Contacts of the helix formed by residues 78 - 87 (chain E) in PDB entry 1XFV
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 LYS 78 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69E THR* 3.8 27.9 - - - +
71E PHE 2.8 28.3 + - - +
72E THR* 5.0 0.8 - - - +
74E GLU* 3.4 41.1 - - + +
75E THR 3.2 4.1 + - - +
77E ASP* 1.3 76.9 - - - +
79E ILE* 1.3 63.1 + - + +
81E GLN* 3.0 12.8 + - - +
82E THR* 2.7 39.3 + - + +
106E PHE 4.1 3.8 - - - -
107E THR 3.0 32.3 - - - +
108E ASP* 4.6 4.0 - - - +
156E ILE* 4.0 25.3 - - + +
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Residues in contact with ILE 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E THR* 5.9 3.1 - - + -
72E THR* 5.0 20.2 - - + +
74E GLU 4.9 6.1 - - - +
75E THR 4.0 17.0 - - - +
76E LEU* 4.3 20.6 - - + -
78E LYS* 1.3 86.3 - - + +
80E GLN* 1.3 54.9 + - - +
81E GLN 2.5 16.1 + - - -
82E THR* 2.8 20.8 + - - +
83E GLN* 2.8 34.8 + - + +
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Residues in contact with GLN 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E LEU* 2.7 41.2 + - + +
77E ASP* 3.9 4.9 - - - +
78E LYS 3.5 0.2 - - - -
79E ILE* 1.3 77.0 - - - +
81E GLN* 1.3 54.6 + - - +
83E GLN* 3.2 26.1 + - - +
84E ASP* 2.5 42.5 - - - +
87E LYS* 5.8 2.1 + - - -
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Residues in contact with GLN 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E ASP* 2.7 27.9 + - - +
78E LYS* 3.1 9.3 - - - +
79E ILE 2.5 6.7 + - - -
80E GLN* 1.3 76.0 - - - +
82E THR* 1.3 62.0 + - - -
83E GLN 3.2 0.7 - - - -
84E ASP* 3.8 6.2 + - + +
85E LEU* 3.3 25.6 + - + +
156E ILE* 3.0 36.3 - - + +
158E ASP 3.7 18.8 + - - +
159E TYR* 4.8 5.2 - - - +
160E ALA 3.9 11.4 + - - -
161E ILE* 4.2 21.5 + - + +
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Residues in contact with THR 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E THR* 5.0 7.7 - - + +
78E LYS* 2.7 28.3 + - + +
79E ILE* 2.8 22.5 + - - +
81E GLN* 1.3 72.0 - - - +
83E GLN* 1.3 69.8 + - - +
85E LEU* 3.0 20.0 - - - +
86E LEU* 3.1 13.8 + - - +
106E PHE* 3.4 46.3 - - + -
156E ILE* 3.6 20.6 - - + -
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Residues in contact with GLN 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E ILE* 2.8 26.4 + - + +
80E GLN* 3.2 34.2 + - - +
82E THR* 1.3 74.3 + - - +
84E ASP* 1.3 55.6 + - - +
85E LEU 2.3 18.9 + - - -
86E LEU* 2.8 19.8 + - - +
87E LYS* 3.1 25.6 + - + +
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Residues in contact with ASP 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E GLN* 2.5 32.8 + - - +
81E GLN* 3.8 7.2 + - + +
82E THR 3.6 0.4 - - - -
83E GLN* 1.3 76.6 - - - +
85E LEU* 1.3 66.8 + - + +
87E LYS* 3.1 39.1 + - - +
88E LYS* 4.0 9.4 - - - +
162E ASN* 5.6 6.7 + - - +
168E GLU* 4.9 0.3 - - - +
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Residues in contact with LEU 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E GLN* 3.3 16.5 + - + +
82E THR* 3.0 11.0 + - - +
83E GLN 2.3 12.3 + - - -
84E ASP* 1.3 70.5 - - + +
86E LEU* 1.3 67.1 + - + +
88E LYS* 2.9 34.7 + - - +
89E ILE* 3.8 1.0 - - - +
106E PHE* 4.3 17.3 - - + -
154E ILE* 5.1 4.5 - - + -
156E ILE* 5.9 4.5 - - + -
161E ILE* 4.0 24.0 - - + -
168E GLU* 2.9 38.1 - - + +
171E TYR* 3.4 39.7 - - + -
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Residues in contact with LEU 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E VAL* 4.0 24.5 - - + -
82E THR* 3.7 11.9 - - - +
83E GLN* 2.8 11.6 + - - +
85E LEU* 1.3 76.7 - - - +
87E LYS* 1.3 57.2 + - - +
88E LYS 2.9 0.2 - - - -
89E ILE* 2.9 41.4 + - + +
94E LEU* 4.9 18.0 - - + +
104E ILE* 4.0 11.4 - - + -
106E PHE* 3.7 23.6 - - + -
171E TYR* 3.0 29.2 - - - +
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Residues in contact with LYS 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E GLN* 5.8 2.4 + - - -
83E GLN* 3.1 20.1 + - + +
84E ASP* 3.1 43.4 + - - +
86E LEU* 1.3 75.5 - - - +
88E LYS* 1.3 61.2 + - + +
89E ILE 3.4 4.3 + - - +
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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