Contacts of the strand formed by residues 40 - 45 (chain B) in PDB entry 3UTR
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 40 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B TYR* 4.0 46.3 + - + +
34B PHE* 3.7 14.8 - - + -
35B SER* 3.5 33.6 - - - +
38B GLY 3.3 3.5 + - - +
39B GLN* 1.3 78.2 + - - +
41B LEU* 1.3 66.6 + - - +
42B ASP* 3.5 25.4 - - - +
43B ILE* 3.8 14.6 - - + -
57B VAL* 4.2 7.2 - - + -
58B ILE 3.6 6.5 - - - +
59B PHE* 3.7 22.4 - - + +
41D LEU* 5.5 1.4 - - - +
97D MET* 4.9 6.9 - - - +
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Residues in contact with LEU 41 (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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39B GLN* 3.9 2.4 + - - +
40B ILE* 1.3 74.9 - - - +
42B ASP* 1.3 62.6 + - - +
58B ILE* 2.7 13.1 + - + +
59B PHE 3.9 6.3 - - - +
60B LYS* 3.7 20.9 - - + +
93B ILE* 3.6 23.0 - - + +
94B ILE* 3.5 32.8 - - + -
97B MET* 4.2 13.9 - - + -
39D GLN* 3.5 28.3 - - - +
40D ILE 5.5 1.6 - - - +
41D LEU* 4.2 30.8 - - + +
93D ILE* 5.7 7.8 - - - +
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Residues in contact with ASP 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LYS* 4.8 8.0 + - - -
31B TYR* 6.3 0.4 - - - -
40B ILE* 3.5 5.8 - - - +
41B LEU* 1.3 82.3 - - - +
43B ILE* 1.3 85.6 + - - +
44B LEU* 3.1 26.7 - - + +
58B ILE* 2.9 38.9 + - + +
93B ILE* 4.5 8.0 - - + +
93D ILE* 5.7 6.0 - - - +
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Residues in contact with ILE 43 (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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27B LYS* 3.6 41.3 + - + +
30B LEU* 3.9 30.1 - - + -
31B TYR* 3.5 47.1 - - + +
40B ILE* 3.8 14.1 - - + -
42B ASP* 1.3 92.5 + - - +
44B LEU* 1.3 66.1 + - - +
45B VAL* 3.9 12.3 + - + -
55B ALA* 4.8 0.7 - - + -
56B PHE 3.4 8.5 - - - +
57B VAL* 4.2 12.8 - - + -
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Residues in contact with LEU 44 (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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18A A 3.8 24.9 - - + +
19A C 3.9 29.8 - - - +
42B ASP* 3.1 32.5 - - + +
43B ILE* 1.3 74.6 - - - +
45B VAL* 1.3 59.4 + - - +
55B ALA* 3.4 6.4 - - - +
56B PHE* 2.9 46.7 + - + +
58B ILE* 4.4 15.3 - - + -
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Residues in contact with VAL 45 (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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23B LYS* 3.5 44.3 + - + +
26B LEU* 3.8 29.6 - - + -
27B LYS* 4.1 26.3 - - + +
30B LEU* 4.4 0.2 - - + -
43B ILE* 3.9 7.6 + - + -
44B LEU* 1.3 78.1 - - - +
46B SER* 1.3 66.7 + - - +
47B ARG* 5.0 3.6 - - + -
54B GLN 4.2 6.7 - - - +
55B ALA* 3.7 22.0 - - + -
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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
------------------------------------------------------------
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