Contacts of the strand formed by residues 220 - 226 (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 ALA 220 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C VAL* 5.0 1.3 - - + -
35C LYS 3.1 3.4 + - - +
36C LEU* 3.2 16.2 - - + -
37C LEU 3.0 22.5 + - - -
218C VAL* 3.4 4.2 - - - +
219C THR* 1.3 82.3 - - - +
221C ILE* 1.3 63.9 + - - +
262C THR* 3.7 1.6 - - - -
263C SER* 3.3 12.6 - - - +
265C ILE* 4.1 8.5 - - + -
343C ILE* 3.8 35.4 - - + -
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Residues in contact with ILE 221 (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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37C LEU* 3.3 17.5 - - + +
39C LEU* 3.8 21.8 - - + -
218C VAL* 3.8 13.5 - - + -
220C ALA* 1.3 76.9 - - - +
222C ILE* 1.3 71.1 + - - +
223C PHE* 3.9 9.9 - - + +
253C ILE* 3.7 13.5 - - + -
259C PHE* 3.5 51.4 - - + -
262C THR* 3.9 2.2 - - + -
263C SER 3.0 6.3 + - - +
264C ILE* 3.7 17.0 - - + -
265C ILE* 2.8 34.6 + - - +
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Residues in contact with ILE 222 (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* 3.9 21.0 - - + +
37C LEU 2.8 7.9 + - - -
38C LEU* 3.5 22.2 - - + -
39C LEU 3.0 24.6 + - - +
49C ILE* 5.0 5.8 - - + -
221C ILE* 1.3 74.8 - - - +
223C PHE* 1.3 58.8 + - - +
224C CYS* 3.8 12.2 + - - -
265C ILE* 3.4 17.7 - - + -
267C PHE* 3.5 51.8 - - + -
336C PHE* 4.1 24.0 - - + -
339C VAL* 4.3 9.2 - - + -
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Residues in contact with PHE 223 (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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39C LEU* 3.4 18.6 - - + -
40C GLY* 4.0 14.6 - - - -
41C ALA 4.8 0.7 - - - -
211C TRP* 5.0 0.4 - + - -
221C ILE* 3.8 8.4 - - + -
222C ILE* 1.3 72.4 - - - +
224C CYS* 1.3 67.1 + - - +
225C VAL* 3.6 25.8 - - + -
246C SER* 4.1 8.3 - - - -
249C LEU* 3.8 26.2 - - + -
250C PHE* 3.6 59.9 - + + -
253C ILE* 4.0 20.4 - - + -
264C ILE* 5.2 1.6 - - + -
265C ILE 2.7 15.8 + - - +
266C LEU* 3.5 4.6 - - + +
267C PHE 2.9 28.2 + - - +
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Residues in contact with CYS 224 (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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38C LEU* 5.6 1.6 - - - -
39C LEU 2.8 13.4 + - - +
40C GLY* 3.5 11.6 - - - -
41C ALA 4.2 1.0 + - - -
44C SER* 3.4 37.5 + - - +
45C GLY 4.4 3.4 - - - -
46C LYS* 4.1 28.0 - - + -
49C ILE* 4.5 6.7 - - - -
222C ILE* 4.1 20.6 - - - -
223C PHE* 1.3 77.6 - - - +
225C VAL* 1.3 64.2 + - - +
246C SER* 5.2 1.0 + - - -
267C PHE* 3.5 15.9 - - - +
269C ASN* 5.2 3.1 - - + -
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Residues in contact with VAL 225 (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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44C SER* 4.4 1.8 - - - -
223C PHE* 3.6 17.7 - - + -
224C CYS* 1.3 77.8 - - - +
226C ALA* 1.3 60.8 + - - +
227C LEU 3.3 1.0 + - - +
229C ASP* 6.1 0.2 - - + -
243C MET* 4.0 20.2 - - + -
246C SER* 4.4 13.2 - - - +
266C LEU* 3.6 15.5 - - + -
267C PHE 2.9 10.4 + - - +
268C LEU* 3.6 13.0 - - + -
269C ASN* 2.6 36.3 + - - -
307C PHE* 3.5 44.6 - - + -
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Residues in contact with ALA 226 (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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43C GLU 4.5 1.6 - - - +
44C SER* 4.1 17.4 - - - -
225C VAL* 1.3 71.4 - - - +
227C LEU* 1.3 65.9 + - - +
228C SER* 3.1 2.7 - - - +
229C ASP* 3.1 43.8 + - - +
243C MET* 3.7 6.6 - - - +
246C SER* 5.3 1.0 + - - -
269C ASN 3.8 5.6 - - - -
270C LYS* 3.6 32.5 - - + +
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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