Contacts of the strand formed by residues 227 - 233 (chain F) in PDB entry 6X34
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 MET 227 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223F PHE* 4.9 2.4 - - - +
224F HIS* 3.3 26.9 + - + +
225F GLY 3.7 5.4 - - - +
226F HIS* 1.3 80.3 - - - +
228F ASP* 1.3 61.1 + - - +
229F GLU* 2.9 16.8 + - + +
359F TYR* 5.0 10.5 - - - +
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Residues in contact with ASP 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223F PHE* 6.3 0.9 - - - -
226F HIS 3.6 2.9 + - - +
227F MET* 1.3 68.6 - - - +
229F GLU* 1.3 60.5 + - - +
249F GLY* 2.9 27.9 - - - +
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Residues in contact with GLU 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223F PHE* 3.3 11.6 - - - +
224F HIS* 2.6 44.3 + - + -
227F MET* 2.9 10.5 + - + +
228F ASP* 1.3 76.3 - - - +
230F CYS* 1.3 57.2 + - - +
247F TYR* 4.4 15.0 - - + +
248F GLU 3.4 19.1 - - - +
249F GLY* 4.4 2.5 - - - -
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Residues in contact with CYS 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221F ARG* 5.7 1.3 - - + -
222F LEU 3.3 21.1 - - - +
223F PHE* 4.0 16.8 - - + +
224F HIS* 4.4 3.6 - - - +
229F GLU* 1.3 78.4 - - - +
231F LEU* 1.3 62.0 + - - +
232F THR* 3.0 14.0 + - - +
247F TYR* 3.3 20.1 - - - -
248F GLU 3.8 7.9 + - - +
252F VAL 5.8 2.0 - - - +
258F SER* 5.5 13.2 - - - +
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Residues in contact with LEU 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F LEU* 3.8 12.5 + - + +
224F HIS* 5.9 0.4 - - - +
230F CYS* 1.3 71.2 - - - +
232F THR* 1.3 58.4 - - - +
245F VAL* 4.1 15.5 - - + -
246F TYR 3.4 8.3 - - - +
247F TYR* 4.7 2.9 - - - +
257F ARG 5.0 0.2 - - - +
258F SER* 5.2 3.1 - - - +
260F TRP* 3.2 24.4 - - + -
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Residues in contact with THR 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F CYS* 3.8 13.2 - - + +
231F LEU* 1.3 73.3 - - - +
233F ILE* 1.3 74.0 + - - +
235F PRO* 5.4 0.4 - - + -
245F VAL* 3.4 6.4 - - - +
246F TYR* 2.8 37.6 + - + +
248F GLU* 4.1 20.2 - - + +
252F VAL* 3.7 23.3 - - + +
257F ARG* 3.2 34.7 + - - +
258F SER* 4.9 3.6 - - - -
260F TRP* 4.3 6.5 - - - -
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Residues in contact with ILE 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232F THR* 1.3 91.5 + - - +
234F SER* 1.3 69.1 + - - +
235F PRO* 3.2 11.3 - - + +
242F ARG* 3.7 35.4 - - + +
244F LEU 4.5 4.9 - - - +
245F VAL* 4.7 7.0 - - + +
246F TYR* 5.0 1.7 - - - +
252F VAL* 5.3 0.3 - - - +
257F ARG* 3.8 23.1 + - + +
260F TRP* 4.9 6.2 - - + -
284F HIS* 3.3 39.3 - - + +
286F THR* 3.9 7.2 - - - +
287F THR* 4.2 4.3 - - - +
291F LEU* 4.9 13.0 - - + -
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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