Contacts of the strand formed by residues 43 - 47 (chain O) in PDB entry 5EEZ
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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11O VAL* 4.0 23.6 - - + -
12O ILE 3.3 7.0 - - - +
13O LYS* 3.8 20.4 - - + -
38O LEU* 5.0 0.4 - - - -
41O GLY 3.7 0.2 + - - -
42O GLU* 1.3 81.4 - - - +
44O LEU* 1.3 63.0 + - - +
45O ILE* 4.0 13.0 - - + +
55P ILE 3.8 0.7 - - - +
56P LYS* 3.4 4.4 - - - +
57P VAL* 2.8 37.8 + - + +
63P ILE* 3.9 24.0 - - + -
70P ILE* 4.5 5.6 - - + -
71P GLU 4.3 2.2 - - - +
72P SER* 3.6 30.0 - - - +
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Residues in contact with LEU 44 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O VAL 3.6 1.9 - - - +
11O VAL* 3.6 1.4 - - - -
12O ILE* 2.8 44.1 + - + +
21O VAL* 3.8 37.0 - - + -
36O GLU* 4.2 18.8 - - + -
38O LEU* 4.0 18.1 - - + +
43O VAL* 1.3 74.4 - - - +
45O ILE* 1.3 61.3 + - - +
46O ALA* 4.1 15.6 + - + -
24P LEU* 4.0 26.5 - - + -
54P ALA* 4.4 8.1 - - + -
55P ILE 3.5 17.9 - - - +
56P LYS* 4.1 9.4 - - + -
101P TRP* 5.5 3.8 - - + -
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Residues in contact with ILE 45 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9O PHE* 3.5 28.9 - - + -
10O VAL 3.4 4.5 - - - +
11O VAL* 4.3 9.0 - - + -
43O VAL* 4.0 15.7 - - + +
44O LEU* 1.3 76.4 - - - +
46O ALA* 1.3 57.6 + - - +
10P VAL* 3.9 31.2 - - + -
12P ILE* 5.4 0.2 - - + -
48P PHE* 3.5 26.6 - - + -
54P ALA* 3.1 4.9 - - - +
55P ILE* 2.8 51.5 + - + +
57P VAL* 4.9 6.5 - - + -
63P ILE* 4.2 19.7 - - + -
65P THR* 4.5 1.8 - - + -
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Residues in contact with ALA 46 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9O PHE* 3.2 4.7 - - - -
10O VAL* 2.8 50.1 + - + +
12O ILE* 5.2 2.5 - - + -
44O LEU* 4.0 16.4 - - + +
45O ILE* 1.3 74.2 - - - +
47O GLN* 1.3 62.5 + - - +
55O ILE* 4.4 2.4 - - + +
53P SER 4.0 2.9 - - - -
54P ALA* 4.1 6.7 - - + -
101P TRP* 3.8 29.6 - - + +
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Residues in contact with GLN 47 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5O THR 3.0 25.4 + - - -
6O ASN* 4.3 0.8 - - - +
7O SER* 3.3 20.8 + - - +
8O ASP 3.3 8.1 - - - +
9O PHE* 3.8 16.6 - - + -
45O ILE 4.4 0.2 + - - -
46O ALA* 1.3 73.8 - - - +
48O PHE* 1.3 72.3 - - - +
49O THR* 3.5 5.1 - - + +
52O THR* 4.6 1.4 - - - -
55O ILE* 4.5 3.6 - - - +
7P SER* 5.5 0.2 - - - -
8P ASP* 5.8 1.4 - - - +
26P ARG* 2.7 29.4 + - - -
48P PHE* 3.5 32.4 - - + +
53P SER* 3.1 20.7 + - - +
101P TRP* 2.8 24.4 + - - -
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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