Contacts of the helix formed by residues 83 - 91 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5C GLU* 3.2 35.1 + - + +
6C ARG* 3.7 16.6 - - - -
7C THR* 3.8 17.7 - - + +
28C PHE* 5.6 1.6 - - + -
33C PHE* 3.7 42.4 - - + -
78C TRP* 3.8 12.6 - - + +
80C GLY 3.4 9.9 - - - +
81C LEU 3.2 1.6 - - - -
82C ASN* 1.3 77.4 - - - +
84C VAL* 1.3 58.6 + - - +
87C GLY* 2.7 31.0 + - - +
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Residues in contact with VAL 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C GLU* 2.8 30.5 + - + +
6C ARG 3.5 24.5 - - - +
7C THR* 3.8 14.0 + - - +
83C VAL* 1.3 73.8 - - - +
85C LYS* 1.3 63.1 + - - +
87C GLY* 3.9 0.7 - - - -
88C ARG* 3.2 22.0 + - + +
120C SER 3.8 11.7 - - - +
121C ASP 4.1 2.5 - - - +
122C SER* 3.7 36.1 - - - +
123C VAL* 4.1 10.3 - - + +
126C ALA* 4.1 9.9 - - + -
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Residues in contact with LYS 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C GLU* 4.1 1.2 + - - -
82C ASN* 3.6 21.4 + - - +
84C VAL* 1.3 80.7 - - + +
86C THR* 1.3 64.7 + - - +
88C ARG* 3.1 13.0 + - + +
89C VAL* 3.0 37.1 + - + +
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Residues in contact with THR 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ALA* 5.0 15.8 + - - +
31C LYS* 3.6 33.0 - - - +
33C PHE* 3.8 18.7 - - + -
81C LEU 4.7 1.0 + - - -
82C ASN* 3.0 27.8 + - - +
85C LYS* 1.3 75.0 - - - +
87C GLY* 1.3 66.8 + - - +
89C VAL* 3.2 11.0 + - + +
90C MET* 2.9 28.0 + - + +
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Residues in contact with GLY 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C THR* 5.4 1.1 - - - -
9C ILE* 5.0 8.3 - - - -
28C PHE* 4.3 20.6 - - - -
33C PHE* 5.0 1.7 - - - -
83C VAL* 2.7 23.5 + - - -
84C VAL 3.9 0.9 - - - -
86C THR* 1.3 72.5 - - - +
88C ARG* 1.3 61.1 + - - +
90C MET* 3.3 5.4 + - - +
91C LEU* 3.1 33.1 + - - +
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Residues in contact with ARG 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C VAL 3.2 15.5 + - - +
85C LYS* 3.1 18.0 + - + +
87C GLY* 1.3 74.3 - - - +
89C VAL* 1.3 65.1 + - + +
91C LEU* 3.3 14.9 + - - +
92C GLY 3.2 27.8 + - - +
94C THR* 4.8 2.4 + - - +
105C ARG* 5.3 1.7 - - - +
118C HIS* 5.0 0.4 - - - -
119C GLY 2.7 34.4 + - - +
120C SER 3.5 12.0 + - - +
121C ASP* 3.6 30.1 + - - +
160C GDP 2.6 45.7 + - - -
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Residues in contact with VAL 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ALA 5.7 4.9 - - - +
99B SER 4.8 6.1 - - - +
100B LYS* 4.3 24.7 - - + +
101B PRO* 3.6 24.8 - - + +
85C LYS* 3.0 34.3 + - + +
86C THR* 3.2 12.8 + - + +
88C ARG* 1.3 75.4 - - + +
90C MET* 1.3 62.7 + - + +
91C LEU 3.4 0.5 + - - -
92C GLY* 3.4 9.2 + - - -
103C THR* 3.5 14.6 - - - +
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Residues in contact with MET 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PRO* 3.9 17.7 - - + +
106B GLY 5.2 4.0 - - - +
107B ASP 6.0 0.4 - - - +
27C ARG* 3.7 40.3 + - + +
28C PHE* 4.1 24.9 - - + +
31C LYS* 4.1 16.2 - - + -
33C PHE* 4.1 23.6 - - - -
86C THR* 2.9 25.8 + - + +
87C GLY* 3.6 5.2 - - - +
89C VAL* 1.3 78.4 - - + +
91C LEU* 1.3 57.0 + - - +
103C THR* 3.3 6.6 - - - -
104C ILE* 2.9 33.3 + - + +
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Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ILE* 4.8 3.4 - - + -
28C PHE* 4.4 8.7 - - + -
87C GLY 3.1 24.8 + - - +
88C ARG* 3.6 16.4 - - - +
89C VAL 3.3 0.6 - - - -
90C MET* 1.3 77.2 - - - +
92C GLY* 1.3 62.7 + - - +
103C THR* 3.9 0.4 - - - -
104C ILE* 3.7 12.0 + - + -
105C ARG* 3.0 51.8 + - - +
117C ILE* 3.4 42.0 - - + -
118C HIS 3.9 3.8 - - - -
119C GLY* 3.6 34.8 - - - +
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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