Contacts of the helix formed by residues 112 - 119 (chain H) in PDB entry 2OME
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 ASP 112 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87H LEU 3.1 17.8 + - - +
88H THR* 4.3 3.1 - - - -
89H ARG* 3.7 31.7 + - - +
92H LEU* 3.5 6.4 - - + +
110H ASN 4.3 0.2 - - - -
111H VAL* 1.3 68.5 - - - +
113H ILE* 1.3 57.4 + - - +
114H LYS* 3.5 10.2 + - - +
115H ALA* 3.2 27.3 + - + +
116H ALA* 2.9 24.1 + - - +
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Residues in contact with ILE 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108H TYR* 3.7 35.0 - - + +
111H VAL* 2.8 24.2 + - + +
112H ASP* 1.3 71.4 + - - +
114H LYS* 1.3 59.8 + - + +
116H ALA* 3.8 6.7 - - - -
117H GLY* 3.1 21.1 + - - -
123H VAL* 3.9 29.6 - - + -
357H VAL* 3.6 24.0 - - + +
358H ASN* 3.1 23.5 + - + +
360H GLU* 3.9 8.3 - - - +
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Residues in contact with LYS 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H ARG* 5.7 1.8 - - - +
112H ASP* 3.2 9.0 + - - +
113H ILE* 1.3 80.0 - - + +
115H ALA* 1.3 66.1 + - - +
117H GLY* 3.5 1.4 + - - -
118H GLU* 3.1 36.4 + - - +
360H GLU* 3.5 29.5 - - + +
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Residues in contact with ALA 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H ARG* 3.5 48.1 - - + +
92H LEU* 3.9 9.6 - - + -
112H ASP* 3.2 24.7 + - - +
114H LYS* 1.3 76.2 - - - +
116H ALA* 1.3 65.8 + - - +
118H GLU* 3.2 2.6 + - - +
119H LEU* 3.0 31.9 + - + +
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Residues in contact with ALA 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92H LEU* 3.6 18.0 - - + +
111H VAL* 5.0 1.3 - - + -
112H ASP 2.9 14.0 + - - +
113H ILE 3.5 5.4 - - - +
115H ALA* 1.3 74.5 - - - +
117H GLY* 1.3 62.2 + - - +
119H LEU* 3.1 9.7 + - - -
121H ILE* 2.8 50.2 + - + +
123H VAL* 3.5 23.3 - - + -
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Residues in contact with GLY 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113H ILE 3.1 11.1 + - - -
114H LYS 3.5 0.6 + - - -
115H ALA 3.3 0.2 - - - -
116H ALA* 1.3 79.6 - - - +
118H GLU* 1.3 59.7 + - - +
120H GLY* 3.2 6.4 + - - -
121H ILE 3.8 4.0 - - - -
358H ASN* 3.5 11.6 - - - +
360H GLU 3.4 18.6 - - - -
361H PHE* 3.7 10.8 - - - -
362H PHE 2.7 26.5 + - - -
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Residues in contact with GLU 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89H ARG* 3.0 26.6 + - - +
114H LYS* 3.1 25.4 + - - +
115H ALA* 3.2 5.4 + - - +
117H GLY* 1.3 77.1 - - - +
119H LEU* 1.3 64.2 + - + +
120H GLY 3.2 3.0 + - - -
360H GLU* 3.7 7.8 + - + +
362H PHE* 4.3 14.7 - - - +
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Residues in contact with LEU 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89H ARG* 4.6 5.6 - - + +
92H LEU* 4.0 26.0 - - + +
93H GLU* 4.0 35.2 - - + +
98H LEU 5.4 0.5 - - - +
115H ALA* 3.0 24.9 + - + +
116H ALA* 3.1 4.0 + - - +
118H GLU* 1.3 79.4 - - + +
120H GLY* 1.3 60.4 + - - +
121H ILE* 3.5 13.1 - - + +
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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