Contacts of the helix formed by residues 76 - 90 (chain N) in PDB entry 5NO6
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 GLY 76 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3F T 3.6 9.2 - - - -
4F G 3.2 18.2 - - - -
68N LEU* 4.4 6.3 - - - -
75N TYR* 1.3 76.1 - - - +
77N ARG* 1.3 56.0 + - - -
79N GLU* 3.4 9.7 + - - +
80N LEU* 2.8 37.3 + - - +
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Residues in contact with ARG 77 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F G 3.5 21.2 + - - +
5F G 5.3 10.3 + - - +
55N LEU* 3.4 34.6 - - - +
58N TYR* 4.6 7.5 - - - -
59N PRO* 3.1 47.0 - - - +
62N GLY* 5.0 10.6 - - - +
68N LEU* 5.1 2.4 - - - +
76N GLY* 1.3 70.9 - - - +
78N ASN* 1.3 69.7 + - - +
80N LEU* 3.1 8.5 + - - +
81N ILE* 2.9 40.5 + - + +
102N ILE* 4.8 12.6 - - - +
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Residues in contact with ASN 78 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F G 2.9 54.2 + - - +
5F G 3.7 6.9 + - - -
77N ARG* 1.3 75.6 - - - +
79N GLU* 1.3 52.9 + - - +
81N ILE* 2.8 8.3 + - - +
82N ALA* 2.8 34.7 + - - +
95N ARG* 3.7 11.4 + - + +
98N VAL* 3.6 34.1 - - + +
99N SER* 3.2 28.0 + - - +
102N ILE* 3.9 7.8 - - - +
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Residues in contact with GLU 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F T 2.5 46.2 + - - +
4F G 3.1 7.5 + - - +
74N MET 4.0 11.3 - - - +
75N TYR* 4.3 10.2 - - + -
76N GLY 3.7 11.9 + - - +
77N ARG 3.3 0.2 - - - -
78N ASN* 1.3 79.0 - - - +
80N LEU* 1.3 58.7 + - - +
82N ALA* 3.4 8.7 + - - +
83N ARG* 2.8 34.5 + - - +
95N ARG* 3.2 36.3 - - + -
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Residues in contact with LEU 80 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58N TYR* 3.3 54.2 + - + +
68N LEU* 4.0 21.1 - - + -
75N TYR* 3.6 37.7 - - + -
76N GLY 2.8 23.4 + - - +
77N ARG* 3.5 7.0 - - - +
79N GLU* 1.3 72.5 - - - +
81N ILE* 1.3 56.3 + - - +
83N ARG* 3.6 18.4 - - - +
84N TYR* 3.2 26.2 + - - +
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Residues in contact with ILE 81 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51N PHE* 3.8 23.8 - - + -
54N ALA* 3.8 29.2 - - + +
55N LEU* 3.7 18.2 - - + +
58N TYR* 5.2 3.1 - - + -
77N ARG* 2.9 60.9 + - - +
78N ASN* 2.8 20.5 + - - +
80N LEU* 1.3 69.0 - - + +
82N ALA* 1.3 52.5 + - - +
84N TYR* 3.0 5.4 + - - +
85N ILE* 2.8 46.0 + - + +
98N VAL* 4.0 12.1 - - + -
102N ILE* 5.5 1.3 - - + -
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Residues in contact with ALA 82 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78N ASN 2.8 14.2 + - - +
79N GLU* 3.5 12.3 - - - +
81N ILE* 1.3 72.6 - - - +
83N ARG* 1.3 61.1 + - - +
85N ILE* 3.5 13.8 + - - +
86N LYS* 3.1 19.9 + - - +
92N THR 3.5 7.8 - - - +
93N ARG 3.2 25.6 - - - +
94N THR* 4.6 7.4 - - - -
95N ARG 4.8 1.1 - - - +
98N VAL* 4.1 7.3 - - + +
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Residues in contact with ARG 83 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58N TYR* 5.7 2.5 - - - +
73N LYS* 5.6 1.6 - - - +
75N TYR* 3.4 42.9 + - - -
79N GLU* 2.8 23.1 + - - +
80N LEU* 3.6 22.0 - - - +
82N ALA* 1.3 73.5 - - - +
84N TYR* 1.3 51.1 + - - +
86N LYS* 2.8 29.0 + - + +
87N LEU* 2.8 33.7 + - + +
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Residues in contact with TYR 84 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50N SER 3.6 17.3 - - - -
53N GLU* 2.7 47.7 + - + +
54N ALA* 3.7 16.6 - - + -
57N ILE* 4.1 21.1 - - + +
58N TYR* 4.5 10.1 - + + +
80N LEU 3.2 14.7 + - - +
81N ILE 3.0 4.4 + - - +
83N ARG* 1.3 78.1 - - - +
85N ILE* 1.3 53.3 + - - +
87N LEU* 3.7 17.2 - - + +
88N ARG* 2.8 65.0 + - + +
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Residues in contact with ILE 85 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43N TRP* 4.0 26.0 - - + -
47N ILE* 3.9 21.5 - - + -
50N SER* 4.5 17.3 - - - +
51N PHE* 4.6 7.2 - - + +
81N ILE* 2.8 39.4 + - + +
82N ALA* 3.5 15.7 - - - +
84N TYR* 1.3 71.0 - - - +
86N LYS* 1.3 55.4 + - - +
89N THR* 2.4 45.9 + - + +
91N LYS* 3.4 17.0 - - + +
92N THR 3.9 7.9 - - - +
93N ARG* 4.8 8.3 - - + -
98N VAL* 4.5 5.2 - - + -
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Residues in contact with LYS 86 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82N ALA 3.1 11.7 + - - +
83N ARG* 2.8 18.8 + - + +
85N ILE* 1.3 71.4 - - - +
87N LEU* 1.3 62.3 + - + +
90N GLY* 2.8 39.9 + - - +
91N LYS 3.4 10.7 + - - +
92N THR* 3.1 41.1 + - + +
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Residues in contact with LEU 87 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83N ARG* 2.8 34.5 + - + +
84N TYR* 3.3 18.1 + - + +
86N LYS* 1.3 76.7 - - + +
88N ARG* 1.3 65.2 + - + +
90N GLY 5.1 0.2 + - - -
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Residues in contact with ARG 88 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50N SER* 3.2 20.6 + - - +
53N GLU* 3.5 25.7 + - - -
84N TYR* 2.8 56.6 + - + +
87N LEU* 1.3 79.6 - - - +
89N THR* 1.3 60.1 + - - +
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Residues in contact with THR 89 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46N ASP* 4.2 17.5 - - + +
47N ILE* 4.2 13.9 - - + -
50N SER* 3.6 25.8 - - - +
85N ILE* 2.4 38.2 + - + +
88N ARG* 1.3 75.0 - - - +
90N GLY* 1.3 54.9 + - - +
91N LYS* 3.0 36.2 + - - +
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Residues in contact with GLY 90 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86N LYS* 2.8 40.3 + - - +
87N LEU 5.1 0.2 + - - -
88N ARG 3.8 0.4 - - - -
89N THR* 1.3 70.0 + - - +
91N LYS* 1.3 63.4 + - - +
92N THR* 3.6 3.8 + - - -
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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