Contacts of the helix formed by residues 83 - 91 (chain F) in PDB entry 1NUE
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 VAL 83 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5F GLU* 3.4 37.1 + - + +
6F ARG 3.9 6.3 - - - -
7F THR* 3.7 18.1 - - + +
28F PHE* 5.6 1.6 - - + -
33F PHE* 3.8 42.4 - - + -
78F TRP* 3.8 20.9 - - + +
80F GLY 3.4 10.1 - - - +
81F LEU 3.2 1.6 - - - -
82F ASN* 1.3 76.7 - - - +
84F VAL* 1.3 56.7 + - - +
87F GLY* 2.7 32.6 + - - +
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Residues in contact with VAL 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F GLU* 2.9 24.6 + - + +
6F ARG 3.6 23.6 - - - +
7F THR* 3.8 16.0 + - - +
83F VAL* 1.3 80.1 - - - +
85F LYS* 1.3 62.3 + - + +
87F GLY* 3.9 0.3 - - - -
88F ARG* 3.2 22.8 + - + +
120F SER 3.7 11.0 - - - +
121F ASP 4.0 3.4 - - - +
122F SER* 3.6 34.8 - - - +
123F VAL* 4.0 17.7 - - + +
126F ALA* 4.2 3.6 - - + -
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Residues in contact with LYS 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F GLU* 4.3 0.8 + - - -
82F ASN* 3.4 23.5 + - - +
84F VAL* 1.3 78.1 - - + +
86F THR* 1.3 67.8 + - - +
88F ARG* 3.3 11.6 + - + +
89F VAL* 3.1 40.2 + - + +
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Residues in contact with THR 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D ALA* 5.2 14.7 + - - +
110D ILE* 6.1 0.3 - - - +
31F LYS* 3.7 31.9 - - - +
33F PHE* 3.9 18.6 - - + -
81F LEU 4.6 1.2 + - - -
82F ASN* 2.9 26.5 + - - +
85F LYS* 1.3 75.6 - - - +
87F GLY* 1.3 66.7 + - - +
89F VAL* 3.1 11.5 + - + +
90F MET* 2.9 27.2 + - + +
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Residues in contact with GLY 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F THR* 5.6 0.2 - - - -
9F ILE* 5.1 7.6 - - - -
28F PHE* 4.3 22.2 - - - -
33F PHE* 5.1 0.8 - - - -
83F VAL* 2.7 26.1 + - - -
84F VAL 3.9 0.7 - - - -
86F THR* 1.3 73.2 - - - +
88F ARG* 1.3 60.3 + - - +
90F MET* 3.2 6.2 + - - +
91F LEU* 3.1 32.1 + - - +
119F GLY* 6.2 0.7 - - - -
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Residues in contact with ARG 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F VAL 3.2 15.0 + - - +
85F LYS* 3.4 15.7 - - + +
87F GLY* 1.3 77.7 - - - +
89F VAL* 1.3 63.4 + - + +
91F LEU* 3.4 12.6 + - - +
92F GLY 3.3 27.8 + - - +
94F THR* 4.8 2.8 + - - -
105F ARG* 5.4 2.1 - - - +
118F HIS* 5.0 0.6 - - - -
119F GLY* 2.7 35.6 + - - +
120F SER 3.5 13.2 + - - +
121F ASP* 3.7 26.9 - - - +
160F GDP 2.6 44.5 + - - -
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Residues in contact with VAL 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D ALA 5.9 3.1 - - - +
99D SER 4.8 6.1 - - - +
100D LYS* 4.6 20.9 - - + +
101D PRO* 3.8 23.6 - - + +
85F LYS* 3.1 32.7 + - + +
86F THR* 3.1 13.0 + - + +
88F ARG* 1.3 76.5 - - + +
90F MET* 1.3 64.4 + - + +
91F LEU 3.4 0.3 + - - -
92F GLY* 3.5 8.5 + - - -
103F THR* 3.6 14.4 - - - +
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Residues in contact with MET 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D PRO* 4.1 16.4 - - + -
106D GLY 5.3 4.0 - - - +
107D ASP 5.9 0.2 - - - +
27F ARG* 3.6 35.7 - - + +
28F PHE* 3.9 32.8 - - + -
31F LYS* 4.2 15.5 - - + -
33F PHE* 3.9 25.8 - - - -
86F THR* 2.9 21.9 + - + +
87F GLY* 3.2 6.9 + - - +
89F VAL* 1.3 77.6 - - + +
91F LEU* 1.3 59.4 + - - +
102F GLY 4.8 0.3 - - - +
103F THR* 3.4 5.9 - - - -
104F ILE* 2.9 31.4 + - + +
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Residues in contact with LEU 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ILE* 4.9 2.7 - - + -
28F PHE* 4.3 9.2 - - + -
87F GLY 3.1 24.2 + - - +
88F ARG* 3.7 16.6 - - - +
89F VAL 3.3 0.2 - - - -
90F MET* 1.3 77.6 - - - +
92F GLY* 1.3 62.4 + - - +
103F THR* 3.9 0.4 - - - -
104F ILE* 3.5 14.7 + - + -
105F ARG* 2.9 51.6 + - - +
117F ILE* 3.5 41.1 - - + -
118F HIS 4.0 3.6 - - - -
119F GLY* 3.6 35.7 - - - +
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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