Contacts of the helix formed by residues 99 - 113 (chain B) in PDB entry 2ONK
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 GLU 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B VAL* 1.3 79.2 - - + +
100B ARG* 1.3 74.8 + - - +
101B VAL* 2.6 32.1 + - - +
102B GLU* 2.7 34.7 + - + +
103B ARG* 2.8 27.0 + - - +
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Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B VAL 3.5 2.1 + - - -
99B GLU* 1.3 79.3 + - - +
101B VAL* 1.3 67.4 + - + +
103B ARG* 2.8 35.6 + - - +
104B ASP* 2.9 13.4 + - + +
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLU* 2.6 22.3 + - - +
100B ARG* 1.3 81.9 - - + +
102B GLU* 1.3 55.6 + - - +
104B ASP* 3.3 9.2 + - + +
105B ARG* 2.9 28.6 + - + +
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Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B VAL* 3.4 11.0 - - + -
99B GLU* 2.7 33.1 + - + +
100B ARG 3.1 0.2 - - - -
101B VAL* 1.3 72.6 - - - +
103B ARG* 1.3 57.8 + - - +
105B ARG* 2.8 46.8 + - - +
106B ARG* 2.9 64.8 + - - +
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Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B TYR* 5.2 1.1 - - - +
92B ALA* 4.5 16.5 + - + +
95B LEU* 2.9 41.5 - - + +
96B ARG* 3.2 61.3 + - - +
98B VAL* 3.3 27.5 + - + -
99B GLU 2.8 8.5 + - - +
100B ARG* 2.8 21.5 + - - +
102B GLU* 1.3 76.5 - - - +
104B ASP* 1.3 58.1 + - - +
105B ARG 3.2 0.2 + - - -
106B ARG* 3.2 6.4 + - - +
107B VAL* 2.8 35.9 + - + +
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Residues in contact with ASP 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B TYR* 2.9 28.1 + - - +
100B ARG* 2.9 13.3 + - + +
101B VAL* 3.6 13.2 - - + +
103B ARG* 1.3 76.1 - - - +
105B ARG* 1.3 66.6 + - - +
107B VAL* 3.6 3.1 - - - +
108B ARG* 2.7 64.6 + - - +
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Residues in contact with ARG 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B VAL* 2.9 15.5 + - + +
102B GLU* 2.8 47.5 + - - +
104B ASP* 1.3 78.8 - - - +
106B ARG* 1.3 64.9 + - - +
108B ARG* 3.6 2.6 - - - +
109B GLU* 2.7 67.5 + - + +
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Residues in contact with ARG 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU* 4.3 18.8 - - + +
98B VAL* 3.6 37.7 - - - +
102B GLU* 2.9 45.1 + - - +
103B ARG 3.6 5.2 - - - +
105B ARG* 1.3 87.2 - - - +
107B VAL* 1.3 61.5 + - - +
109B GLU* 3.4 12.8 - - - +
110B MET* 3.0 27.5 + - - +
142B VAL* 3.8 17.2 + - + +
144B GLN* 3.1 26.8 + - - -
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B TYR* 4.0 31.0 - - + +
91B ILE* 3.9 33.3 - - + +
92B ALA* 4.1 21.3 - - + -
95B LEU* 4.0 17.7 - - + -
103B ARG* 2.8 34.4 + - + +
104B ASP* 3.6 7.4 - - - +
105B ARG 3.0 0.2 + - - -
106B ARG* 1.3 71.2 - - - +
108B ARG* 1.3 53.7 + - - +
110B MET* 2.9 7.1 + - - +
111B ALA* 2.6 32.2 + - - +
120B LEU* 4.6 4.7 - - + -
142B VAL* 4.6 1.1 - - - -
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Residues in contact with ARG 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B TYR* 4.2 11.6 - - + -
104B ASP* 2.7 50.8 + - - +
105B ARG* 3.9 2.5 - - - +
107B VAL* 1.3 81.5 - - + +
109B GLU* 1.3 66.6 + - - +
111B ALA* 3.6 7.9 - - + +
112B GLU* 2.8 28.3 + - - +
117B ALA* 4.8 2.8 - - + +
120B LEU* 3.9 28.1 - - + +
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Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ARG* 2.7 57.8 + - + +
106B ARG* 3.4 10.2 - - - +
108B ARG* 1.3 71.5 - - - +
110B MET* 1.3 61.4 + - - +
112B GLU* 3.7 5.2 - - - +
113B LYS* 2.9 60.2 + - - +
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Residues in contact with MET 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ILE* 5.1 0.7 - - + -
106B ARG 3.0 11.9 + - - +
107B VAL 2.9 8.3 + - - +
109B GLU* 1.3 79.2 - - - +
111B ALA* 1.3 64.2 + - - +
112B GLU 3.1 1.8 - - - -
113B LYS* 3.6 19.1 - - + -
114B LEU* 3.1 44.3 + - + +
116B ILE* 4.8 0.3 - - - +
138B ALA* 4.1 11.9 - - + +
141B LEU* 3.6 32.5 - - - -
142B VAL* 3.6 27.4 - - + -
176B PHE* 3.9 18.4 - - + -
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ILE* 4.6 5.6 - - + +
107B VAL 2.6 19.4 + - - +
108B ARG* 3.6 9.9 - - - +
110B MET* 1.3 72.3 - - - +
112B GLU* 1.3 57.8 + - - +
115B GLY 3.3 3.1 + - - -
116B ILE* 2.8 46.2 + - + +
117B ALA* 2.9 24.6 + - + +
120B LEU* 3.7 21.8 - - + -
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ARG 2.8 16.4 + - - +
109B GLU* 3.7 5.2 - - - +
111B ALA* 1.3 75.3 - - - +
113B LYS* 1.3 58.0 + - + +
114B LEU 2.8 10.7 + - - -
115B GLY* 3.0 12.4 + - - +
117B ALA* 4.0 17.9 - - + +
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B GLU* 2.9 57.0 + - + +
110B MET* 3.3 19.2 + - + +
112B GLU* 1.3 75.0 - - + +
114B LEU* 1.3 66.3 + - - +
115B GLY 3.7 0.2 - - - -
171B PHE* 5.7 5.7 - - - -
175B GLU* 5.4 7.7 + - + +
176B PHE* 4.0 33.0 - - + -
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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