Contacts of the helix formed by residues 146 - 152 (chain C) in PDB entry 2ONL
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 LEU 146 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144C GLY 3.5 3.5 + - - -
145C GLU* 1.3 74.6 - - + +
147C PHE* 1.3 86.3 + - + +
148C SER 3.1 2.6 + - - -
149C ARG* 3.3 6.8 + - - +
150C ILE* 3.1 44.2 + - + +
166C ILE* 4.9 14.8 - - + -
170C ILE* 5.5 5.4 - - + -
189C PRO* 5.3 0.2 - - + -
192C LEU* 3.0 54.6 + - + +
193C LEU* 4.6 0.4 - - - +
194C TYR* 4.9 7.3 - - + -
203C LEU* 4.5 19.7 - - + -
252C ILE* 5.6 4.7 - - + -
256C LEU* 4.6 10.8 - - + -
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Residues in contact with PHE 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C GLU* 3.4 12.1 + - - +
146C LEU* 1.3 119.2 - - + +
148C SER* 1.3 58.2 + - - +
150C ILE* 4.6 7.4 - - + -
151C GLN* 2.8 33.0 + - - +
189C PRO* 4.3 15.0 - - + +
192C LEU* 4.5 2.2 - - + -
252C ILE* 4.4 20.4 - - + -
255C ILE* 3.6 39.5 - - + -
256C LEU* 4.5 15.3 - - + -
342C LEU* 4.5 10.5 - - + -
349C TRP* 3.4 43.9 + + + +
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Residues in contact with SER 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C GLY* 5.4 0.7 - - - -
145C GLU* 2.8 48.0 + - - +
147C PHE* 1.3 78.3 - - - +
149C ARG* 1.3 62.4 + - - +
151C GLN* 4.5 3.6 - - - +
152C ASP* 2.6 30.6 - - - +
353C LYS* 5.4 0.7 + - - -
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Residues in contact with ARG 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C GLY 5.5 7.0 - - - +
144C GLY* 5.7 1.3 - - - -
145C GLU 2.9 10.1 + - - +
146C LEU 3.7 7.2 - - - +
148C SER* 1.3 75.7 - - - +
150C ILE* 1.3 74.1 + - + +
152C ASP* 3.1 20.1 + - - +
153C ARG* 3.7 45.5 + - - +
194C TYR* 4.4 26.0 - - + -
197C LYS* 5.1 22.0 + - - +
198C ARG* 5.9 1.0 - - - +
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Residues in contact with ILE 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C LEU* 3.1 37.2 + - + +
147C PHE* 4.6 6.5 - - + +
149C ARG* 1.3 77.5 - - + +
151C GLN* 1.3 69.7 + - - +
152C ASP 2.8 4.2 + - - -
153C ARG* 3.3 23.7 + - - +
158C PHE* 3.7 53.8 - - + -
166C ILE* 4.5 2.7 - - + -
194C TYR* 6.1 3.4 - - + +
256C LEU* 4.6 5.8 - - + -
338C THR* 6.4 0.7 - - - -
339C SER* 3.9 24.9 - - - -
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Residues in contact with GLN 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C PHE 2.8 23.3 + - - +
148C SER* 4.7 3.6 + - - +
149C ARG 3.2 1.0 - - - -
150C ILE* 1.3 79.4 - - - +
152C ASP* 1.3 82.8 + - - +
153C ARG 3.9 3.5 + - - +
339C SER* 4.1 6.2 - - - +
342C LEU* 5.2 7.3 - - + +
343C LYS* 3.0 70.4 - - + +
346C LYS* 4.2 12.8 - - - +
349C TRP* 3.6 27.0 + - - +
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Residues in contact with ASP 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C SER* 2.6 26.6 - - - +
149C ARG* 3.1 14.4 + - - +
150C ILE 2.8 3.0 + - - -
151C GLN* 1.3 98.7 + - - +
153C ARG* 1.3 56.1 + - - +
154C GLY* 3.9 2.7 + - - -
343C LYS* 2.4 29.0 + - - +
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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