Contacts of the helix formed by residues 212 - 226 (chain A) in PDB entry 2WOE
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 TYR 212 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ALA* 3.4 28.7 - - + -
162A LEU* 3.6 12.5 - - + +
199A ASP* 4.6 5.0 + - - +
210A SER* 3.2 15.9 + - - +
211A ALA* 1.3 76.1 - - - +
213A ILE* 1.3 69.3 + - + +
214A VAL* 3.1 38.3 + - + +
215A ASP* 3.2 20.8 + - - -
216A THR* 2.9 24.6 + - - -
401A AR6 3.4 56.9 + + - +
278C ARG* 5.9 1.6 - - - -
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Residues in contact with ILE 213 (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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124A ALA* 2.8 28.5 + - + +
125A GLY 3.9 5.4 - - - +
126A ASN* 3.7 23.1 - - + -
129A ALA* 3.7 17.5 - - + -
162A LEU* 3.8 34.1 - - + +
163A SER* 4.1 6.1 - - - +
166A ALA* 3.4 33.9 - - + -
200A PHE* 4.1 3.4 - - + -
211A ALA 3.4 3.1 + - - -
212A TYR* 1.3 72.5 - - + +
214A VAL* 1.3 63.0 + - + +
216A THR* 3.8 6.5 - - + -
217A MET* 2.9 36.7 + - + +
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Residues in contact with VAL 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LEU* 3.8 18.2 - - + -
199A ASP* 3.4 39.3 - - + -
200A PHE* 3.8 15.9 - - + +
212A TYR* 3.1 39.6 - - + +
213A ILE* 1.3 75.2 - - + +
215A ASP* 1.3 68.2 + - - +
217A MET* 3.9 0.9 - - - +
218A GLN* 2.9 41.3 + - + +
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Residues in contact with ASP 215 (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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208A GLN* 3.1 37.4 - - - +
209A SER* 4.3 0.9 - - - -
210A SER* 2.7 49.9 + - - +
212A TYR* 3.2 21.0 + - - +
214A VAL* 1.3 75.8 - - - +
216A THR* 1.3 61.2 + - - +
218A GLN* 3.7 8.6 - - - +
219A THR* 2.9 30.5 + - - -
274C MET* 5.2 3.8 - - - +
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Residues in contact with THR 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASN* 2.7 39.1 + - + +
210A SER 2.9 17.6 + - - -
212A TYR 2.9 12.2 + - - -
213A ILE* 3.8 7.0 - - + -
215A ASP* 1.3 76.7 - - - +
217A MET* 1.3 59.3 + - - +
219A THR* 3.3 2.8 + - - -
220A VAL* 2.9 34.1 + - + +
243A ASP* 4.5 0.3 + - - +
246A THR* 4.8 0.2 - - + -
247A THR* 4.1 21.6 - - + +
250A LEU* 3.7 30.5 - - + -
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Residues in contact with MET 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ALA* 3.8 27.4 - - + +
169A THR* 4.3 6.3 - - + -
170A LEU* 3.8 44.9 - - + -
193A LEU* 3.9 22.7 - - + -
200A PHE* 3.7 20.2 - - + -
213A ILE* 2.9 28.0 + - + +
216A THR* 1.3 73.5 - - - +
218A GLN* 1.3 65.7 + - - +
220A VAL* 4.5 4.7 - - - +
221A LEU* 3.0 48.6 + - + +
250A LEU* 4.9 6.7 - - - -
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Residues in contact with GLN 218 (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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199A ASP 2.9 25.1 - - - -
200A PHE* 3.7 11.4 - - - +
201A HIS 3.0 24.1 + - - +
202A PHE* 3.6 17.1 - - + +
205A TYR* 3.8 12.1 - - + -
206A LYS* 5.7 5.2 - - - +
208A GLN* 4.5 9.9 + - - +
214A VAL* 2.9 31.3 + - + +
215A ASP* 3.7 15.1 - - - +
217A MET* 1.3 75.9 - - - +
219A THR* 1.3 58.3 + - - +
222A HIS* 3.0 33.1 + - - +
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Residues in contact with THR 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A TYR* 2.7 31.7 + - - +
208A GLN 2.8 19.4 + - - -
209A SER* 3.3 11.1 - - - -
215A ASP 2.9 10.2 + - - -
216A THR 3.6 3.6 - - - -
218A GLN* 1.3 75.4 - - - +
220A VAL* 1.3 67.8 + - - +
222A HIS* 3.7 0.3 - - - +
223A TYR* 3.1 44.8 + - + +
237A THR* 4.3 5.2 - - + -
240A GLN* 4.4 4.9 - - + -
