Contacts of the strand formed by residues 222 - 229 (chain F) in PDB entry 3Q2K
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 THR 222 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E TYR 3.8 13.9 - - - +
155E MET* 3.4 24.5 - - + -
234E MET* 3.7 21.5 - - + +
184F ALA* 5.1 0.9 - - - -
185F PHE* 4.8 0.4 - - - -
210F THR* 3.2 4.3 - - - -
211F ALA 2.8 29.9 + - - +
213F LEU* 3.7 6.7 - - + +
220F GLU* 3.4 6.0 - - - +
221F ASP* 1.3 96.9 + - - +
223F GLY* 1.3 62.5 + - - +
239F VAL 3.5 5.8 - - - +
240F THR* 3.2 16.7 + - - +
242F LEU* 3.4 10.2 - - - +
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Residues in contact with GLY 223 (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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155E MET* 3.4 1.6 - - - +
234E MET* 4.2 5.2 - - - -
185F PHE* 3.6 20.2 - - - -
209F TYR 3.2 11.4 - - - -
210F THR* 3.8 1.8 - - - -
222F THR* 1.3 77.2 - - - +
224F VAL* 1.3 68.2 + - - +
239F VAL 2.9 35.6 + - - +
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Residues in contact with VAL 224 (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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155E MET* 3.7 12.1 - - + -
226E ALA* 4.0 16.7 - - + +
234E MET* 4.2 5.6 - - + -
235E GLY* 3.6 42.8 - - - +
236E SER* 4.1 5.6 - - - -
185F PHE* 4.0 3.7 - - - -
208F ALA* 3.3 4.2 - - - +
209F TYR* 2.8 37.1 + - + +
223F GLY* 1.3 80.4 - - - +
225F ALA* 1.3 71.3 + - - +
236F SER* 4.9 0.4 - - - -
237F ILE 3.3 4.5 - - - +
238F ASN* 3.6 26.2 - - - +
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Residues in contact with ALA 225 (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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185F PHE* 4.4 1.1 - - + -
206F VAL* 5.0 0.9 - - + -
207F TYR 3.3 10.1 - - - +
208F ALA* 4.1 4.0 - - + -
224F VAL* 1.3 79.7 - - - +
226F ALA* 1.3 62.9 - - - +
227F LEU* 3.8 7.2 - - + +
236F SER* 3.1 4.9 - - - -
237F ILE* 2.8 53.8 + - + -
335F ILE* 4.0 27.4 - - + -
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Residues in contact with ALA 226 (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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207E TYR* 4.6 11.4 - - + +
209E TYR* 3.8 19.3 - - + -
224E VAL* 4.1 15.3 - - + +
226E ALA* 4.1 23.1 - - + +
206F VAL* 3.1 8.0 - - - +
207F TYR 2.9 34.7 + - - +
224F VAL 4.2 0.6 - - - -
225F ALA* 1.3 71.3 - - - +
227F LEU* 1.3 60.1 + - - +
235F GLY 3.7 5.6 - - - -
236F SER* 4.3 2.9 - - - -
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Residues in contact with LEU 227 (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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209E TYR* 3.6 7.9 - - - -
156F VAL* 6.2 0.2 - - + -
196F LEU* 4.0 29.6 - - + -
203F VAL* 4.6 7.4 - - + -
205F SER 3.6 5.8 - - - +
206F VAL* 3.1 31.9 - - + -
225F ALA* 3.8 13.2 - - + +
226F ALA* 1.3 76.9 - - - +
228F ARG* 1.3 60.2 + - - +
229F TRP* 4.0 30.5 - - + -
234F MET* 3.3 6.6 - - - +
235F GLY 2.9 30.8 + - - +
236F SER* 3.9 28.5 - - - +
237F ILE* 4.2 2.0 - - + +
331F LEU* 4.4 7.0 - - + -
335F ILE* 5.2 1.6 - - + -
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Residues in contact with ARG 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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209E TYR* 3.5 47.8 - - + +
210E THR 5.3 6.2 + - - -
339E ALA 5.4 5.1 + - - -
203F VAL* 3.6 3.0 - - - +
204F GLU* 2.5 65.6 + - - +
205F SER* 3.1 16.8 + - - +
227F LEU* 1.3 73.7 - - - +
229F TRP* 1.3 61.4 + - - +
232F GLY* 4.8 6.1 - - - +
233F ALA 3.6 9.2 - - - +
234F MET* 4.4 11.4 - - + +
344F ARG* 4.4 11.3 - - - +
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Residues in contact with TRP 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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156F VAL* 3.6 27.6 - - + -
196F LEU* 3.3 36.0 + - + -
200F VAL* 3.5 22.3 - - + +
201F GLY 3.2 32.8 + - - -
202F PRO 3.5 12.3 - - - +
203F VAL* 3.4 13.8 - - + +
204F GLU* 3.8 3.4 - - - +
227F LEU* 4.0 22.4 - - + -
228F ARG* 1.3 82.6 - - - +
230F ARG* 1.3 66.4 + - - +
231F HIS* 3.7 25.4 - + + +
232F GLY* 2.8 15.1 + - - -
233F ALA* 3.0 26.7 + - + +
234F MET 3.8 21.5 - - - -
235F GLY* 3.8 5.8 - - - -
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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