Contacts of the helix formed by residues 114 - 120 (chain I) 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 GLY 114 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107I LEU 4.7 0.6 + - - -
108I VAL* 3.0 28.8 + - - +
109I VAL 4.3 0.7 - - - -
111I GLY 2.9 11.6 + - - -
113I SER* 1.3 82.7 - - - +
115I LEU* 1.3 72.5 + - - +
116I ILE 3.7 0.7 - - - -
117I GLY 3.3 10.2 + - - -
118I SER* 3.3 7.3 + - - -
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Residues in contact with LEU 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H LEU* 5.0 17.7 - - + -
26H ALA* 5.8 6.3 - - + -
30H LEU* 6.5 0.9 - - + -
108I VAL 3.8 4.6 + - - +
109I VAL* 4.9 6.1 - - + +
114I GLY* 1.3 76.4 - - - +
116I ILE* 1.3 70.7 + - + +
118I SER* 3.1 7.1 + - - -
119I PHE* 3.2 31.7 + - + -
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Residues in contact with ILE 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H LEU* 3.9 18.4 - - + -
109I VAL* 3.0 33.5 + - + +
110I PHE* 4.3 28.9 - - + -
115I LEU* 1.3 81.4 - - + +
117I GLY* 1.3 54.5 + - - +
118I SER 2.8 0.2 + - - -
119I PHE* 4.2 10.1 - - + -
120I SER* 2.7 52.4 + - - +
124I PHE* 4.6 2.0 - - + -
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Residues in contact with GLY 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109I VAL 2.7 12.5 + - - -
110I PHE* 3.3 33.6 - - - +
111I GLY 3.4 8.5 - - - -
112I SER* 4.0 12.5 - - - -
114I GLY 3.3 0.8 + - - -
115I LEU 3.0 2.2 + - - -
116I ILE* 1.3 73.0 - - - +
118I SER* 1.3 57.0 + - - +
120I SER* 3.8 14.2 - - - +
122I LEU 5.5 0.3 - - - +
123I LYS* 6.0 1.4 - - - -
124I PHE* 4.9 3.1 - - - -
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Residues in contact with SER 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112I SER* 2.5 24.7 + - - +
113I SER 3.5 5.9 + - - -
114I GLY 3.3 6.9 + - - -
115I LEU 3.1 7.7 + - - -
116I ILE 3.0 0.2 - - - -
117I GLY* 1.3 74.6 - - - +
119I PHE* 1.3 68.5 + - - +
120I SER 2.9 16.0 + - - +
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Residues in contact with PHE 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115I LEU* 3.2 30.7 + - + +
116I ILE* 2.9 12.4 + - + +
118I SER* 1.3 85.8 - - - +
120I SER* 1.3 55.9 + - - +
121I PRO* 4.0 5.8 - - - +
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Residues in contact with SER 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I ILE* 2.7 25.6 + - - -
117I GLY 3.8 9.8 - - - +
118I SER 2.9 10.6 - - - +
119I PHE* 1.3 80.2 - - - +
121I PRO* 1.3 69.7 - - - +
122I LEU* 3.3 13.0 + - - +
123I LYS* 5.5 0.5 - - - +
124I PHE* 3.2 33.3 - - - -
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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