Contacts of the strand formed by residues 70 - 76 (chain F) in PDB entry 5BOU
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 70 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65F VAL* 3.4 9.5 - - - +
66F VAL* 2.8 51.2 + - + +
67F ASP* 5.1 0.9 - - + -
68F ARG 3.8 0.4 - - - -
69F HIS* 1.3 115.2 - - + +
71F GLY* 1.3 72.0 + - - +
72F CYS* 4.1 13.5 - - - -
92F ALA* 5.6 4.5 - - + -
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Residues in contact with GLY 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F PHE* 3.6 40.9 - - - -
63F ILE* 5.1 4.0 - - - -
64F GLN 3.6 5.4 - - - -
65F VAL* 4.6 1.8 - - - -
69F HIS 4.3 0.4 + - - -
70F ILE* 1.3 79.7 - - - +
72F CYS* 1.3 67.6 + - - -
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Residues in contact with CYS 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F PHE* 5.5 1.6 - - - -
62F LYS 4.5 0.5 - - - +
63F ILE* 3.5 7.2 - - - +
64F GLN* 2.7 44.1 + - - +
66F VAL* 3.7 26.5 - - - -
70F ILE* 4.1 9.4 - - - -
71F GLY* 1.3 80.2 - - - -
73F VAL* 1.3 61.6 + - - +
74F TYR* 4.9 4.5 - - + -
85F VAL* 4.0 23.3 - - + -
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Residues in contact with VAL 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F SER* 3.8 16.0 + - - +
34F ILE 4.0 21.5 - - - +
44F PHE* 4.4 18.5 - - + -
45F ALA 4.6 1.3 - - - +
46F VAL* 3.8 32.8 - - + -
62F LYS* 5.3 3.6 - - + -
63F ILE* 3.9 23.3 - - + +
72F CYS* 1.3 73.7 - - - +
74F TYR* 1.3 71.4 + - - +
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Residues in contact with TYR 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F THR* 5.3 1.7 + - - -
33F SER* 3.9 7.5 + - - -
46F VAL* 5.0 4.7 - - - +
62F LYS* 4.2 19.8 + - + +
64F GLN* 2.6 32.9 + - + -
72F CYS* 4.9 4.5 - - + -
73F VAL* 1.3 87.4 - - - +
75F SER* 1.3 68.1 + - - +
77F LEU 5.0 1.6 - - - -
78F ILE* 3.6 47.8 + - + +
81F GLY* 3.5 32.3 - - - -
82F ARG* 3.4 18.2 - - - +
84F LEU* 6.3 1.8 - - + -
85F VAL* 3.9 10.5 - - + -
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Residues in contact with SER 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F VAL* 3.6 37.7 - - - +
31F THR* 2.7 31.5 + - - +
33F SER* 2.7 29.7 + - - -
74F TYR* 1.3 78.1 + - - +
76F GLY* 1.3 59.4 + - - +
78F ILE* 5.6 0.4 - - - -
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Residues in contact with GLY 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F ALA 3.5 23.1 - - - -
27F VAL* 3.9 5.8 - - - -
30F GLY* 4.0 15.1 - - - -
31F THR 4.9 0.2 - - - +
74F TYR* 6.2 0.2 - - - -
75F SER* 1.3 76.2 - - - +
77F LEU* 1.3 66.8 + - - +
78F ILE* 3.3 16.3 + - - +
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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