Contacts of the helix formed by residues 76 - 83 (chain A) in PDB entry 2B2T
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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30A THR* 4.0 7.2 - - + +
57A GLU* 3.3 42.1 - - + +
58A ILE 3.8 14.8 - - - +
59A GLN* 3.9 10.1 - - + -
60A TYR* 4.6 1.6 - - - -
75A GLU* 1.3 77.5 - - - +
77A GLU* 1.3 65.4 + - - +
78A GLU* 2.9 12.0 + - - +
79A THR* 2.9 42.1 + - + +
80A LEU* 3.1 14.4 + - - +
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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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58A ILE* 4.7 3.2 + - + +
60A TYR* 4.2 14.0 + - + -
76A THR* 1.3 73.4 - - - +
78A GLU* 1.3 55.9 + - - +
80A LEU* 3.6 6.2 - - - +
81A LYS* 3.2 55.3 + - + +
88A MSE 4.5 0.6 - - + +
91A LEU* 3.3 28.5 - - + +
95A LYS* 2.7 33.3 + - - +
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Residues in contact with GLU 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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57A GLU* 5.3 4.9 - - - +
76A THR* 2.9 9.8 + - - +
77A GLU* 1.3 77.5 - - - +
79A THR* 1.3 60.9 + - + +
80A LEU 3.1 1.8 - - - -
81A LYS* 3.3 10.5 + - + +
82A GLN* 2.8 59.2 + - + +
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Residues in contact with THR 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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30A THR* 3.8 21.8 - - - +
75A GLU* 2.7 26.1 + - - +
76A THR* 2.9 37.0 + - + +
78A GLU* 1.3 77.9 - - + +
80A LEU* 1.3 52.9 + - - +
82A GLN* 3.2 14.8 + - - +
83A GLN* 2.8 49.1 + - - +
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Residues in contact with LEU 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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16A ILE* 4.0 15.5 - - + -
19A PHE* 4.6 11.0 - - + -
60A TYR* 5.1 2.0 - - + -
62A ILE* 3.7 22.2 - - + -
64A TRP* 4.1 10.3 - - + -
75A GLU* 3.6 27.4 - - + -
76A THR 3.1 14.7 + - - +
77A GLU* 3.6 12.6 - - - +
79A THR* 1.3 82.1 + - - +
81A LYS* 1.3 61.5 + - - +
83A GLN* 3.3 2.5 + - - +
84A ASN 3.1 17.2 + - - -
85A VAL* 3.5 28.5 + - + +
88A MSE 3.9 17.3 - - - -
91A LEU* 4.5 13.9 - - + -
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Residues in contact with LYS 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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77A GLU* 3.2 43.7 + - + +
78A GLU* 3.3 9.4 + - + +
80A LEU* 1.3 79.8 - - - +
82A GLN* 1.3 62.4 + - + +
84A ASN* 3.2 15.8 + - - +
85A VAL 5.5 0.2 - - - +
88A MSE 3.3 31.9 - - + -
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Residues in contact with GLN 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 GLU* 2.8 49.6 + - + +
79A THR* 3.5 15.5 - - - +
81A LYS* 1.3 75.5 - - + +
83A GLN* 1.3 59.7 + - + +
84A ASN* 2.9 11.9 + - - +
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Residues in contact with GLN 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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13A PHE* 4.2 11.1 - - - -
14A GLU* 5.3 1.2 + - - +
31A GLY* 5.3 5.1 - - - -
64A TRP* 4.2 14.6 - - - -
75A GLU* 3.2 34.9 + - - +
79A THR* 2.8 31.4 + - - +
80A LEU* 5.2 0.3 - - - +
82A GLN* 1.3 72.2 - - + +
84A ASN* 1.3 70.4 + - - +
85A VAL* 3.3 15.0 + - + +
4D M3L 5.5 4.2 - - - -
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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