247A THR* 3.8 26.5 - - + +
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Residues in contact with VAL 220 (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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170A LEU* 5.0 4.7 - - + -
216A THR* 2.9 26.4 + - + +
217A MET* 4.1 5.8 - - - +
219A THR* 1.3 75.3 - - - +
221A LEU* 1.3 62.5 + - + +
223A TYR* 4.0 0.7 - - - +
224A TYR* 2.9 29.0 + - + +
237A THR* 5.1 3.4 + - - -
247A THR* 3.6 37.0 - - + +
250A LEU* 3.8 16.6 - - + -
251A ALA* 4.1 18.9 - - - +
254A LEU* 3.8 28.0 - - + -
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Residues in contact with LEU 221 (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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170A LEU* 5.4 0.2 - - + -
173A MET* 3.6 33.4 - - + -
190A ALA* 4.2 12.6 - - + +
193A LEU* 4.6 11.4 - - + -
194A VAL* 5.8 1.1 - - + -
200A PHE* 5.7 1.6 - - + +
202A PHE* 3.9 34.1 - - + -
217A MET* 3.0 42.4 + - + +
220A VAL* 1.3 77.1 - - + +
222A HIS* 1.3 65.3 + - - +
224A TYR* 4.4 2.5 - - + -
225A PHE* 3.0 41.9 + - + +
254A LEU* 4.3 13.5 - - + -
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Residues in contact with HIS 222 (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 PHE* 3.6 13.0 - - + -
203A GLU* 2.6 32.7 + - - +
205A TYR* 3.4 44.8 - + + +
218A GLN 3.0 21.8 + - - +
219A THR 3.7 2.0 - - - +
221A LEU* 1.3 77.1 - - - +
223A TYR* 1.3 91.1 + + - +
225A PHE* 3.9 0.3 - - - +
226A VAL* 3.1 50.0 + - + +
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Residues in contact with TYR 223 (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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32A LYS* 4.1 9.0 + - - -
205A TYR* 3.9 17.8 - + - -
219A THR* 3.1 28.3 + - + +
220A VAL 4.3 0.4 - - - +
222A HIS* 1.3 101.3 + + - +
224A TYR* 1.3 54.8 + - - +
226A VAL* 4.0 3.8 - - + -
227A THR* 2.7 38.5 + - - +
233A CYS* 4.3 4.7 - - - +
236A GLN* 3.6 47.4 + - + -
237A THR* 3.2 35.0 - - - +
240A GLN* 2.7 38.0 + - + +
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Residues in contact with TYR 224 (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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173A MET* 5.5 0.9 - - - -
177A LEU* 3.2 23.0 - - + +
183A MET* 3.1 46.3 - - + +
186A CYS* 4.3 7.6 - - + -
220A VAL* 2.9 21.0 + - + +
221A LEU* 3.9 3.1 - - + +
223A TYR* 1.3 77.1 - - - +
225A PHE* 1.3 98.4 + + - +
226A VAL 3.5 0.2 + - - -
227A THR* 3.5 9.8 + - - +
233A CYS* 3.9 17.8 - - - -
251A ALA* 5.7 0.9 - - - -
254A LEU* 3.9 39.0 - - + -
255A ALA* 4.2 9.2 - - + -
258A THR* 2.7 33.7 + - - +
259A TYR* 4.7 4.6 + + - -
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Residues in contact with PHE 225 (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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173A MET* 4.2 3.4 - - + -
183A MET* 3.6 21.9 - - + +
186A CYS* 3.5 28.9 - - + -
187A ARG* 2.9 63.6 + - + +
190A ALA* 3.7 21.1 - - + -
202A PHE* 3.8 20.6 - + + -
203A GLU* 5.8 0.4 - - - +
221A LEU* 3.0 39.4 + - + +
222A HIS 4.1 1.6 - - - +
224A TYR* 1.3 99.0 - + - +
226A VAL* 1.3 63.0 + - + +
227A THR 3.4 3.4 + - - +
600A GOL 4.2 5.6 - - - -
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Residues in contact with VAL 226 (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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203A GLU* 4.1 9.4 - - - +
222A HIS* 3.1 49.8 + - + +
223A TYR* 3.9 11.4 - - + +
224A TYR 3.3 0.2 - - - -
225A PHE* 1.3 80.4 - - + +
227A THR* 1.3 60.6 + - - +
236A GLN* 4.4 14.6 + - - +
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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