Contacts of the helix formed by residues 106 - 122 (chain A) in PDB entry 1ON2
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 SER 106 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LEU* 1.3 75.4 - - - +
107A TRP* 1.3 60.4 + - - +
108A ASN* 3.7 8.9 + - - +
109A SER* 2.9 27.2 + - - -
110A ILE* 3.0 10.8 + - - +
93B LYS* 3.9 20.4 - - - +
97B ASP* 2.7 37.4 + - - -
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Residues in contact with TRP 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU* 5.4 3.8 + - - -
69A ILE* 6.3 0.9 - - + -
72A ARG* 3.4 61.7 - - + -
73A LEU* 4.3 11.0 - - + -
75A TYR* 4.7 0.9 - + - -
76A ARG* 3.7 39.2 - - + +
105A LEU 5.3 1.3 - - - -
106A SER* 1.3 73.0 - - - +
108A ASN* 1.3 60.5 + - - +
110A ILE* 3.5 29.2 - - + +
111A ASP* 2.8 42.9 + - - +
93B LYS* 5.7 0.6 - - - +
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Residues in contact with ASN 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A SER* 3.0 1.1 - - - +
107A TRP* 1.3 78.8 - - - +
109A SER* 1.3 56.3 + - - +
111A ASP* 3.2 11.5 + - - +
112A ARG* 3.0 44.4 + - - +
89B VAL* 3.3 19.7 - - - +
90B ASP* 2.8 51.8 - - - +
93B LYS* 3.5 34.4 - - + +
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Residues in contact with SER 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 4.1 17.5 - - - -
106A SER* 2.9 10.4 + - - -
108A ASN* 1.3 76.8 - - - +
110A ILE* 1.3 60.3 + - - +
112A ARG* 3.3 1.9 + - - +
113A ILE* 2.9 38.9 + - - +
84B LEU* 3.9 10.5 - - - +
87B ILE* 4.9 0.2 - - - +
89B VAL* 3.5 28.3 - - - +
97B ASP* 2.6 27.4 + - - -
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Residues in contact with ILE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG* 5.3 0.2 - - - +
75A TYR* 4.3 10.7 + - + -
76A ARG* 3.6 38.8 - - + -
79A LEU* 3.5 21.6 - - + +
80A LEU* 4.2 20.4 - - + -
105A LEU* 4.2 22.2 - - + +
106A SER 3.0 13.9 + - - +
107A TRP* 3.5 35.7 - - + +
108A ASN 3.2 0.2 - - - -
109A SER* 1.3 75.3 - - - +
111A ASP* 1.3 66.3 + - - +
113A ILE* 3.2 4.5 + - + +
114A GLY* 3.0 19.4 + - - -
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Residues in contact with ASP 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG* 4.7 12.6 + - - -
107A TRP* 2.8 32.9 + - - +
108A ASN* 3.2 12.1 + - - +
110A ILE* 1.3 79.3 - - - +
112A ARG* 1.3 82.2 + - - +
114A GLY* 3.2 11.0 + - - -
115A ASP* 3.2 17.2 + - - +
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Residues in contact with ARG 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ASN* 3.0 32.9 + - - +
109A SER 3.8 4.0 - - - +
111A ASP* 1.3 90.8 + - - +
113A ILE* 1.3 66.0 + - - +
115A ASP* 2.6 34.0 + - + +
116A LEU* 3.0 21.5 + - - +
87B ILE* 2.6 37.7 - - + +
88B GLY 3.4 28.2 + - - -
89B VAL* 3.7 12.1 - - + +
90B ASP* 5.6 0.8 + - - -
130B LEU* 5.5 0.3 - - - +
134B GLN* 3.5 34.1 + - - +
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Residues in contact with ILE 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU* 4.2 14.8 - - + -
80A LEU* 3.9 24.0 - - + -
83A PHE* 3.8 43.3 - - + -
105A LEU* 4.3 16.4 - - + -
109A SER* 2.9 26.6 + - - +
110A ILE* 3.2 6.9 + - - +
112A ARG* 1.3 76.5 - - - +
114A GLY* 1.3 58.6 + - - +
116A LEU* 3.1 7.7 + - + +
117A VAL* 2.9 27.6 + - + +
83B PHE* 4.9 10.3 - - + -
84B LEU* 5.5 1.6 - - + -
87B ILE* 4.0 17.9 - - + -
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Residues in contact with GLY 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR* 4.6 7.4 - - - -
79A LEU* 3.8 20.6 - - - +
