.1 9.4 - - - +
49E PHE* 2.9 47.2 + - + +
51E TYR* 3.5 41.6 - - + -
60E ASN* 2.7 47.5 + - - +
61E PHE 3.4 18.4 - - - -
62E GLU* 3.8 30.5 + - - +
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Residues in contact with PHE 37 (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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35E PRO* 5.4 5.2 - - + -
36E ARG* 1.3 79.4 - - - +
38E TYR* 1.3 60.3 + - - +
46E CYS 4.5 2.0 - - - -
47E THR 3.4 6.7 - - - +
48E MET* 3.9 39.5 - - + -
49E PHE* 3.9 2.2 - - - -
60E ASN* 3.4 5.4 - - - -
61E PHE* 2.7 44.6 + - - +
62E GLU 3.7 18.2 - - - -
63E THR* 3.5 22.9 - - - +
64E ILE* 3.7 43.5 - - + -
67E CYS* 4.1 12.8 - - + -
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Residues in contact with TYR 38 (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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23E LEU 5.0 0.4 - - - -
24E PRO* 5.0 0.9 - - + -
25E ALA* 3.7 35.4 - - + -
37E PHE* 1.3 72.9 - - - +
39E PHE* 1.3 68.3 + - - +
40E ASN* 3.0 41.5 + - + -
46E CYS* 3.4 0.5 - - - -
47E THR* 2.7 77.3 + - + +
48E MET 4.2 0.7 - - - -
49E PHE* 3.5 28.9 - + + -
59E ASN* 3.2 30.1 - - - +
67E CYS* 3.8 7.0 - - - -
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Residues in contact with PHE 39 (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* 3.7 49.4 - + + -
21E CYS* 3.5 30.8 - - + +
23E LEU 4.5 1.4 - - - +
38E TYR* 1.3 74.6 - - - +
40E ASN* 1.3 65.1 + - - +
41E THR* 3.7 15.5 + - + +
44E GLY* 3.4 30.5 - - - -
45E LYS 4.0 4.3 - - - -
46E CYS* 4.2 13.0 - - - -
59E ASN* 2.8 30.7 + - - +
67E CYS* 3.8 5.3 - - - -
71E CYS* 3.5 47.8 - - + -
72E GLY* 4.6 4.7 - - - -
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Residues in contact with ASN 40 (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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38E TYR* 3.0 32.7 + - + -
39E PHE* 1.3 73.5 - - - +
41E THR* 1.3 54.2 + - - +
42E GLU* 3.0 34.7 + - - +
43E THR* 3.0 29.1 + - - +
44E GLY* 2.7 36.4 + - - -
45E LYS 3.0 13.8 + - - +
47E THR* 3.5 11.6 + - - +
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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