Contacts of the helix formed by residues 76 - 87 (chain B) in PDB entry 4BT9
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 THR 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A ASP* 5.1 0.2 + - - -
110A GLN* 2.9 26.2 + - - +
72B LYS* 2.8 34.6 + - + -
75B ASN* 1.3 80.0 + - - +
77B GLU* 1.3 65.9 + - + +
78B TRP 3.4 0.9 - - - -
79B SER* 3.2 6.5 + - - -
80B GLU* 3.0 45.5 + - + +
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Residues in contact with GLU 77 (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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42B TRP* 2.7 31.9 + - + +
45B LYS* 2.6 35.2 + - - -
46B LEU* 4.0 5.9 - - + +
49B LEU* 5.4 0.7 - - - +
69B LYS* 5.7 2.8 + - - -
72B LYS* 3.1 6.8 + - + +
73B ARG* 3.4 38.9 - - + +
76B THR* 1.3 80.9 - - + +
78B TRP* 1.3 57.9 + - + +
80B GLU* 3.2 13.0 + - - +
81B LEU* 2.9 27.3 + - - +
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Residues in contact with TRP 78 (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 GLU* 2.8 45.3 + - + +
21A LEU* 3.7 34.5 - - + -
22A VAL* 4.0 15.5 - - + -
25A LEU* 4.6 2.7 - - + -
93A PHE* 3.9 19.3 - + - -
97A LEU* 4.1 21.2 - - + +
101A ARG* 3.7 7.9 + - - +
104A PHE* 4.2 12.6 - + + -
46B LEU* 4.0 24.0 - - + +
73B ARG* 2.9 38.0 + - + +
74B LEU* 3.9 20.8 + - + +
76B THR 3.4 0.2 - - - -
77B GLU* 1.3 75.1 - - + +
79B SER* 1.3 57.8 + - - +
81B LEU* 3.7 31.3 - - + +
82B GLU* 3.0 27.7 + - - +
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Residues in contact with SER 79 (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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101A ARG* 3.6 24.8 + - - +
74B LEU 4.8 0.7 + - - -
75B ASN 3.3 18.0 + - - -
76B THR* 3.2 11.0 + - - -
77B GLU 3.2 0.4 - - - -
78B TRP* 1.3 75.7 - - - +
80B GLU* 1.3 60.3 + - - +
82B GLU* 3.4 4.9 + - - +
83B ASN* 3.0 35.8 + - - -
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Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B TRP* 3.7 17.9 - - + -
76B THR* 3.0 36.8 + - + +
77B GLU* 3.8 13.3 - - - +
79B SER* 1.3 73.0 - - - +
81B LEU* 1.3 65.7 + - - +
83B ASN* 3.3 14.9 + - - +
84B LEU* 3.1 21.0 + - - +
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.6 28.7 - - + -
93A PHE* 4.5 3.8 - - + -
39B ILE* 4.5 19.1 - - + -
42B TRP* 3.5 39.1 - - + -
46B LEU* 3.9 12.1 - - + -
77B GLU 2.9 16.5 + - - +
78B TRP* 3.7 31.0 - - + +
79B SER 3.3 0.2 - - - -
80B GLU* 1.3 74.1 - - - +
82B GLU* 1.3 67.3 + - - +
84B LEU* 3.1 3.1 + - + +
85B VAL* 2.9 42.0 + - + +
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Residues in contact with GLU 82 (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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93A PHE* 5.2 0.7 - - - -
94A ILE* 3.7 33.1 - - + +
97A LEU* 3.7 13.2 - - + +
98A THR* 4.6 3.9 + - - -
101A ARG* 2.7 38.7 + - - -
78B TRP 3.0 16.0 + - - +
79B SER* 3.5 6.9 - - - +
81B LEU* 1.3 77.4 - - - +
83B ASN* 1.3 65.9 + - - +
85B VAL* 3.2 8.3 + - - +
86B LEU* 3.0 36.6 + - + +
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Residues in contact with ASN 83 (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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79B SER* 3.0 24.4 + - - +
80B GLU* 3.5 14.6 - - - +
81B LEU 3.2 0.2 - - - -
82B GLU* 1.3 80.5 - - - +
84B LEU* 1.3 62.2 + - - +
86B LEU* 3.4 9.4 + - - +
87B LYS* 3.2 21.5 + - - +
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Residues in contact with LEU 84 (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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35B LYS* 3.1 30.6 - - + +
38B GLN* 4.0 29.6 - - + +
39B ILE* 3.7 28.0 - - + -
42B TRP* 3.9 26.0 - - + -
80B GLU 3.1 13.1 + - - +
81B LEU 3.1 6.7 + - - +
83B ASN* 1.3 74.6 - - - +
85B VAL* 1.3 64.9 + - - +
87B LYS* 3.1 31.6 + - + +
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Residues in contact with VAL 85 (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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25A LEU* 4.6 2.7 - - + -
28A TYR* 3.8 22.0 + - + -
32A GLU* 5.1 0.3 - - - +
90A SER* 3.6 30.5 + - - -
93A PHE* 4.1 21.8 - - + -
94A ILE* 3.9 16.4 - - + -
35B LYS* 2.7 25.8 + - - +
39B ILE* 4.1 16.6 - - + -
81B LEU* 2.9 28.8 + - + +
82B GLU 3.6 7.9 - - - +
84B LEU* 1.3 75.4 - - - +
86B LEU* 1.3 56.6 + - - +
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Residues in contact with LEU 86 (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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88A ASP* 5.9 1.1 - - - +
90A SER* 3.9 11.9 - - - +
94A ILE* 3.8 30.5 - - + -
82B GLU* 3.0 43.5 + - + +
83B ASN* 3.4 10.5 + - - +
84B LEU 3.1 0.2 - - - -
85B VAL* 1.3 75.0 - - - +
87B LYS* 1.3 64.7 + - - +
88B ASP* 3.3 5.0 + - - +
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Residues in contact with LYS 87 (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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35B LYS* 2.7 27.1 + - - +
83B ASN 3.2 11.1 + - - +
84B LEU* 3.1 32.0 + - + +
86B LEU* 1.3 76.9 - - - +
88B ASP* 1.3 64.3 + - - +
89B MET* 3.5 29.3 + - + +
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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