Contacts of the strand formed by residues 227 - 240 (chain C) in PDB entry 2Q2U
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 LYS 227 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204C PHE* 3.8 25.8 + - + +
205C LYS 3.6 1.3 - - - -
206C ASN* 3.8 37.0 + - - +
222C THR* 3.9 24.5 - - - +
223C HIS 3.5 13.7 - - - +
224C LYS* 3.1 41.3 + - + +
225C SER 3.2 3.3 + - - +
226C GLY* 1.3 74.9 - - - +
228C VAL* 1.3 63.9 + - - +
229C GLU 3.7 2.3 + - - -
11I G 4.5 14.1 + - - -
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Residues in contact with VAL 228 (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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204C PHE* 3.4 2.7 - - - -
205C LYS* 2.9 65.2 + - + +
207C THR* 3.6 25.6 - - + +
226C GLY* 3.8 0.6 + - - -
227C LYS* 1.3 73.0 - - - +
229C GLU* 1.3 63.2 + - - +
230C GLU* 3.4 4.8 + - - +
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Residues in contact with GLU 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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202C ALA* 3.5 31.6 - - + +
204C PHE* 3.5 29.2 - - + -
227C LYS 3.7 3.4 + - - -
228C VAL* 1.3 70.9 - - - +
230C GLU* 1.3 65.5 + - - +
260C TRP* 4.9 6.9 - - - -
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Residues in contact with GLU 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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224A LYS* 5.9 4.0 - - - +
202C ALA* 3.7 14.0 - - - +
203C LEU* 2.7 50.2 + - + +
205C LYS* 3.5 41.1 + - + +
228C VAL* 3.4 5.6 + - - +
229C GLU* 1.3 80.8 - - - +
231C ASP* 1.3 63.4 + - - +
232C VAL* 3.1 16.0 + - + +
260C TRP* 5.1 0.3 + - - -
10I T 5.9 0.2 - - - +
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Residues in contact with ASP 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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224A LYS* 3.8 25.3 + - + +
225A SER* 3.1 39.5 + - - +
229C GLU 4.1 0.6 + - - -
230C GLU* 1.3 77.8 + - - +
232C VAL* 1.3 68.7 + - - +
260C TRP* 3.2 27.4 + - - +
27F G 4.5 3.8 + - - -
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Residues in contact with VAL 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A SER* 4.2 15.0 - - - +
202C ALA* 3.5 2.9 - - - -
203C LEU* 2.7 57.3 + - + -
230C GLU* 3.1 11.7 + - + +
231C ASP* 1.3 89.1 - - + +
233C MET* 1.3 57.2 + - - +
256C ARG* 3.7 16.2 - - + +
257C ARG* 4.2 21.5 - - + +
260C TRP* 3.5 14.6 - - - +
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Residues in contact with MET 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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200C MET* 4.3 6.5 - - + -
201C THR 3.6 6.3 - - - +
203C LEU* 3.8 5.1 - - - +
232C VAL* 1.3 73.5 - - - +
234C GLY* 1.3 67.7 + - - +
235C SER* 3.1 32.1 - - - +
236C ILE* 3.8 9.6 - - + -
251C PHE* 3.3 48.5 - - + -
256C ARG* 2.9 47.9 + - - +
259C PHE* 3.8 20.2 - - + -
260C TRP* 3.0 27.1 - - + +
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Residues in contact with GLY 234 (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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201C THR 2.6 15.6 + - - -
202C ALA 4.0 3.1 - - - -
203C LEU* 3.6 21.5 - - - -
232C VAL 3.6 1.0 + - - -
233C MET* 1.3 79.5 - - - +
235C SER* 1.3 59.3 + - - +
248C GLY* 3.3 5.5 - - - +
256C ARG* 3.1 16.5 + - - -
11I G 3.2 24.6 - - - +
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Residues in contact with SER 235 (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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201C THR* 3.0 46.0 + - - +
233C MET* 3.1 4.8 - - - +
234C GLY* 1.3 78.4 - - - +
236C ILE* 1.3 71.2 + - - +
246C SER* 4.1 9.0 + - - -
247C ILE 3.3 16.2 - - - -
248C GLY* 3.8 1.1 - - - -
11I G 3.5 5.6 - - - -
12I G 3.1 27.7 + - - -
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Residues in contact with ILE 236 (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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197C ILE* 4.3 17.3 - - + -
199C SER 3.6 7.2 - - - +
200C MET* 3.4 36.6 - - + +
233C MET* 3.8 12.1 - - + -
235C SER* 1.3 81.7 - - - +
237C GLU* 1.3 64.8 + - - +
238C VAL* 3.6 19.1 + - + +
246C SER* 3.4 5.1 - - - -
247C ILE* 2.8 46.5 + - + +
251C PHE* 3.8 20.9 - - + -
259C PHE* 4.3 9.6 - - + -
271C VAL* 4.6 9.0 - - + -
289C PHE* 4.7 2.5 - - + -
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Residues in contact with GLU 237 (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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197C ILE* 3.8 0.5 - - - -
198C ILE* 3.0 38.6 + - + +
199C SER* 2.9 40.7 + - - +
200C MET* 4.9 1.0 - - - +
201C THR* 5.9 0.8 + - - +
236C ILE* 1.3 71.8 - - - +
238C VAL* 1.3 62.9 + - - +
244C VAL* 3.6 26.9 - - + +
245C PHE 3.6 7.6 - - - +
246C SER* 3.7 12.7 + - - +
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Residues in contact with VAL 238 (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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195C ALA* 3.5 23.1 - - + -
196C THR 3.2 8.1 - - - +
197C ILE* 3.8 19.1 - - + +
198C ILE* 4.3 6.1 - - - -
236C ILE* 3.8 24.9 - - + +
237C GLU* 1.3 81.0 - - - +
239C ASP* 1.3 59.9 + - - +
243C VAL 3.6 1.0 - - - +
244C VAL* 3.3 24.4 - - - +
245C PHE* 2.9 42.0 + - + +
247C ILE* 4.2 10.1 - - + -
271C VAL* 4.5 8.3 - - + -
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Residues in contact with ASP 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C ALA* 3.5 3.8 - - - -
196C THR* 2.8 41.0 + - - +
198C ILE* 4.2 13.4 - - + +
238C VAL* 1.3 70.5 - - - +
240C TYR* 1.3 58.0 + - - +
241C ASP* 3.3 5.1 + - - -
242C GLY* 2.9 44.4 + - - +
243C VAL 3.2 2.8 - - - +
244C VAL* 4.2 12.5 - - + +
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Residues in contact with TYR 240 (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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191C LYS* 3.6 15.1 + - - -
193C ALA* 3.5 27.3 - - + +
194C GLU 2.9 28.7 - - - -
195C ALA* 3.8 9.1 - - + +
238C VAL 3.9 1.0 + - - -
239C ASP* 1.3 68.5 - - - +
241C ASP* 1.3 79.3 + - + +
242C GLY 3.2 1.3 + - - -
243C VAL* 2.7 28.9 + - + +
245C PHE* 3.5 21.1 - + + -
273C PHE* 4.0 10.1 - + - -
275C TYR* 4.0 21.1 + + - -
284C PRO* 4.4 13.5 - - + -
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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