Contacts of the strand formed by residues 226 - 233 (chain C) in PDB entry 2OB2
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 GLY 226 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C PHE* 3.5 18.7 - - - -
196C THR 3.0 13.0 - - - -
225C HIS* 1.3 77.0 - - - +
227C LEU* 1.3 60.5 + - - +
327C GLN* 3.5 7.3 - - - +
328C TRP* 2.9 42.5 + - - +
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Residues in contact with LEU 227 (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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88C ALA* 3.7 24.7 - - + +
92C PHE* 3.7 34.1 - - + -
196C THR 2.7 9.2 + - - +
197C ILE* 3.2 12.5 - - + +
198C VAL 2.9 26.4 + - - +
226C GLY* 1.3 72.6 - - - +
228C TRP* 1.3 61.2 + - - +
229C ILE* 3.7 24.0 - - + -
325C LYS* 4.1 25.8 - - + -
326C ALA 3.2 12.6 - - - +
327C GLN* 3.6 24.7 - - + +
328C TRP* 3.9 4.3 - - - -
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Residues in contact with TRP 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C LEU* 3.7 20.6 - - + -
198C VAL* 3.3 28.6 - - + +
200C SER* 2.8 23.7 + - - -
204C LEU* 4.5 7.9 - - + -
215C LEU* 3.9 6.7 - - + -
216C ILE* 3.4 51.8 - - + -
219C ILE* 3.8 20.6 - - + -
220C MET* 3.7 18.6 - - + -
227C LEU* 1.3 73.4 - - - +
229C ILE* 1.3 72.7 + - - +
230C SER* 3.8 6.3 - - - -
275C TRP* 3.3 26.6 - - - +
324C MET* 3.3 8.0 - - + +
325C LYS* 3.5 1.6 - - - -
326C ALA* 2.8 35.7 + - + -
328C TRP* 3.7 10.9 - + + -
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Residues in contact with ILE 229 (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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85C ILE* 3.8 19.1 - - + +
88C ALA* 3.7 28.7 - - + -
89C ILE* 3.4 32.8 - - + -
197C ILE* 3.7 9.6 - - + -
198C VAL 2.7 11.0 + - - +
199C ILE* 3.3 7.8 - - + +
200C SER 2.9 25.8 + - - +
227C LEU* 3.7 26.7 - - + -
228C TRP* 1.3 78.6 - - - +
230C SER* 1.3 63.1 + - - +
323C LEU* 3.6 26.9 - - + -
324C MET 3.5 5.6 - - - +
325C LYS* 4.4 3.4 - - + -
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Residues in contact with SER 230 (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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200C SER* 3.0 24.6 + - - -
204C LEU* 3.6 6.1 - - - +
228C TRP* 3.8 11.9 + - - -
229C ILE* 1.3 74.3 - - - +
231C TYR* 1.3 62.3 + - - +
232C ASP* 3.9 0.2 + - - -
271C TYR* 2.7 28.7 + - - -
275C TRP* 3.9 12.3 - - - -
322C ILE* 3.8 1.2 - - - +
323C LEU* 3.5 3.5 - - - -
324C MET* 2.7 44.5 + - - +
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Residues in contact with TYR 231 (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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77C GLY* 4.2 6.2 + - - -
81C ARG* 3.5 50.0 + - + +
85C ILE* 4.1 12.6 - - + -
200C SER 3.0 5.1 + - - +
201C GLU* 4.2 10.1 - - + -
202C SMC 2.9 41.6 + - - -
230C SER* 1.3 76.7 + - - +
232C ASP* 1.3 68.2 + - - +
271C TYR* 4.2 0.2 - - - -
286C MET* 3.6 30.1 - - + +
318C GLN* 4.6 2.4 + - - -
321C TYR* 3.2 37.0 - + + +
322C ILE 3.2 18.6 - - - -
323C LEU* 4.1 18.2 - - + -
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Residues in contact with ASP 232 (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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200C SER 4.9 0.5 - - - +
202C SMC 3.8 5.1 - - - -
203C LEU 4.0 0.3 + - - -
204C LEU* 3.5 20.3 + - - +
205C CYS* 3.1 41.0 + - + +
230C SER* 3.9 1.6 + - - -
231C TYR* 1.3 82.8 - - - +
233C PRO* 1.3 71.3 - - + +
271C TYR* 2.2 46.1 + - + +
321C TYR* 3.4 6.2 - - - -
322C ILE* 2.9 33.3 + - - +
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Residues in contact with PRO 233 (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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202C SMC 3.5 27.4 - - + -
205C CYS* 4.1 6.6 - - + +
232C ASP* 1.3 99.6 - - + +
234C ILE* 1.4 62.7 + - - +
247C MET* 3.3 26.7 - - + -
259C MET* 3.9 19.5 - - + -
262C LEU* 3.4 18.1 - - + +
265C TYR 4.7 1.7 - - - +
271C TYR* 5.0 2.4 - - - -
320C HIS 3.2 9.0 - - - +
321C TYR* 3.7 15.2 - - + -
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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