110A ILE 3.0 13.0 + - - -
111A ASP 3.2 5.3 + - - -
112A ARG 3.2 0.4 - - - -
113A ILE* 1.3 78.1 - - - +
115A ASP* 1.3 56.9 + - - +
117A VAL* 3.4 3.3 + - - +
118A GLN* 3.1 27.3 + - - +
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Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ASP 3.2 8.1 + - - +
112A ARG* 2.6 45.1 + - + +
114A GLY* 1.3 72.8 - - - +
116A LEU* 1.3 60.7 + - - +
118A GLN* 3.5 8.1 + - - +
119A TYR* 3.0 26.5 + - - +
87B ILE 6.0 0.7 - - - +
130B LEU* 3.8 8.7 - - + +
133B ILE* 3.7 33.9 - - + +
134B GLN* 3.6 16.2 - - + +
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE* 3.3 36.1 - - + -
112A ARG 3.0 12.8 + - - +
113A ILE* 3.4 9.9 - - - +
115A ASP* 1.3 75.2 - - - +
117A VAL* 1.3 64.0 + - - +
119A TYR* 3.1 17.4 - - + +
120A PHE* 3.3 26.9 + - + -
83B PHE* 4.3 2.9 - - + -
87B ILE* 4.0 23.3 - - + -
116B LEU* 3.5 16.8 - - + -
120B PHE* 3.6 37.0 - - + -
130B LEU* 3.9 13.4 - - + +
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Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 3.9 19.1 - - + -
82A GLN* 3.5 26.0 - - - +
83A PHE* 3.9 34.5 - - + +
86A ILE* 3.4 25.2 - - + +
113A ILE* 2.9 18.9 + - + +
114A GLY 3.7 5.2 - - - +
115A ASP 3.3 0.2 - - - -
116A LEU* 1.3 78.0 - - - +
118A GLN* 1.3 61.3 + - - +
120A PHE* 3.4 4.8 + - - +
121A GLU* 2.8 32.7 + - + +
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Residues in contact with GLN 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A GLY 3.1 17.1 + - - +
115A ASP* 3.7 9.9 - - - +
117A VAL* 1.3 74.9 - - - +
119A TYR* 1.3 67.3 + - - +
121A GLU* 3.1 8.8 + - + +
122A GLU* 3.1 47.9 + - + +
133B ILE* 3.5 28.1 - - + +
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Residues in contact with TYR 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ASP 3.0 15.6 + - - +
116A LEU 3.1 9.8 + - - +
118A GLN* 1.3 76.7 - - - +
120A PHE* 1.3 84.9 + + - +
122A GLU* 3.4 6.8 + - - +
126A ARG* 2.7 68.6 + - - +
119B TYR* 2.7 44.3 + + - -
120B PHE* 4.0 10.8 - + - -
126B ARG* 3.6 21.9 - - - +
129B ASP* 3.8 21.2 + - + +
130B LEU* 3.9 25.8 - - + -
133B ILE* 4.8 5.8 - - + +
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Residues in contact with PHE 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ILE* 4.0 18.4 - - + -
87A ILE* 5.3 1.6 - - + -
116A LEU* 3.3 35.7 + - + -
117A VAL 4.1 2.9 - - - +
118A GLN 3.3 0.2 - - - -
119A TYR* 1.3 103.1 - + - +
121A GLU* 1.3 63.6 + - - +
122A GLU 3.4 0.4 - - - -
123A ASP 3.5 16.3 + - - +
124A ASP 4.3 0.2 + - - -
126A ARG* 3.7 37.9 - - + -
127A LYS* 3.1 39.1 - - + +
130A LEU* 3.9 18.8 - - + -
116B LEU* 3.5 33.9 - - + -
119B TYR* 4.0 11.4 - + - -
120B PHE* 4.5 0.7 - + - -
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Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLN* 2.9 27.7 + - - +
86A ILE* 3.7 13.4 - - - +
117A VAL* 2.8 34.8 + - + +
118A GLN* 3.1 11.4 + - + +
120A PHE* 1.3 80.1 - - - +
122A GLU* 1.3 59.8 + - - +
123A ASP 3.5 0.9 + - - -
124A ASP* 5.0 6.1 - - - +
127A LYS* 3.8 12.5 + - - -
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Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A GLN* 3.1 40.5 + - + +
119A TYR* 3.4 0.4 - - - +
121A GLU* 1.3 76.0 - - - +
123A ASP* 1.3 62.3 + - - +
126A ARG* 3.2 32.3 + - - +
133B ILE* 3.7 18.4 - - - +
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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
------------------------------------------------------------
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