Contacts of the helix formed by residues 157 - 165 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A VAL* 3.8 11.1 - - + +
180A LYS 3.3 23.4 - - - +
181A THR* 3.5 10.2 + - - +
182A THR* 3.1 25.7 + - + +
153B LEU* 3.0 18.8 + - + +
156B LYS* 1.3 77.1 - - - +
158B SER* 1.3 63.3 + - - +
159B TYR 3.5 0.4 - - - -
160B PRO* 3.4 9.9 - - - +
161B ARG* 2.8 56.2 + - - +
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Residues in contact with SER 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A THR* 3.6 24.4 + - - +
70B PHE* 4.0 5.6 - - - -
73B PHE* 3.5 8.5 - - - -
74B LEU* 3.4 32.3 - - - +
77B GLU* 4.3 4.7 + - - -
79B SER* 4.0 3.3 + - - -
82B ASN* 5.3 0.3 + - - -
154B MET* 3.3 14.2 + - - +
157B ASP* 1.3 76.9 + - - +
159B TYR* 1.3 58.1 + - - +
161B ARG* 3.2 15.0 + - - +
162B PHE* 2.9 23.4 + - - +
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Residues in contact with TYR 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TRP 2.7 28.6 + - - -
54B ALA 3.5 11.8 + - - -
56B SER* 3.0 16.9 - - - -
57B PHE* 3.4 51.8 - + + -
60B LEU* 3.6 22.2 - - + -
70B PHE* 3.9 8.0 - + + -
154B MET 2.9 21.7 + - - +
155B GLU* 3.6 14.6 - - + +
158B SER* 1.3 70.9 - - - +
160B PRO* 1.4 71.6 - - + +
162B PHE* 3.1 5.3 + + - +
163B LEU* 3.1 42.5 + - + +
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Residues in contact with PRO 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLN* 6.1 0.7 - - - +
155B GLU 3.3 20.0 - - - +
156B LYS* 3.6 16.4 - - - +
157B ASP 3.4 14.6 - - - +
159B TYR* 1.4 93.0 - - + +
161B ARG* 1.3 61.3 + - + +
163B LEU* 3.3 17.9 + - + +
164B ARG* 3.4 17.0 + - - +
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Residues in contact with ARG 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A THR* 4.9 2.6 - - - +
182A THR 4.1 4.2 + - - -
185A VAL* 3.4 38.0 - - - +
73B PHE* 3.7 11.0 - - + -
77B GLU* 2.9 37.0 + - - -
157B ASP* 2.8 56.9 + - - +
158B SER* 3.2 11.1 + - - +
160B PRO* 1.3 76.4 - - + +
162B PHE* 1.3 67.5 + - - +
164B ARG* 3.1 8.6 + - - +
165B SER* 3.0 22.2 + - - -
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Residues in contact with PHE 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B TRP* 4.1 7.4 - + + -
60B LEU* 3.7 26.5 - - + -
66B GLY 5.0 0.2 - - - -
69B ALA* 3.8 40.6 - - + -
70B PHE* 3.9 16.6 - + + -
73B PHE* 3.5 41.1 - + + -
158B SER 2.9 10.3 + - - +
159B TYR* 3.1 9.6 + + - +
161B ARG* 1.3 75.9 - - - +
163B LEU* 1.3 74.1 + - + +
165B SER* 2.7 29.8 + - - -
167B MET* 4.7 5.6 - - + -
168B TYR* 3.2 46.4 - + + +
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Residues in contact with LEU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B TRP 4.3 0.9 - - - +
54B ALA* 3.8 38.8 - - + +
159B TYR* 3.1 49.9 + - + +
160B PRO* 3.7 11.0 - - + +
161B ARG 3.2 0.6 - - - -
162B PHE* 1.3 93.8 - - + +
164B ARG* 1.3 62.0 + - + +
165B SER 3.5 0.2 - - - -
168B TYR* 3.5 32.1 - - + -
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Residues in contact with ARG 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LYS* 4.8 4.9 - - - +
65A GLU* 3.2 42.0 + - - +
68A GLN* 4.4 18.4 + - - +
160B PRO 3.4 11.6 + - - +
161B ARG* 3.1 10.8 + - - +
163B LEU* 1.3 78.8 - - + +
165B SER* 1.3 64.5 + - - +
166B LYS 3.9 0.2 + - - -
169B LEU* 5.6 1.2 - - - +
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Residues in contact with SER 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B PHE* 3.6 26.1 - - - -
161B ARG 3.0 10.4 + - - -
162B PHE* 2.7 23.7 + - - -
163B LEU 3.5 0.7 - - - +
164B ARG* 1.3 81.1 - - - +
166B LYS* 1.3 63.8 + - - +
167B MET* 3.6 8.1 + - - +
168B TYR* 2.9 19.1 + - - +
169B LEU* 3.0 24.7 + - - +
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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