Contacts of the strand formed by residues 44 - 50 (chain E) in PDB entry 1U3H
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 ALA 44 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35E TYR* 3.0 6.3 - - - -
36E GLN* 2.5 51.1 + - + +
42E GLY 4.9 1.8 - - - +
43E PRO* 1.3 77.0 - - - +
45E LEU* 1.3 67.2 + - - +
106F GLN 5.8 0.9 - - - -
108F PHE* 5.2 0.2 - - - -
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Residues in contact with LEU 45 (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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31E TYR* 4.6 5.8 - - - +
33E PRO* 3.9 25.6 - - + -
34E TRP 3.5 13.5 - - - +
35E TYR* 3.6 15.6 - - + -
44E ALA* 1.3 76.6 - - - +
46E LEU* 1.3 66.7 + - - +
47E ILE* 3.8 16.6 - - - +
48E SER* 4.4 7.4 - - - +
105F GLU* 3.1 57.0 + - + +
106F GLN 5.2 1.4 + - - -
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Residues in contact with LEU 46 (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 TRP* 2.7 20.2 + - + +
36E GLN* 4.3 25.4 - - + +
44E ALA 3.3 0.6 + - - -
45E LEU* 1.3 77.0 - - - +
47E ILE* 1.3 76.1 + - + +
58E ASP* 5.0 6.4 - - - +
62E PHE* 3.8 52.4 - - + -
75E LEU* 4.0 19.1 - - + -
88E TYR* 4.2 17.0 - - + -
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Residues in contact with ILE 47 (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 TRP* 3.1 22.4 + - + +
45E LEU* 3.8 4.3 - - - +
46E LEU* 1.3 103.0 - - + +
48E SER* 1.3 68.7 + - - +
56E LYS* 3.3 37.2 - - + +
58E ASP* 4.4 16.6 - - + +
62E PHE* 4.0 22.7 - - + +
64E ILE* 3.1 31.8 - - + +
75E LEU* 4.3 8.7 - - + -
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Residues in contact with SER 48 (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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31E TYR* 3.5 32.9 + - - -
32E PHE 3.7 4.7 - - - -
33E PRO* 3.5 17.0 - - - -
45E LEU* 4.4 10.2 - - - +
47E ILE* 1.3 75.0 - - - +
49E ILE* 1.3 61.4 + - - +
56E LYS* 2.9 35.0 + - - +
64E ILE* 3.8 3.1 - - - -
70H ARG* 5.3 1.6 + - - -
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Residues in contact with ILE 49 (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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30E ASP 3.9 0.2 - - - +
31E TYR* 3.7 5.2 - - - -
32E PHE* 3.0 48.5 + - + +
48E SER* 1.3 77.2 - - - +
50E LEU* 1.3 72.8 + - - +
53E SER* 3.1 33.4 - - - +
54E ASP 4.2 0.4 - - - -
55E LYS 4.0 10.5 - - - +
56E LYS* 3.9 25.8 - - + +
64E ILE* 3.7 26.7 - - + +
66E PHE* 3.7 18.8 - - + -
73E LEU* 4.6 4.9 - - + -
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Residues in contact with LEU 50 (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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30E ASP* 3.2 25.6 - - + +
31E TYR* 4.0 26.0 - - + -
49E ILE* 1.3 81.1 - - - +
51E SER* 1.3 54.4 + - - +
52E VAL* 2.5 29.6 + - + +
53E SER* 3.0 24.3 + - - +
66E PHE* 5.5 0.2 - - - -
69H GLU* 4.0 44.0 - - + +
70H ARG* 4.6 20.4 - - + +
73H ALA* 4.2 13.7 - - + -
77H THR* 6.2 0.7 - - + -
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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