Contacts of the strand formed by residues 227 - 240 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A PHE* 3.8 28.2 + - + +
205A LYS 3.6 1.6 - - - -
206A ASN* 3.8 36.1 + - - +
222A THR* 3.9 24.7 - - - +
223A HIS 3.6 13.7 - - - +
224A LYS* 3.1 40.4 + - + +
225A SER 3.2 3.1 + - - +
226A GLY* 1.3 75.4 - - - +
228A VAL* 1.3 62.8 + - - +
229A GLU 3.7 1.9 + - - -
257C ARG* 5.2 0.6 + - - -
11E G 4.5 14.5 + - - -
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Residues in contact with VAL 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A PHE* 3.4 3.0 - - - -
205A LYS* 2.9 61.9 + - + +
207A THR* 3.6 18.2 - - + -
226A GLY 3.8 0.2 - - - -
227A LYS* 1.3 73.7 - - - +
229A GLU* 1.3 65.2 + - - +
230A GLU* 3.4 5.3 + - - +
257C ARG* 3.7 30.7 - - - +
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Residues in contact with GLU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ALA* 3.5 32.8 - - + +
204A PHE* 3.5 29.1 - - + -
227A LYS 3.7 3.0 + - - -
228A VAL* 1.3 72.0 - - - +
230A GLU* 1.3 65.6 + - - +
260A TRP* 4.9 6.6 - - - -
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Residues in contact with GLU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ALA* 3.8 8.1 - - - +
203A LEU* 2.7 48.6 + - + +
205A LYS* 3.5 42.3 + - + +
228A VAL* 3.4 5.8 + - - +
229A GLU* 1.3 87.6 - - - +
231A ASP* 1.3 63.5 + - - +
232A VAL* 3.1 14.6 + - + +
260A TRP* 5.1 0.7 + - - -
10E T 5.9 0.2 - - - +
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Residues in contact with ASP 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A GLU 4.1 0.2 + - - -
230A GLU* 1.3 77.8 + - - +
232A VAL* 1.3 67.4 + - + +
257A ARG 5.5 0.3 - - - +
260A TRP* 3.2 30.4 + - - +
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ALA* 3.5 3.8 - - - -
203A LEU* 2.7 57.1 + - + -
230A GLU* 3.1 11.7 + - + +
231A ASP* 1.3 90.7 - - - +
233A MET* 1.3 57.2 + - - +
253A ALA 5.8 0.4 - - - +
256A ARG* 3.6 15.7 - - + +
257A ARG* 4.1 28.9 - - + +
260A TRP* 3.5 14.2 - - - +
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Residues in contact with MET 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A MET* 4.3 7.4 - - + -
201A THR 3.6 6.1 - - - +
203A LEU* 3.7 4.9 - - - +
232A VAL* 1.3 73.5 - - - +
234A GLY* 1.3 68.1 + - - +
235A SER* 3.1 33.0 - - - +
236A ILE* 3.8 9.6 - - + -
251A PHE* 3.3 47.3 - - + -
256A ARG* 2.9 51.2 + - - +
259A PHE* 3.8 20.2 - - + -
260A TRP* 3.0 24.0 - - + +
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Residues in contact with GLY 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A THR 2.6 15.4 + - - -
202A ALA 4.0 3.1 - - - -
203A LEU* 3.6 21.7 - - - +
232A VAL 3.6 1.0 + - - -
233A MET* 1.3 78.8 - - - +
235A SER* 1.3 57.6 + - - +
248A GLY* 3.3 5.4 - - - +
256A ARG* 3.1 16.6 + - - -
11E G 3.1 25.5 - - - +
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Residues in contact with SER 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A THR* 2.9 47.8 + - - +
233A MET* 3.1 5.0 - - - +
234A GLY* 1.3 79.0 - - - +
236A ILE* 1.3 69.6 + - - +
246A SER* 4.2 8.4 + - - -
247A ILE 3.3 13.9 - - - -
248A GLY* 3.8 2.0 - - - -
11E G 3.5 5.4 - - - -
12E G 3.1 27.8 + - - -
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Residues in contact with ILE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ILE* 4.3 16.8 - - + -
199A SER 3.6 7.4 - - - +
200A MET* 3.4 36.8 - - + +
233A MET* 3.8 12.3 - - + -
235A SER* 1.3 82.2 - - - +
237A GLU* 1.3 63.2 + - - +
238A VAL* 3.6 19.4 + - + +
246A SER* 3.5 5.0 - - - -
247A ILE* 2.8 43.9 + - + +
251A PHE* 3.8 20.4 - - + -
259A PHE* 4.3 9.6 - - + -
271A VAL* 4.6 9.0 - - + -
289A PHE* 4.7 2.9 - - + -
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Residues in contact with GLU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ILE* 3.7 0.7 - - - -
198A ILE* 3.0 36.0 + - + +
199A SER* 2.9 39.2 + - - +
200A MET* 4.8 0.8 - - - +
201A THR* 5.8 1.0 + - - -
235A SER* 5.5 0.2 + - - -
236A ILE* 1.3 72.3 - - - +
238A VAL* 1.3 63.5 + - - +
244A VAL* 3.6 30.4 - - + +
245A PHE 3.7 5.6 - - - +
246A SER* 3.7 15.1 + - - +
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Residues in contact with VAL 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A ALA* 3.5 23.6 - - + -
196A THR 3.2 8.3 - - - +
197A ILE* 3.8 17.3 - - + +
198A ILE* 4.4 6.1 - - - -
236A ILE* 3.7 26.5 - - + +
237A GLU* 1.3 82.9 - - - +
239A ASP* 1.3 59.3 + - - +
243A VAL 3.6 0.9 - - - +
244A VAL* 3.3 24.4 - - - +
245A PHE* 2.9 40.3 + - + +
247A ILE* 4.3 10.1 - - + -
271A VAL* 4.5 7.4 - - + -
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Residues in contact with ASP 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A ALA* 3.5 3.6 - - - -
196A THR* 2.8 42.4 + - - +
198A ILE* 4.1 13.9 - - + +
238A VAL* 1.3 71.3 - - - +
240A TYR* 1.3 57.6 + - - +
241A ASP* 3.3 5.6 + - - -
242A GLY* 2.8 43.6 + - - +
243A VAL 3.2 2.6 - - - +
244A VAL* 4.2 13.3 - - + +
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Residues in contact with TYR 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A LYS* 3.5 15.6 + - - -
193A ALA* 3.5 27.9 - - + +
194A GLU 2.9 29.2 - - - -
195A ALA* 3.8 10.0 - - + +
238A VAL 3.9 0.8 + - - -
239A ASP* 1.3 68.0 - - - +
241A ASP* 1.3 78.6 + - + +
242A GLY 3.2 1.3 + - - -
243A VAL* 2.7 28.9 + - + +
245A PHE* 3.5 27.6 - + + -
273A PHE* 4.0 9.2 - + - -
275A TYR* 3.9 22.6 + + - -
284A PRO* 4.4 7.9 - - + -
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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