Contacts of the helix formed by residues 229 - 240 (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 THR 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A THR* 4.2 0.5 + - - -
228A ASP* 1.3 94.2 + - - +
230A PHE* 1.3 64.5 + - - +
231A LYS* 3.6 6.5 + - - +
232A SER* 2.6 33.3 + - - +
233A CYS* 3.0 25.5 + - - +
259A TYR* 3.6 14.0 + - - -
263A ASP* 5.5 5.6 - - - +
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Residues in contact with PHE 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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16A GLY* 3.7 27.1 - - - -
19A VAL* 4.1 4.7 - - + -
229A THR* 1.3 73.7 - - - +
231A LYS* 1.3 67.2 + - - +
233A CYS* 3.5 0.5 - - - +
234A LEU* 3.0 48.2 + - + +
252A GLY* 3.5 26.0 - - - -
255A ALA* 3.7 8.7 - - + -
256A GLY* 3.5 23.6 - - - -
259A TYR* 3.5 18.0 - - + +
260A GLY 5.5 0.4 - - - -
263A ASP* 3.5 23.3 + - + +
264A ILE* 3.8 29.2 - - + -
265A PRO* 3.9 14.4 - - + -
268A TRP* 3.9 13.7 - + - -
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Residues in contact with LYS 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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43A ARG* 6.2 0.7 - - - +
229A THR* 3.3 6.3 + - - +
230A PHE* 1.3 81.0 - - - +
232A SER* 1.3 57.7 + - - +
234A LEU 3.3 1.4 + - - -
235A ILE* 2.9 52.1 + - + +
263A ASP 4.5 2.8 + - - +
265A PRO* 3.9 23.5 - - + +
268A TRP* 3.8 27.4 - - + -
500A TLA 2.7 38.2 + - - -
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Residues in contact with SER 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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227A THR* 3.7 9.3 - - - -
228A ASP* 4.1 4.5 + - - -
229A THR* 2.6 35.2 + - - -
231A LYS* 1.3 75.8 - - - +
233A CYS* 1.3 68.2 + - - +
235A ILE* 4.6 5.6 - - - +
236A GLN* 3.0 46.0 + - - +
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Residues in contact with CYS 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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223A TYR* 4.4 0.9 - - - +
224A TYR* 3.9 24.9 - - - -
227A THR* 3.2 27.3 + - - +
229A THR 3.0 17.0 + - - +
230A PHE 3.5 4.7 - - - +
232A SER* 1.3 78.3 + - - +
234A LEU* 1.3 57.1 + - - +
236A GLN* 4.0 1.2 - - - +
237A THR* 2.9 34.0 + - - -
251A ALA* 3.8 25.6 - - - -
255A ALA* 4.1 20.0 - - + -
259A TYR* 5.2 1.8 - - + -
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Residues in contact with LEU 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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19A VAL* 5.3 0.4 - - + -
20A GLY* 3.5 19.7 - - - +
23A LEU* 4.3 5.2 - - + -
230A PHE* 3.0 45.9 + - + +
231A LYS 3.9 3.4 - - - +
233A CYS* 1.3 78.2 - - + +
235A ILE* 1.3 61.4 - - - +
237A THR* 3.7 1.7 - - - -
238A VAL* 2.9 40.9 - - + -
248A GLY* 3.1 35.4 - - - +
251A ALA* 4.0 8.7 - - + +
252A GLY* 3.8 21.8 - - - +
268A TRP* 4.0 15.3 - - + -
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Residues in contact with ILE 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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23A LEU* 5.0 0.9 - - + -
41A ILE* 3.6 29.4 - - + -
42A HIS 4.5 1.3 - - - +
43A ARG* 3.6 29.4 - - + -
231A LYS* 2.9 47.6 + - + +
232A SER* 4.1 5.4 - - - +
234A LEU* 1.3 75.4 + - - +
236A GLN* 1.3 66.6 + - + +
238A VAL* 4.0 5.8 - - - -
239A ASN* 2.8 34.3 + - - +
268A TRP* 3.8 17.3 - - + -
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Residues in contact with GLN 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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223A TYR* 3.6 40.4 + - + -
226A VAL* 4.4 7.0 + - - +
227A THR* 3.4 28.9 - - + +
232A SER* 3.0 28.0 + - - +
233A CYS 4.0 1.3 - - - +
235A ILE* 1.3 80.7 - - + +
237A THR* 1.3 63.5 + - - +
239A ASN* 3.7 4.0 + - - +
240A GLN 3.5 12.3 + - - -
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Residues in contact with THR 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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219A THR* 4.3 9.2 + - + +
220A VAL* 5.1 3.4 + - + -
223A TYR* 3.2 25.2 - - + +
233A CYS* 2.9 21.9 + - - -
234A LEU* 3.3 3.8 - - - -
236A GLN* 1.3 76.7 - - - +
238A VAL* 1.3 64.3 + - - +
240A GLN* 3.2 19.4 + - - +
241A GLY 4.1 1.6 + - - +
247A THR* 3.5 51.1 + - - +
248A GLY* 3.8 2.5 - - - +
251A ALA* 3.6 17.0 - - + +
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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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20A GLY 4.4 0.9 - - - +
23A LEU* 4.0 22.4 - - + -
24A GLY* 3.6 35.4 - - - +
27A VAL* 3.4 20.7 - - + +
35A ILE* 3.6 0.2 - - - +
42A HIS* 4.2 12.3 - - + +
234A LEU* 2.9 28.6 - - + -
235A ILE* 3.5 7.6 - - - +
237A THR* 1.3 74.5 - - - +
239A ASN* 1.3 68.6 + - - +
240A GLN 3.2 0.2 - - - -
241A GLY* 3.0 17.0 + - - -
244A ALA* 3.8 16.0 - - - +
248A GLY* 4.0 14.6 - - - -
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Residues in contact with ASN 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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32A LYS* 3.6 25.5 - - - +
35A ILE* 3.4 22.9 - - - +
40A GLY 4.4 1.4 - - - +
41A ILE* 3.5 13.4 - - - +
42A HIS* 2.8 49.8 + - - +
235A ILE* 2.8 38.0 + - + +
236A GLN* 4.1 4.3 - - - +
238A VAL* 1.3 76.2 - - - +
240A GLN* 1.3 63.5 + - - +
241A GLY 3.1 1.7 + - - -
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Residues in contact with GLN 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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31A THR* 5.0 0.2 - - - -
32A LYS* 3.6 44.1 + - - +
205A TYR* 3.3 28.5 - - - +
207A GLY* 3.4 30.1 + - - -
209A SER* 3.9 14.9 + - - +
219A THR* 4.4 2.5 - - + -
223A TYR* 2.7 37.2 + - + +
236A GLN 3.5 4.0 + - - -
237A THR 3.2 15.8 + - - +
238A VAL 3.2 0.8 - - - -
239A ASN* 1.3 76.7 - - - +
241A GLY* 1.3 61.3 + - - +
242A GLY 3.9 0.2 + - - -
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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