Contacts of the helix formed by residues 78 - 85 (chain A) in PDB entry 5JNT
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 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A ARG* 4.1 8.5 + - - +
76A GLN 3.6 14.1 - - - +
77A ILE* 1.3 74.4 - - - +
79A LYS* 1.3 65.0 + - - +
80A GLU* 3.4 12.7 + - - +
81A ASP* 2.9 44.4 + - - +
82A PHE* 3.7 12.4 - - - -
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Residues in contact with LYS 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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78A THR* 1.3 73.7 - - - +
80A GLU* 1.3 60.0 + - - +
82A PHE* 3.3 27.2 + - + +
83A ALA* 3.9 4.5 + - - +
102A LYS 5.0 0.6 + - - -
105A GLN* 3.5 43.5 + - - +
106A VAL* 3.7 23.4 - - + +
108A THR 5.1 0.3 - - - +
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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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78A THR* 3.2 10.5 + - - +
79A LYS* 1.3 79.1 - - - +
81A ASP* 1.4 64.3 + - - +
83A ALA* 2.9 17.8 + - + +
84A THR* 3.1 31.4 + - + +
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Residues in contact with ASP 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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9A LEU* 4.1 4.5 - - + -
40A ARG* 4.5 4.3 + - - -
75A ARG* 2.8 43.7 + - - -
77A ILE* 3.4 18.0 - - + +
78A THR* 2.9 31.7 + - - +
80A GLU* 1.4 79.1 - - - +
82A PHE* 1.4 61.9 + - - +
84A THR* 3.8 6.1 + - - -
85A PHE* 3.1 47.0 + - + +
88A ILE* 4.2 3.4 - - - +
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Residues in contact with PHE 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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77A ILE* 3.7 22.0 - - + -
78A THR 3.7 19.7 - - - -
79A LYS* 3.3 15.4 + - + +
80A GLU 3.1 0.8 - - - -
81A ASP* 1.4 77.5 - - - +
83A ALA* 1.4 60.0 + - - +
88A ILE* 3.7 26.2 - - + -
99A LEU* 3.8 12.8 - - + -
102A LYS* 3.7 33.0 - - + -
103A SER* 3.8 32.1 - - - -
106A VAL* 4.0 13.0 - - + -
108A THR 3.6 10.3 - - - +
109A CYS* 3.4 9.8 - - - -
110A LYS 2.9 23.0 + - - -
111A ALA* 3.2 10.7 + - - +
113A ILE* 3.9 5.8 - - + -
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Residues in contact with ALA 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 LYS 3.9 2.6 + - - +
80A GLU* 2.9 14.7 + - + +
82A PHE* 1.4 80.8 - - - +
84A THR* 1.3 62.1 + - + +
108A THR* 3.6 33.8 + - + +
110A LYS* 3.3 24.2 + - - +
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Residues in contact with THR 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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7A SER* 3.4 8.1 + - - -
40A ARG* 3.0 30.6 + - - +
80A GLU* 3.1 35.6 + - + +
81A ASP* 3.8 2.8 + - - -
83A ALA* 1.3 82.3 - - + +
85A PHE* 1.3 69.1 + - - +
110A LYS* 2.9 19.8 + - - +
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Residues in contact with PHE 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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7A SER* 3.3 4.5 - - - -
8A VAL 3.5 28.5 - - - -
9A LEU* 3.5 31.4 - - + -
40A ARG* 3.3 47.6 - - + -
42A ASP* 4.0 21.1 - - + -
75A ARG* 4.3 0.9 - - - -
81A ASP* 3.1 43.6 + - + +
84A THR* 1.3 85.3 + - - +
86A ASP* 1.3 59.6 + - - +
87A TYR 3.8 11.2 - - - +
88A ILE* 4.3 7.6 - - + -
110A LYS* 3.5 6.5 - - - +
111A ALA* 3.1 28.9 + - - +
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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