Contacts of the strand formed by residues 184 - 191 (chain C) 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 ILE 184 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182C THR 4.1 0.4 + - - -
183C GLY* 1.3 78.8 - - - +
185C VAL* 1.3 63.9 + - - +
186C GLU* 4.3 0.9 + - + -
199C PHE* 4.1 28.0 - - + -
200C ASP 3.5 8.1 - - - +
201C VAL* 4.3 15.9 - - + -
210C LYS* 3.3 34.8 - - + +
211C TRP* 4.6 2.5 - - + -
213C HIS* 4.0 10.1 - - + -
214C CYS* 4.4 17.3 - - + -
76D THR 4.4 2.8 - - - +
77D GLU* 2.7 30.6 + - - +
78D PHE* 4.0 30.5 - - + -
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Residues in contact with VAL 185 (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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181C THR* 4.3 13.7 - - + -
182C THR 4.7 0.9 - - - +
184C ILE* 1.3 79.5 - - - +
186C GLU* 1.3 69.2 + - - +
187C THR* 4.0 4.3 + - - +
198C MET 3.6 1.6 - - - +
199C PHE* 3.4 1.8 - - - -
200C ASP* 2.8 50.8 + - + +
77D GLU* 4.0 10.8 - - - +
161D ARG* 3.5 55.4 - - - +
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Residues in contact with GLU 186 (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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184C ILE* 4.2 1.4 + - + -
185C VAL* 1.3 79.4 - - - +
187C THR* 1.3 71.0 + - - +
188C HIS* 6.2 0.2 - - - +
197C LYS* 4.3 15.6 - - - +
198C MET 3.3 6.5 - - - +
199C PHE* 3.5 43.9 - - + -
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Residues in contact with THR 187 (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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50C VAL* 4.5 11.8 - - + +
58C GLU* 4.0 15.9 + - - +
185C VAL* 5.3 4.5 - - - +
186C GLU* 1.3 78.8 - - - +
188C HIS* 1.3 73.6 + - - +
197C LYS* 3.7 2.8 - - - -
198C MET* 2.7 72.7 + - + +
200C ASP* 6.4 0.9 - - + -
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Residues in contact with HIS 188 (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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58C GLU* 3.5 14.0 - - - +
187C THR* 1.3 82.1 + - - +
189C PHE* 1.3 69.2 + - - +
195C TYR* 3.2 39.3 + + + +
196C PHE 3.1 13.9 - - - +
197C LYS* 4.7 2.2 - - + -
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Residues in contact with PHE 189 (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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36C LEU* 4.8 0.9 - - + -
53C MET* 3.7 20.9 - - + -
57C HIS* 3.7 30.7 - + + +
58C GLU* 3.4 34.5 - - + -
188C HIS* 1.3 81.2 - - - +
190C THR* 1.3 63.6 + - - +
191C PHE* 4.5 0.7 - - + -
195C TYR* 3.8 3.5 - - - -
196C PHE* 2.8 73.1 + + + +
198C MET* 3.7 35.2 - - + -
336C PHE* 3.7 22.2 - + - -
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Residues in contact with THR 190 (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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31C ALA* 5.6 4.7 - - + -
57C HIS* 4.1 17.0 + - - +
189C PHE* 1.3 79.9 + - - +
191C PHE* 1.3 69.5 + - - +
193C ASP* 4.5 9.6 - - - +
194C LEU 3.2 21.7 + - - +
195C TYR* 3.6 21.2 - - + +
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Residues in contact with PHE 191 (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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57C HIS* 3.2 42.2 - + + +
189C PHE* 4.5 1.8 - - + -
190C THR* 1.3 79.3 - - - +
192C LYS* 1.3 83.4 + - + +
193C ASP 3.2 1.8 - - - -
194C LEU* 2.8 25.0 + - - +
196C PHE* 3.9 13.2 - + + -
336C PHE* 3.9 7.9 - + - -
337C ASP* 3.2 29.6 - - - -
340C THR* 3.4 38.8 - - + -
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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