Contacts of the strand formed by residues 227 - 240 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204B PHE* 3.8 27.8 + - + +
205B LYS 3.6 1.8 - - - -
206B ASN* 3.9 37.6 + - - +
222B THR* 3.9 24.9 - - - +
223B HIS 3.6 13.7 - - - +
224B LYS* 3.2 40.7 + - + +
225B SER 3.2 3.2 + - - +
226B GLY* 1.3 73.6 - - - +
228B VAL* 1.3 64.2 + - - +
229B GLU 3.7 2.1 + - - -
11G G 4.5 14.5 + - - -
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Residues in contact with VAL 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B PHE* 3.4 2.1 - - - -
205B LYS* 2.9 61.8 + - + +
207B THR* 3.6 24.2 - - + +
225B SER 5.9 0.7 - - - +
226B GLY* 3.9 0.6 - - - -
227B LYS* 1.3 75.2 - - - +
229B GLU* 1.3 64.9 + - - +
230B GLU* 3.4 4.9 + - - +
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Residues in contact with GLU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B ALA* 3.5 32.4 - - + +
204B PHE* 3.5 30.0 - - + -
227B LYS 3.7 3.0 + - - -
228B VAL* 1.3 72.0 - - - +
230B GLU* 1.3 66.0 + - - +
231B ASP 4.1 0.2 + - - -
260B TRP* 4.9 6.6 - - - -
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Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B ALA* 3.7 15.1 - - - +
203B LEU* 2.7 50.6 + - + +
205B LYS* 3.5 41.9 + - + +
228B VAL* 3.4 5.8 + - - +
229B GLU* 1.3 79.6 - - - +
231B ASP* 1.3 64.6 + - - +
232B VAL* 3.1 15.0 + - + +
260B TRP* 5.0 0.7 + - - -
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Residues in contact with ASP 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B GLU 4.1 0.4 + - - -
230B GLU* 1.3 78.0 + - - +
232B VAL* 1.3 68.7 + - + +
257B ARG 5.5 0.3 - - - +
260B TRP* 3.2 29.2 + - - +
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Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ALA* 3.5 3.5 - - - -
203B LEU* 2.7 58.1 + - + -
230B GLU* 3.1 11.1 + - + +
231B ASP* 1.3 90.3 - - - +
233B MET* 1.3 56.5 + - - +
253B ALA 5.8 0.7 - - - +
256B ARG* 3.7 16.4 - - + +
257B ARG* 4.1 29.6 - - + +
260B TRP* 3.5 14.0 - - - +
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Residues in contact with MET 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B MET* 4.3 7.2 - - + -
201B THR 3.6 6.7 - - - +
203B LEU* 3.8 4.7 - - - +
232B VAL* 1.3 73.3 - - - +
234B GLY* 1.3 68.0 + - - +
235B SER* 3.1 32.3 - - - +
236B ILE* 3.8 9.6 - - + -
251B PHE* 3.3 47.6 - - + -
256B ARG* 2.9 48.3 + - + +
259B PHE* 3.8 20.9 - - + -
260B TRP* 3.0 27.7 - - + +
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Residues in contact with GLY 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B THR 2.6 15.6 + - - -
202B ALA 4.0 2.9 - - - -
203B LEU* 3.6 22.0 - - - +
232B VAL 3.6 1.0 + - - -
233B MET* 1.3 78.8 - - - +
235B SER* 1.3 59.1 + - - +
248B GLY* 3.4 5.2 - - - +
256B ARG* 3.1 16.9 + - - -
11G G 3.1 25.3 - - - +
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Residues in contact with SER 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B THR* 2.9 46.6 + - - +
233B MET* 3.1 4.2 - - - +
234B GLY* 1.3 78.4 - - - +
236B ILE* 1.3 70.9 + - - +
246B SER* 4.2 8.4 + - - -
247B ILE 3.3 14.4 - - - -
248B GLY* 3.8 2.2 - - - -
11G G 3.4 5.8 - - - -
12G G 3.1 27.8 + - - -
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Residues in contact with ILE 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B ILE* 4.3 16.2 - - + -
199B SER 3.6 7.4 - - - +
200B MET* 3.5 37.0 - - + +
233B MET* 3.8 12.1 - - + -
235B SER* 1.3 82.6 - - - +
237B GLU* 1.3 64.1 + - - +
238B VAL* 3.6 19.5 + - + +
246B SER* 3.5 4.7 - - - -
247B ILE* 2.8 43.6 + - + +
251B PHE* 3.8 20.2 - - + -
259B PHE* 4.3 9.9 - - + -
271B VAL* 4.6 9.2 - - + -
289B PHE* 4.7 2.0 - - + -
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Residues in contact with GLU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B ILE* 3.7 0.7 - - - +
198B ILE* 3.0 25.7 + - + +
199B SER* 3.0 34.8 + - - +
200B MET* 4.8 1.0 - - - +
201B THR* 5.8 1.2 + - - +
236B ILE* 1.3 71.9 - - - +
238B VAL* 1.3 63.5 + - - +
244B VAL* 3.6 20.9 - - + +
245B PHE 3.7 8.1 - - - +
246B SER* 3.7 12.6 + - - +
104C ASP* 3.3 20.4 - - - +
106C LEU* 3.1 20.8 - - - +
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Residues in contact with VAL 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B ALA* 3.5 23.6 - - + -
196B THR 3.2 8.1 - - - +
197B ILE* 3.8 17.3 - - + +
198B ILE* 4.3 6.1 - - - -
236B ILE* 3.7 25.8 - - + +
237B GLU* 1.3 82.7 - - - +
239B ASP* 1.3 60.8 + - - +
240B TYR 3.8 0.2 + - - -
243B VAL 3.6 1.0 - - - +
244B VAL* 3.3 6.9 - - - +
245B PHE* 3.0 56.7 + - + +
247B ILE* 4.3 10.3 - - + -
271B VAL* 4.5 7.4 - - + -
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Residues in contact with ASP 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ALA* 3.4 3.8 - - - -
196B THR* 2.8 36.7 + - - +
198B ILE* 4.1 13.6 - - + +
238B VAL* 1.3 70.9 - - - +
240B TYR* 1.3 57.9 + - - +
241B ASP 3.3 5.2 + - - -
242B GLY 2.8 40.0 + - - -
243B VAL 3.2 2.8 - - - +
244B VAL* 4.2 12.6 - - + -
106C LEU 4.5 1.5 - - - +
107C LYS* 4.1 5.2 - - - +
108C LYS* 3.6 48.0 + - - +
111C ASP* 4.0 4.0 - - - +
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Residues in contact with TYR 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B LYS* 3.5 15.1 + - - -
193B ALA* 3.5 28.1 - - + +
194B GLU 2.8 29.4 - - - -
195B ALA* 3.8 9.3 - - + +
238B VAL 3.8 1.0 + - - -
239B ASP* 1.3 67.6 - - - +
241B ASP* 1.3 78.5 + - + +
242B GLY 3.2 1.3 + - - -
243B VAL* 2.7 29.4 + - + +
245B PHE* 3.5 21.1 - + + -
273B PHE* 4.0 8.7 - + - -
275B TYR* 4.0 21.7 + + - -
284B PRO* 4.4 13.2 - - + -
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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