Contacts of the strand formed by residues 43 - 47 (chain U) in PDB entry 5EEY
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 VAL 43 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11U VAL* 4.0 14.8 - - + -
12U ILE 3.3 6.5 - - - +
13U LYS* 3.7 26.7 - - + -
38U LEU* 4.9 0.9 - - - -
41U GLY 3.8 0.4 + - - -
42U GLU* 1.3 78.3 - - - +
44U LEU* 1.3 61.8 + - - +
45U ILE* 4.0 22.9 - - + -
55V ILE 3.7 0.9 - - - +
56V LYS* 3.3 7.1 - - - +
57V VAL* 2.7 38.3 + - + +
63V ILE* 4.0 23.1 - - + -
70V ILE* 4.5 6.5 - - + -
71V GLU 4.3 2.5 - - - +
72V SER* 3.8 25.3 - - - +
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Residues in contact with LEU 44 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10U VAL 3.8 1.6 - - - +
11U VAL* 3.6 1.0 - - - -
12U ILE* 2.8 40.7 + - + +
21U VAL* 3.7 35.2 - - + -
36U GLU* 4.3 17.7 - - + -
38U LEU* 4.1 18.1 - - + +
42U GLU 4.3 0.2 + - - -
43U VAL* 1.3 74.1 - - - +
45U ILE* 1.3 63.3 + - - +
46U ALA* 4.0 16.1 + - + -
24V LEU* 3.9 27.8 - - + -
54V ALA* 4.3 7.4 - - + -
55V ILE 3.5 13.7 - - - +
56V LYS* 4.1 11.7 - - + -
101V TRP* 5.2 5.6 - - + -
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Residues in contact with ILE 45 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9U PHE* 3.5 35.4 - - + -
10U VAL 3.4 3.6 - - - +
11U VAL* 4.2 10.3 - - + -
43U VAL* 4.0 16.6 - - + -
44U LEU* 1.3 76.2 - - - +
46U ALA* 1.3 59.4 + - - +
10V VAL* 4.0 28.3 - - + -
48V PHE* 3.7 20.0 - - + -
54V ALA* 3.1 3.6 - - - -
55V ILE* 2.7 53.8 + - + +
57V VAL* 4.8 7.4 - - + -
63V ILE* 4.3 20.9 - - + -
65V THR* 4.5 1.8 - - + -
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Residues in contact with ALA 46 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9U PHE* 3.1 5.6 - - - -
10U VAL* 2.9 46.2 + - + +
12U ILE* 5.3 1.3 - - + -
44U LEU* 4.0 19.0 - - + +
45U ILE* 1.3 74.6 - - - +
47U GLN* 1.3 61.0 + - - +
55U ILE* 4.5 2.2 - - + +
48V PHE* 5.0 0.2 - - - -
53V SER 4.1 3.8 - - - -
54V ALA* 4.1 4.5 - - + -
101V TRP* 3.8 29.8 - - + +
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Residues in contact with GLN 47 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5U THR 2.9 28.2 + - - -
6U ASN* 4.3 1.6 + - - +
7U SER* 3.4 19.1 + - - +
8U ASP 3.4 8.3 - - - +
9U PHE* 3.8 9.6 - - + -
46U ALA* 1.3 73.0 - - - +
48U PHE* 1.3 72.8 + - - +
49U THR* 3.4 4.9 - - + +
52U THR* 4.6 1.7 - - - -
55U ILE* 4.6 3.2 - - - +
8V ASP* 5.7 0.6 - - - +
26V ARG* 2.8 30.8 + - - -
48V PHE* 3.5 35.9 - - + +
53V SER* 3.1 22.1 + - - +
101V TRP* 2.8 29.5 + - - -
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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