Contacts of the helix formed by residues 157 - 164 (chain D) in PDB entry 2ODE
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 157 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179C VAL* 3.8 11.1 - - + +
180C LYS 3.2 25.3 - - - +
181C THR* 3.3 10.2 + - - +
182C THR* 2.9 28.6 + - - +
153D LEU* 3.0 18.5 + - + +
156D LYS* 1.3 79.3 - - - +
158D SER* 1.3 65.5 + - - +
159D TYR 3.4 0.2 - - - -
160D PRO* 3.5 9.0 - - - +
161D ARG* 2.9 54.0 + - - +
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Residues in contact with SER 158 (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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182C THR* 3.6 24.4 - - - +
70D PHE* 4.1 4.5 - - - -
73D PHE* 3.4 7.9 - - - -
74D LEU* 3.6 31.6 - - - +
77D GLU* 4.4 5.4 - - - -
79D SER* 3.9 3.6 + - - -
82D ASN* 5.2 0.2 + - - -
153D LEU 3.8 0.2 + - - -
154D MET* 3.4 15.7 + - - +
157D ASP* 1.3 74.3 - - - +
159D TYR* 1.3 61.0 + - - +
161D ARG* 3.2 17.3 + - - +
162D PHE* 2.9 24.8 + - - +
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Residues in contact with TYR 159 (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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56D SER* 3.3 28.6 + - - -
57D PHE* 3.5 45.8 - + + -
60D LEU* 3.9 20.8 - - + +
70D PHE* 3.9 7.2 - + + -
154D MET 2.9 18.2 + - - +
155D GLU* 3.4 21.5 - - + +
158D SER* 1.3 76.9 - - - +
160D PRO* 1.4 66.7 - - + +
162D PHE* 3.1 14.9 + + - +
163D LEU* 3.0 59.6 + - + +
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Residues in contact with PRO 160 (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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155D GLU 3.2 18.6 - - - +
156D LYS* 3.6 16.8 - - - +
157D ASP 3.5 13.0 - - - +
159D TYR* 1.4 91.2 - - + +
161D ARG* 1.3 59.8 + - + +
163D LEU* 3.5 13.4 + - + +
164D ARG* 3.5 29.3 + - - +
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Residues in contact with ARG 161 (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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181C THR* 4.9 2.2 - - - +
182C THR 4.1 3.6 + - - -
185C VAL* 3.5 40.0 - - - +
73D PHE* 3.7 11.5 - - + -
77D GLU* 2.9 32.3 + - - -
157D ASP* 2.9 56.2 + - - +
158D SER* 3.2 12.9 + - - +
160D PRO* 1.3 75.7 - - + +
162D PHE* 1.3 65.9 + - - +
163D LEU 3.2 0.2 - - - -
164D ARG* 3.1 12.0 + - - +
165D SER* 3.0 22.7 + - - -
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Residues in contact with PHE 162 (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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60D LEU* 3.7 27.4 - - + -
69D ALA* 3.6 41.1 - - + -
70D PHE* 3.7 24.2 - + + -
73D PHE* 3.4 38.0 - + + -
158D SER 2.9 15.8 + - - +
159D TYR* 3.3 23.3 - + - +
161D ARG* 1.3 71.3 - - - +
163D LEU* 1.3 61.9 + - + +
165D SER* 2.7 25.2 + - - -
167D MET* 4.9 2.7 - - + -
168D TYR* 3.0 50.8 - + + +
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Residues in contact with LEU 163 (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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159D TYR* 3.0 61.1 + - + +
160D PRO* 3.7 13.5 - - + +
161D ARG 3.2 0.2 - - - -
162D PHE* 1.3 80.7 - - + +
164D ARG* 1.3 61.7 + - + +
165D SER 3.3 0.2 - - - -
168D TYR* 3.1 48.3 - - + +
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Residues in contact with ARG 164 (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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160D PRO* 3.5 17.2 + - - +
161D ARG* 3.1 12.6 + - - +
163D LEU* 1.3 79.7 - - + +
165D SER* 1.3 63.8 + - - +
166D LYS 3.7 1.0 + - - -
169D LEU* 5.6 1.9 - - - +
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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