Contacts of the helix formed by residues 99 - 113 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97G ASN 4.5 0.2 + - - -
98G VAL* 1.3 80.7 - - + +
100G ARG* 1.3 73.7 + - - +
101G VAL* 2.6 33.2 + - - +
102G GLU* 2.7 34.2 + - + +
103G ARG* 2.8 26.7 + - - +
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Residues in contact with ARG 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G VAL 3.5 1.7 + - - -
99G GLU* 1.3 80.2 + - - +
101G VAL* 1.3 68.1 + - + +
103G ARG* 2.8 36.3 + - - +
104G ASP* 2.9 14.7 + - + +
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Residues in contact with VAL 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G GLU* 2.6 21.3 + - - +
100G ARG* 1.3 81.9 - - + +
102G GLU* 1.3 56.3 + - - +
104G ASP* 3.3 9.4 + - + +
105G ARG* 2.9 28.9 + - + +
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Residues in contact with GLU 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G VAL* 3.4 11.2 - - + -
99G GLU* 2.7 31.6 + - + +
100G ARG 3.1 0.2 - - - -
101G VAL* 1.3 72.4 - - - +
103G ARG* 1.3 57.9 + - - +
105G ARG* 2.8 46.8 + - - +
106G ARG* 2.9 64.8 + - - +
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Residues in contact with ARG 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G ALA* 4.5 14.9 + - + +
95G LEU* 2.9 41.5 - - + +
96G ARG* 3.2 62.7 + - - +
98G VAL* 3.3 27.1 + - + -
99G GLU 2.8 9.3 + - - +
100G ARG* 3.1 20.9 - - - +
102G GLU* 1.3 77.1 - - - +
104G ASP* 1.3 57.5 + - - +
105G ARG 3.2 0.2 + - - -
106G ARG* 3.2 6.5 + - - +
107G VAL* 2.8 37.7 + - + +
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Residues in contact with ASP 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G TYR* 2.8 29.2 + - - +
100G ARG* 2.9 12.7 + - + +
101G VAL* 3.6 13.0 - - + +
103G ARG* 1.3 76.8 - - - +
105G ARG* 1.3 66.1 + - - +
107G VAL* 3.6 2.4 - - - +
108G ARG* 2.7 63.9 + - - +
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Residues in contact with ARG 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G VAL* 2.9 14.7 + - + +
102G GLU* 2.8 48.1 + - - +
103G ARG 3.1 0.2 - - - -
104G ASP* 1.3 78.4 - - - +
106G ARG* 1.3 64.8 + - - +
108G ARG* 3.1 2.7 + - - +
109G GLU* 2.7 70.8 + - + +
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Residues in contact with ARG 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G LEU* 4.3 14.6 - - + +
98G VAL* 3.6 37.1 - - - +
102G GLU* 2.9 45.6 + - - +
103G ARG 3.6 4.7 - - - +
105G ARG* 1.3 86.4 - - - +
107G VAL* 1.3 62.1 + - - +
109G GLU* 3.4 12.7 - - - +
110G MET* 3.0 26.3 + - - +
142G VAL* 3.7 25.4 + - + +
144G GLN* 3.1 26.7 + - - -
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Residues in contact with VAL 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G TYR* 3.8 32.1 - - + +
91G ILE* 4.0 28.7 - - + +
92G ALA* 3.9 29.4 - - + +
95G LEU* 3.9 10.3 - - + -
103G ARG* 2.8 34.0 + - + +
104G ASP* 3.6 7.4 - - - +
106G ARG* 1.3 71.6 - - - +
108G ARG* 1.3 60.8 + - - +
110G MET* 3.0 5.9 + - - +
111G ALA* 2.8 27.2 + - - +
120G LEU* 4.6 7.4 - - + -
142G VAL* 4.7 0.9 - - - -
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Residues in contact with ARG 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G TYR* 4.0 18.1 - - + -
104G ASP* 2.7 51.0 + - - +
105G ARG* 3.9 2.2 - - - +
107G VAL* 1.3 80.4 - - - +
109G GLU* 1.3 63.0 + - - +
111G ALA* 3.5 8.0 - - - +
112G GLU* 2.9 27.7 + - - +
117G ALA* 4.8 3.4 - - + +
120G LEU* 3.9 24.9 - - + +
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Residues in contact with GLU 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105G ARG* 2.7 56.5 + - + +
106G ARG* 3.4 10.8 - - - +
108G ARG* 1.3 74.4 - - - +
110G MET* 1.3 60.5 + - - +
112G GLU* 3.4 5.8 + - - +
113G LYS* 3.0 57.8 + - + +
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Residues in contact with MET 110 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91G ILE* 5.1 2.5 - - + -
106G ARG 3.0 16.3 + - - +
107G VAL 3.6 2.9 - - - +
109G GLU* 1.3 77.4 - - - +
111G ALA* 1.3 65.7 + - - +
112G GLU 3.1 2.0 - - - -
113G LYS* 3.6 19.1 - - + -
114G LEU* 3.1 45.5 + - + +
138G ALA* 4.1 9.6 - - + +
141G LEU* 3.6 33.2 - - - -
142G VAL* 3.6 27.1 - - + -
176G PHE* 3.9 17.9 - - + -
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Residues in contact with ALA 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G ILE* 4.5 5.1 - - + +
107G VAL 2.8 18.7 + - - +
108G ARG* 3.2 9.6 + - - +
110G MET* 1.3 74.6 - - - +
112G GLU* 1.3 58.9 + - - +
115G GLY 3.3 3.5 + - - -
116G ILE* 2.8 45.1 + - + +
117G ALA* 2.9 23.1 + - + +
120G LEU* 3.7 21.5 - - + -
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Residues in contact with GLU 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108G ARG 2.9 15.9 + - - +
109G GLU* 3.7 5.4 - - - +
111G ALA* 1.3 75.9 - - - +
113G LYS* 1.3 59.1 + - + +
114G LEU 2.8 11.2 + - - -
115G GLY* 3.0 12.8 + - - +
117G ALA* 4.0 16.2 - - + +
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Residues in contact with LYS 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G GLU* 3.0 53.9 + - + +
110G MET* 3.3 18.8 + - + -
112G GLU* 1.3 75.4 - - + +
114G LEU* 1.3 66.2 + - - +
171G PHE* 5.6 5.4 - - - -
175G GLU* 5.4 7.2 + - + +
176G PHE* 4.0 33.2 - - + -
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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