Contacts of the helix formed by residues 75 - 86 (chain N) in PDB entry 2ZJQ
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 ASN 75 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69N ALA* 3.9 3.0 - - - +
70N ARG* 3.7 23.1 - - + +
74N MET* 1.3 85.9 - - - +
76N TYR* 1.3 69.5 + - - +
77N SER* 2.8 20.8 + - - -
78N THR* 2.4 52.4 + - - +
79N PHE* 2.6 13.1 + - - -
1022X A 2.6 40.2 + - - +
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Residues in contact with TYR 76 (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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62N ILE* 3.5 36.3 - - + +
65N ILE* 3.8 33.4 - - + -
66N ASN* 3.1 36.5 - - + +
69N ALA* 3.8 1.6 - - - +
70N ARG* 3.7 0.4 - - - +
75N ASN* 1.3 68.6 - - - +
77N SER* 1.3 65.2 + - - +
79N PHE* 4.2 5.2 - - - -
80N ILE* 2.7 56.9 + - + +
92N ARG* 6.0 1.4 - - - -
1021X A 4.3 5.6 - - - +
1022X A 4.3 2.2 - - - +
1163X C 3.1 38.6 - - - -
1164X C 2.4 28.0 + - - -
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Residues in contact with SER 77 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75N ASN* 2.7 22.0 + - - -
76N TYR* 1.3 84.0 - - - +
78N THR* 1.3 63.9 + - - -
81N ASN* 3.2 16.5 + - - +
1021X A 3.8 3.4 - - - -
1022X A 3.2 23.4 + - - -
1162X A 3.4 34.0 + - - -
1163X C 3.5 22.0 + - - +
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Residues in contact with THR 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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74N MET* 3.9 17.2 - - + +
75N ASN* 2.4 33.4 + - - +
77N SER* 1.3 77.4 + - - +
79N PHE* 1.3 65.3 + - - +
80N ILE 3.1 1.0 + - - -
81N ASN* 3.4 1.4 + - - -
82N GLY* 3.2 19.4 + - - -
117N ARG* 3.1 52.4 + - - +
1162X A 5.0 1.8 - - - -
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Residues in contact with PHE 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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65N ILE* 4.2 6.7 - - + -
69N ALA* 4.0 9.2 - - + -
74N MET* 3.1 36.5 - - - +
75N ASN 2.6 21.9 + - - +
76N TYR* 3.8 1.8 - - - +
78N THR* 1.3 75.0 - - - +
80N ILE* 1.3 84.4 + - + +
83N LEU* 2.9 48.3 - - + +
95N LEU* 3.7 23.6 - - + -
106N PHE* 3.4 39.9 - + - -
109N LEU* 4.5 3.1 - - + -
110N VAL* 3.7 25.8 - - + -
113N SER* 3.3 8.1 + - - -
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Residues in contact with ILE 80 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65N ILE* 4.1 1.3 - - + -
76N TYR* 2.7 72.6 + - + +
77N SER 3.8 2.2 - - - +
79N PHE* 1.3 100.8 - - + +
81N ASN* 1.3 68.3 + - - +
82N GLY 2.9 2.1 + - - -
83N LEU* 3.3 4.6 + - + +
84N LYS* 3.0 19.6 + - + +
92N ARG* 4.3 26.6 + - - +
95N LEU* 4.0 15.3 - - + -
1009X C 5.6 2.0 - - - +
1163X C 4.5 15.0 - - - +
1164X C 5.2 1.1 - - - +
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Residues in contact with ASN 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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77N SER 3.2 7.9 + - - +
78N THR* 3.4 4.0 + - - +
80N ILE* 1.3 77.0 - - - +
82N GLY* 1.3 51.5 + - - +
84N LYS* 3.0 24.0 + - - +
85N ARG* 2.6 65.1 + - - +
117N ARG* 4.0 16.0 - - - +
1162X A 3.3 54.4 - - - +
1163X C 3.8 8.4 - - - -
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Residues in contact with GLY 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 THR 3.2 11.2 + - - -
80N ILE 2.9 2.0 - - - -
81N ASN* 1.3 74.4 - - - +
83N LEU* 1.3 57.6 + - - -
85N ARG* 2.6 39.2 + - - +
86N ALA* 3.0 5.4 + - - +
113N SER* 2.6 28.7 - - - -
116N ALA* 4.3 2.9 - - - +
117N ARG* 4.7 6.9 - - - +
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Residues in contact with LEU 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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79N PHE* 2.9 58.1 - - + +
80N ILE* 3.3 6.1 + - + +
82N GLY* 1.3 72.7 - - - +
84N LYS* 1.3 58.5 + - - +
86N ALA* 2.5 33.8 + - - +
89N ASP* 3.5 37.0 - - + +
91N ASN* 4.3 9.9 - - - +
92N ARG* 4.0 12.3 - - - +
95N LEU* 4.5 9.9 - - + -
109N LEU* 3.6 30.1 - - + +
112N ALA* 6.3 0.2 - - + -
113N SER* 3.2 20.7 + - - +
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Residues in contact with LYS 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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80N ILE* 3.0 11.3 + - + +
81N ASN* 3.0 22.0 + - - +
82N GLY 2.9 0.2 - - - -
83N LEU* 1.3 78.0 - - - +
85N ARG* 1.3 63.2 + - - +
86N ALA 3.1 0.7 + - - -
87N ASN* 3.3 15.5 + - - +
89N ASP 4.7 0.4 - - - -
90N LEU* 6.1 0.4 - - - -
92N ARG* 3.1 27.9 - - - +
1009X C 5.4 0.6 + - - -
1010X U 4.2 11.1 + - - -
1162X A 4.6 3.8 + - - -
1163X C 3.1 38.4 + - - +
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Residues in contact with ARG 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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81N ASN* 2.6 48.4 + - - +
82N GLY* 2.6 22.1 + - - +
84N LYS* 1.3 71.9 - - - +
86N ALA* 1.3 54.2 + - - +
87N ASN* 3.2 7.1 + - - +
116N ALA* 2.9 34.5 + - + +
117N ARG* 5.1 13.5 + - - +
1162X A 6.0 1.2 - - - -
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Residues in contact with ALA 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 GLY 3.0 6.6 + - - +
83N LEU* 2.5 20.0 + - - +
85N ARG* 1.3 73.3 - - - +
87N ASN* 1.3 51.8 + - - +
88N ILE* 2.4 28.2 + - + +
89N ASP* 2.4 47.6 + - - +
112N ALA 5.8 1.8 - - - +
113N SER* 6.4 0.7 - - - -
116N ALA* 4.7 12.3 - - + -
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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