Contacts of the helix formed by residues 99 - 113 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97F ASN 5.3 0.7 - - - +
98F VAL* 1.3 89.2 - - + +
100F ARG* 1.3 71.4 + - - +
101F VAL* 3.5 12.3 - - + -
102F GLU* 2.9 26.6 + - + +
103F ARG* 3.1 13.8 + - - +
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Residues in contact with ARG 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F GLU* 1.3 72.4 - - - +
101F VAL* 1.3 76.8 + - + +
103F ARG* 2.8 27.6 + - - +
104F ASP* 3.1 17.7 + - + +
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Residues in contact with VAL 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F GLU* 4.2 14.4 - - + +
100F ARG* 1.3 85.1 - - + +
102F GLU* 1.3 68.8 + - + +
104F ASP* 3.7 5.8 + - - +
105F ARG* 3.3 22.9 + - - +
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Residues in contact with GLU 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F VAL* 3.0 29.9 - - + +
99F GLU* 2.9 19.3 + - + +
100F ARG 2.8 3.2 + - - -
101F VAL* 1.3 77.2 - - + +
103F ARG* 1.3 49.4 + - - -
105F ARG* 3.1 34.0 + - - +
106F ARG* 2.8 67.2 + - - +
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Residues in contact with ARG 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F TYR* 4.5 3.1 - - + +
92F ALA* 4.9 12.8 - - + -
95F LEU* 3.0 43.2 + - + +
96F ARG* 4.0 26.9 + - - +
98F VAL* 3.7 23.1 + - + +
99F GLU* 3.1 4.1 + - - +
100F ARG* 2.8 29.1 + - - +
102F GLU* 1.3 71.6 - - - +
104F ASP* 1.3 68.0 + - - +
106F ARG* 4.4 5.4 - - - -
107F VAL* 2.8 32.7 + - + +
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Residues in contact with ASP 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F TYR* 3.2 20.8 + - - +
100F ARG* 3.1 14.8 + - + +
101F VAL* 4.0 8.8 - - - +
103F ARG* 1.3 79.3 - - - +
105F ARG* 1.3 61.8 + - - +
107F VAL* 3.9 1.0 - - - +
108F ARG* 2.6 67.4 + - - +
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Residues in contact with ARG 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F VAL 3.3 11.3 + - - +
102F GLU* 3.1 33.2 + - - +
103F ARG 3.1 0.2 - - - -
104F ASP* 1.3 77.0 + - - +
106F ARG* 1.3 87.2 + - - +
107F VAL 2.8 4.0 + - - -
108F ARG* 2.9 16.1 + - - +
109F GLU* 3.0 42.6 + - + +
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Residues in contact with ARG 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F LEU* 3.6 22.1 - - + +
98F VAL* 4.0 12.0 - - - +
102F GLU* 2.8 51.6 + - - +
103F ARG 3.8 3.8 - - - +
105F ARG* 1.3 89.0 - - - +
107F VAL* 1.3 61.1 + - - +
109F GLU* 3.8 16.7 - - - +
110F MET* 3.6 15.1 + - - +
142F VAL* 3.4 39.3 + - + +
143F ILE* 5.1 2.0 - - - +
144F GLN* 3.0 26.5 + - - -
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Residues in contact with VAL 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F TYR* 4.2 28.9 - - + +
91F ILE* 3.6 35.4 - - + +
92F ALA* 3.9 19.7 - - + +
95F LEU* 3.7 22.7 - - + -
103F ARG 2.8 23.8 - - - +
104F ASP* 3.9 4.9 - - - +
105F ARG 2.8 5.1 + - - -
106F ARG* 1.3 69.9 - - - +
108F ARG* 1.3 61.0 + - - +
109F GLU 3.1 1.6 - - - -
110F MET* 3.1 5.7 + - - +
111F ALA* 2.8 24.8 + - - +
120F LEU* 4.7 3.4 - - + -
142F VAL* 4.8 1.3 - - + -
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Residues in contact with ARG 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F TYR* 3.9 19.9 - - + -
104F ASP* 2.6 42.4 + - - +
105F ARG* 2.9 7.3 + - - +
107F VAL* 1.3 69.0 - - - +
109F GLU* 1.3 65.9 + - + +
111F ALA* 3.7 10.4 - - - +
112F GLU* 3.1 26.2 + - - +
117F ALA* 4.8 3.2 - - + +
120F LEU* 4.3 21.8 - - + +
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Residues in contact with GLU 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F ARG* 3.0 51.2 + - + +
106F ARG* 3.8 13.8 - - - +
107F VAL 3.1 0.2 - - - -
108F ARG* 1.3 78.7 - - + +
110F MET* 1.3 57.7 + - + +
112F GLU* 3.3 5.3 + - - +
113F LYS* 2.9 42.6 + - - +
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Residues in contact with MET 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F ILE* 5.1 0.7 - - + -
106F ARG 3.6 6.4 + - - +
107F VAL 3.1 8.1 + - - +
109F GLU* 1.3 75.7 - - + +
111F ALA* 1.3 65.4 + - - +
112F GLU 3.1 1.8 - - - -
113F LYS* 3.6 19.3 - - + -
114F LEU* 3.1 45.7 + - + +
116F ILE* 4.8 0.2 - - - +
138F ALA* 4.1 11.7 - - + +
141F LEU* 3.6 32.3 - - - -
142F VAL* 3.6 29.8 - - + -
176F PHE* 3.9 17.5 - - + -
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Residues in contact with ALA 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F ILE* 4.6 5.1 - - + +
107F VAL 2.8 16.4 + - - +
108F ARG* 3.7 8.5 - - - +
110F MET* 1.3 77.1 - - - +
112F GLU* 1.3 57.9 + - - +
115F GLY 3.3 2.9 + - - -
116F ILE* 2.8 45.7 + - + +
117F ALA* 2.9 23.6 + - + +
120F LEU* 3.7 21.8 - - + -
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Residues in contact with GLU 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F ARG 3.1 16.7 + - - +
109F GLU* 3.6 5.3 - - - +
110F MET 3.1 0.4 - - - -
111F ALA* 1.3 76.4 - - - +
113F LYS* 1.3 57.8 + - + +
114F LEU 2.8 11.1 + - - -
115F GLY* 3.0 13.1 + - - +
117F ALA* 4.0 16.3 - - + +
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Residues in contact with LYS 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F GLU* 2.9 29.9 + - - +
110F MET* 3.3 21.5 + - + +
112F GLU* 1.3 75.2 - - - +
114F LEU* 1.3 66.0 + - - +
115F GLY 3.7 0.2 - - - -
171F PHE* 5.6 5.4 - - - -
175F GLU* 5.4 7.2 + - + +
176F PHE* 4.0 31.6 - - + -
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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