Contacts of the strand formed by residues 41 - 49 (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 GLY 41 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37F LYS* 3.8 3.3 - - - +
38F CYS* 2.9 35.9 + - - +
39F ASN 3.7 0.8 - - - -
40F ASP* 1.3 79.7 - - - +
42F VAL* 1.3 70.8 + - - +
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Residues in contact with VAL 42 (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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36F ILE 3.4 7.4 - - - +
37F LYS* 4.2 20.0 - - + -
38F CYS* 3.9 1.5 - - - -
41F GLY* 1.3 80.0 - - - +
43F VAL* 1.3 67.9 + - - +
44F PHE* 3.7 36.1 - - + -
69F HIS 6.1 0.7 - - - +
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Residues in contact with VAL 43 (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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35F GLY* 3.3 4.7 - - - -
36F ILE* 2.8 51.8 + - + +
38F CYS* 4.9 13.9 - - + -
42F VAL* 1.3 80.7 - - - +
44F PHE* 1.3 77.6 + - - +
45F ALA* 5.4 4.0 - - + -
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Residues in contact with PHE 44 (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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34F ILE 3.6 12.1 - - - +
35F GLY* 4.5 6.5 - - - -
42F VAL* 3.7 37.5 - - + -
43F VAL* 1.3 86.0 - - - +
45F ALA* 1.3 62.6 + - - +
63F ILE* 4.0 27.3 - - + +
71F GLY* 3.6 45.5 - - - -
72F CYS* 5.5 0.4 - - - -
73F VAL* 4.4 20.2 - - + -
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Residues in contact with ALA 45 (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* 3.5 2.9 - - - -
34F ILE* 2.8 55.3 + - + +
43F VAL* 5.4 4.7 - - + -
44F PHE* 1.3 75.3 - - - +
46F VAL* 1.3 61.7 + - - +
63F ILE* 4.5 5.4 - - - -
73F VAL* 4.6 1.7 - - - +
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Residues in contact with VAL 46 (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* 4.2 4.9 - - - +
32F THR 3.5 12.8 - - - +
33F SER* 3.9 11.2 - - - -
45F ALA* 1.3 77.5 - - - +
47F GLU* 1.3 73.7 + - - +
48F LYS* 3.8 15.8 + - + +
62F LYS* 4.2 28.0 - - + -
63F ILE* 4.1 23.5 - - + +
73F VAL* 3.8 13.9 - - + -
74F TYR 5.0 3.8 - - - +
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Residues in contact with GLU 47 (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* 3.0 33.4 + - - +
32F THR* 2.8 50.3 + - - +
46F VAL* 1.3 76.6 - - - +
48F LYS* 1.3 63.9 + - - +
49F LEU* 3.6 29.7 - - + +
62F LYS* 4.1 1.2 + - - -
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Residues in contact with LYS 48 (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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46F VAL* 3.8 15.5 + - + +
47F GLU* 1.3 77.9 - - - +
49F LEU* 1.3 65.1 + - - +
50F ILE* 3.4 10.7 + - - +
58F GLN* 4.5 17.4 - - - +
59F LYS 4.6 0.2 - - - +
60F ASN* 3.0 45.0 + - - +
61F VAL* 4.2 4.9 - - - +
62F LYS* 4.0 30.7 - - + +
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Residues in contact with LEU 49 (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* 3.8 27.5 - - + +
47F GLU* 3.6 27.1 + - + +
48F LYS* 1.3 70.8 - - - +
50F ILE* 1.3 61.4 + - - +
51F THR* 3.2 15.5 + - - +
55F LEU* 4.2 5.5 - - - +
62F LYS* 5.5 0.6 - - - +
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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