Contacts of the helix formed by residues 146 - 152 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144D GLY 3.3 2.2 + - - -
145D GLU* 1.3 73.4 - - + +
147D PHE* 1.3 73.8 + - + +
149D ARG* 3.6 2.9 + - - +
150D ILE* 2.8 39.5 + - + +
166D ILE* 3.6 22.9 - - + -
170D ILE* 4.3 6.7 - - + -
189D PRO* 5.4 1.1 - - + +
192D LEU* 3.1 47.0 + - + +
194D TYR* 3.4 27.8 - - + +
203D LEU* 4.0 18.2 - - + -
252D ILE* 6.2 2.2 - - + -
256D LEU* 5.5 2.9 - - + -
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Residues in contact with PHE 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D GLU* 3.2 7.3 - - - +
146D LEU* 1.3 89.0 - - + +
148D SER* 1.3 57.9 + - - +
149D ARG 2.9 5.6 + - - -
150D ILE* 3.0 23.2 + - + +
151D GLN* 2.8 33.6 + - - +
189D PRO* 4.0 25.8 - - + -
252D ILE* 4.9 12.1 - - + -
255D ILE* 3.1 33.2 - - + -
256D LEU* 4.4 20.2 - - + -
338D THR* 5.7 2.0 - - + -
342D LEU* 3.9 18.4 - - + +
349D TRP* 3.1 48.9 - + + +
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Residues in contact with SER 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D GLY* 6.2 0.2 - - - -
145D GLU* 3.3 26.6 + - - +
147D PHE* 1.3 77.2 - - - +
149D ARG* 1.3 57.6 + - - +
151D GLN* 4.1 18.6 + - - +
152D ASP* 2.9 28.8 - - - +
346D LYS* 5.4 2.1 - - - -
349D TRP* 5.5 4.8 + - - +
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Residues in contact with ARG 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D GLY* 2.7 35.1 + - - -
144D GLY* 4.3 2.4 - - - -
145D GLU 3.2 14.8 + - - +
146D LEU 3.7 6.1 - - - +
147D PHE 2.9 0.6 - - - -
148D SER* 1.3 78.6 - - - +
150D ILE* 1.3 63.5 + - + +
152D ASP* 3.3 17.1 - - - +
153D ARG* 4.2 4.9 + - - +
194D TYR* 3.1 27.7 - - + +
196D SER 2.7 29.9 + - - -
197D LYS* 3.0 24.0 + - - +
198D ARG 4.7 0.6 + - - -
199D PRO* 6.0 0.4 - - - +
201D ALA* 4.0 7.9 - - - +
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Residues in contact with ILE 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D LEU* 2.8 43.5 - - + +
147D PHE* 3.0 30.9 + - + +
149D ARG* 1.3 74.5 - - + +
151D GLN* 1.3 69.8 + - - +
152D ASP 2.9 1.7 + - - -
153D ARG* 2.9 52.7 - - - +
158D PHE* 4.2 23.8 - - + -
166D ILE* 4.8 3.6 - - + -
256D LEU* 4.8 9.6 - - + -
338D THR* 4.9 2.7 - - + +
339D SER* 3.5 12.5 + - - +
342D LEU* 4.6 10.1 - - + -
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Residues in contact with GLN 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D PHE 2.8 21.7 + - - +
148D SER* 4.1 13.3 + - - -
150D ILE* 1.3 76.6 - - - +
152D ASP* 1.3 66.3 + - - +
153D ARG 3.1 4.7 + - - -
339D SER* 4.1 11.6 + - - +
342D LEU* 3.4 35.1 - - + +
343D LYS* 2.6 50.5 + - - +
346D LYS* 2.6 47.1 + - - +
349D TRP* 4.4 9.9 - - - -
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Residues in contact with ASP 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D SER* 2.9 23.3 + - - +
149D ARG* 3.3 9.7 - - - +
150D ILE 2.9 3.6 + - - -
151D GLN* 1.3 94.1 + - - +
153D ARG* 1.3 65.4 + - - +
343D LYS* 4.3 7.8 - - - +
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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