Contacts of the helix formed by residues 76 - 86 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A LYS* 2.8 31.4 + - + -
74A LEU 3.4 0.4 - - - -
75A ASN* 1.3 80.1 + - - +
77A GLU* 1.3 65.5 + - - +
78A TRP 3.3 1.3 - - - -
79A SER* 3.1 16.7 + - - -
80A GLU* 3.3 26.7 + - + +
110B GLN* 3.3 20.5 + - - -
148B GLU* 5.9 1.1 - - - +
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Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TRP* 2.8 30.0 + - + +
45A LYS* 2.5 37.5 + - - -
46A LEU* 4.5 2.8 - - + +
69A LYS* 5.5 5.0 + - - -
72A LYS* 3.3 3.4 + - + +
73A ARG* 3.0 41.4 + - + +
76A THR* 1.3 79.5 - - - +
78A TRP* 1.3 63.8 + - + +
80A GLU* 3.0 17.7 + - - +
81A LEU* 3.0 21.1 + - - +
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Residues in contact with TRP 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 3.8 25.1 - - + +
73A ARG* 2.9 38.5 + - + +
74A LEU* 3.9 20.8 + - + +
76A THR 3.3 0.4 - - - -
77A GLU* 1.3 76.8 - - + +
79A SER* 1.3 57.3 + - - +
81A LEU* 3.7 28.5 - - + +
82A GLU* 2.9 28.4 + - - +
18B GLU* 2.8 44.3 + - + +
21B LEU* 3.6 39.0 - - + -
22B VAL* 3.9 12.3 - - + -
25B LEU* 4.9 1.8 - - + -
93B PHE* 3.9 19.7 - + - -
97B LEU* 4.2 18.3 - - + +
101B ARG* 3.6 11.0 + - - +
104B PHE* 4.3 9.0 - + + -
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Residues in contact with SER 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LEU 5.1 1.0 + - - -
75A ASN 4.0 13.1 + - - -
76A THR* 3.1 12.9 + - - -
78A TRP* 1.3 76.0 - - - +
80A GLU* 1.3 60.2 + - - +
82A GLU* 3.4 5.1 + - - +
83A ASN* 3.0 35.5 + - - -
101B ARG* 3.3 23.7 + - - +
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Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TRP* 3.9 16.2 - - + -
76A THR* 3.3 20.3 + - + +
77A GLU* 3.0 27.4 + - - +
79A SER* 1.3 74.2 - - - +
81A LEU* 1.3 65.3 + - - +
83A ASN* 3.3 12.1 + - - +
84A LEU* 3.2 21.0 + - - +
184B THR* 6.1 0.7 - - - +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ILE* 4.7 12.1 - - + -
42A TRP* 3.8 42.9 - - + +
46A LEU* 3.8 14.8 - - + -
77A GLU 3.0 15.0 + - - +
78A TRP* 3.7 31.6 - - + +
80A GLU* 1.3 73.6 - - - +
82A GLU* 1.3 66.0 + - - +
84A LEU* 3.1 3.8 + - + +
85A VAL* 3.0 34.7 + - + +
25B LEU* 3.7 30.1 - - + -
93B PHE* 4.9 2.9 - - + -
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A TRP 2.9 16.6 + - - +
79A SER* 3.5 6.8 + - - +
81A LEU* 1.3 76.3 - - - +
83A ASN* 1.3 65.0 + - - +
85A VAL* 3.2 8.9 + - - +
86A LEU* 3.0 35.8 + - + +
93B PHE* 5.0 1.1 - - - -
94B ILE* 3.7 33.3 - - + +
97B LEU* 3.8 15.0 - - + -
98B THR* 4.7 4.9 + - - -
101B ARG* 2.7 37.5 + - - -
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Residues in contact with ASN 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A SER* 3.0 24.5 + - - +
80A GLU* 3.5 12.4 - - - +
81A LEU 3.2 0.2 - - - -
82A GLU* 1.3 81.4 - - - +
84A LEU* 1.3 60.3 - - - +
86A LEU* 3.4 12.1 + - - +
87A LYS* 3.2 21.1 + - - +
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LYS* 3.1 29.1 - - + -
38A GLN* 3.9 40.2 - - + +
39A ILE* 3.8 26.2 - - + -
42A TRP* 4.0 25.4 - - + -
80A GLU 3.2 10.9 + - - +
81A LEU* 3.1 10.8 + - + +
83A ASN* 1.3 74.5 - - - +
85A VAL* 1.3 64.6 + - - +
87A LYS* 3.1 35.7 + - + +
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LYS* 2.7 23.2 + - - +
39A ILE* 4.0 19.7 - - + -
81A LEU* 3.0 20.9 + - + +
82A GLU* 3.6 9.2 - - - +
84A LEU* 1.3 75.8 - - - +
86A LEU* 1.3 56.1 + - - +
25B LEU* 4.2 12.1 - - + -
28B TYR* 3.7 20.9 + - + -
90B SER* 3.6 31.1 + - - -
93B PHE* 4.1 29.4 - - + -
94B ILE* 4.3 5.4 - - + -
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLU* 3.0 40.1 + - + +
83A ASN* 3.7 12.1 - - - +
84A LEU 3.2 0.4 - - - -
85A VAL* 1.3 76.0 - - - +
87A LYS* 1.3 62.7 + - - +
88A ASP* 3.3 4.7 + - - +
88B ASP* 5.7 1.8 - - - +
90B SER* 4.1 11.0 - - - +
94B ILE* 3.9 31.2 - - + -
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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