Contacts of the strand formed by residues 25 - 28 (chain X) in PDB entry 2OU0
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 TYR 25 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17X ILE* 3.6 20.4 - - + -
18X TYR* 3.4 3.6 - - - -
19X LYS* 3.7 39.3 + - + -
23X GLY 4.0 1.7 + - - -
24X TYR* 1.3 70.9 - - - +
26X THR* 1.3 55.6 + - - +
32X LEU* 3.7 1.6 - - - +
33X LEU* 2.8 30.1 + - - +
34X THR* 3.5 12.8 + - + +
36X SER 3.5 17.2 + - - -
37X PRO* 3.6 22.5 + - + -
38X SER 3.7 1.3 - - - -
39X LEU* 3.6 45.5 + - + +
42X ALA* 3.5 32.1 - - + -
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Residues in contact with THR 26 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X ILE* 3.3 5.9 - - - +
18X TYR* 2.6 71.2 + - + +
20X ASP* 3.4 18.0 + - + +
24X TYR 2.8 19.3 + - - -
25X TYR* 1.3 73.4 + - - +
27X ILE* 1.3 63.6 + - - +
30X GLY* 3.7 5.6 - - - -
31X HIS 3.3 30.3 - - - +
32X LEU* 4.0 6.6 - - + +
33X LEU* 3.9 5.5 - - - +
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Residues in contact with ILE 27 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14X ARG 3.7 4.7 - - - +
15X LEU 3.6 17.7 - - - +
16X LYS 3.7 12.8 - - - -
17X ILE* 3.6 15.5 - - + +
18X TYR* 3.6 7.6 - - - -
26X THR* 1.3 73.8 - - - +
28X GLY* 1.3 69.3 + - - +
30X GLY 3.8 0.5 + - - -
31X HIS* 3.0 40.0 + - - +
33X LEU* 4.2 13.0 - - + -
46X LEU* 3.6 45.5 - - + -
56X GLY 3.7 3.6 - - - +
58X ILE* 3.7 24.9 - - + -
66X LEU* 4.4 10.3 - - + -
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Residues in contact with GLY 28 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12X GLY 3.7 0.7 - - - +
13X LEU* 3.5 3.2 - - - -
14X ARG 2.7 44.0 + - - -
18X TYR* 3.8 6.4 + - - -
27X ILE* 1.3 76.0 - - - +
29X ILE* 1.3 64.3 + - - -
30X GLY 3.5 3.3 + - - -
31X HIS* 5.4 0.9 - - - -
58X ILE* 4.4 3.4 - - - -
63X ALA* 3.9 24.0 - - - -
66X LEU* 6.3 0.4 - - - -
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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