Contacts of the helix formed by residues 250 - 265 (chain B) in PDB entry 1WOI
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 250 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B PHE* 3.6 3.1 - - - -
234B ASP* 5.3 2.2 - - + -
237B VAL* 4.6 13.0 - - + -
248B GLY 4.9 2.9 - - - +
249B LEU* 1.3 77.8 - - - +
251B TYR* 1.3 65.8 + - - +
252B ALA* 3.5 6.6 + - - +
253B GLN* 3.0 39.2 + - - +
254B GLY 3.1 14.7 + - - -
247C ASP* 4.0 9.9 - - - -
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Residues in contact with TYR 251 (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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233B PHE* 3.8 15.5 - + - -
237B VAL* 4.5 16.2 - - + +
238B ILE* 5.8 1.8 - - + -
249B LEU 4.0 0.4 + - - -
250B THR* 1.3 73.7 - - - +
252B ALA* 1.3 58.3 + - - +
254B GLY* 3.3 1.2 + - - -
255B MET* 2.9 34.5 + - + +
288B LEU* 3.3 32.3 - - + -
289B MET* 6.0 2.0 - - - -
291B ARG* 3.0 26.2 + - - +
292B LEU* 3.3 38.6 - - + +
295B GLU* 2.7 29.1 + - - -
246C PRO* 3.5 28.5 - - + -
247C ASP* 3.1 23.8 + - - +
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Residues in contact with ALA 252 (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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250B THR* 3.1 5.4 - - - +
251B TYR* 1.3 83.5 - - - +
253B GLN* 1.3 57.1 + - + +
255B MET* 3.4 5.1 + - - +
256B LYS* 2.9 51.1 + - - +
247C ASP* 3.1 26.6 + - + +
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Residues in contact with GLN 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B MET* 3.5 15.5 - - - +
207B VAL* 3.9 24.5 + - + +
208B THR* 4.8 6.7 + - - +
211B LEU* 5.1 9.0 - - + +
248B GLY 4.0 1.0 - - - +
249B LEU* 3.5 18.1 - - + -
250B THR* 3.0 44.3 + - - +
252B ALA* 1.3 73.6 - - + +
254B GLY* 1.3 66.4 + - - +
256B LYS* 3.2 12.6 + - + +
257B ILE* 3.2 28.6 + - - +
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Residues in contact with GLY 254 (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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142B LEU* 3.8 12.9 - - - +
233B PHE* 3.8 20.4 - - - -
249B LEU* 4.2 10.6 - - - +
250B THR 3.1 8.7 + - - -
251B TYR 3.7 2.9 - - - -
253B GLN* 1.3 78.8 - - - +
255B MET* 1.3 57.0 + - - +
257B ILE* 3.4 5.9 + - - +
258B LEU* 3.1 33.3 + - - +
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Residues in contact with MET 255 (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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251B TYR* 2.9 25.6 + - + +
252B ALA* 3.7 6.3 - - - +
254B GLY* 1.3 75.7 - - - +
256B LYS* 1.3 54.4 + - - +
258B LEU* 3.9 9.9 - - + +
259B ALA* 2.7 41.4 + - + +
292B LEU* 3.6 23.0 - - + +
295B GLU* 3.3 48.2 - - + +
296B THR* 3.4 37.9 - - - +
299B GLU* 4.0 13.7 - - + +
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Residues in contact with LYS 256 (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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211B LEU* 4.7 19.1 - - + -
215B LEU* 3.9 14.5 - - + +
252B ALA* 2.9 42.0 + - - +
253B GLN* 3.2 11.4 + - + +
255B MET* 1.3 76.5 - - + +
257B ILE* 1.3 58.4 + - - +
259B ALA* 3.7 6.2 - - - +
260B ALA* 3.0 29.6 + - - +
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Residues in contact with ILE 257 (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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140B VAL* 4.7 8.1 - - + -
142B LEU* 4.0 21.8 - - + -
179B VAL* 3.7 29.8 - - + -
207B VAL* 4.6 6.1 - - + -
211B LEU* 4.5 8.7 - - + -
214B VAL* 4.6 4.9 - - + -
215B LEU* 3.9 17.7 - - + -
218B LEU* 3.7 29.1 - - + +
249B LEU* 4.1 17.7 - - + -
253B GLN 3.2 15.4 + - - +
254B GLY* 3.6 6.1 - - - +
256B LYS* 1.3 75.0 - - - +
258B LEU* 1.3 66.6 + - - +
260B ALA 3.3 1.4 + - - -
261B ALA* 3.1 21.1 + - - +
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Residues in contact with LEU 258 (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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140B VAL* 5.1 4.3 - - + +
142B LEU* 3.9 20.9 - - + -
226B PHE* 3.5 41.4 - - + -
228B VAL* 4.1 17.5 - - + -
254B GLY 3.1 21.2 + - - +
255B MET* 3.9 12.3 - - + +
257B ILE* 1.3 76.7 - - - +
259B ALA* 1.3 57.5 + - - +
261B ALA 3.5 0.2 + - - -
262B ALA* 2.9 32.7 + - - +
270B LEU* 5.5 0.4 - - + -
292B LEU* 3.9 30.3 - - + -
296B THR* 3.6 24.0 - - + +
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Residues in contact with ALA 259 (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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255B MET* 2.7 26.6 + - + +
256B LYS* 3.7 7.2 - - - +
257B ILE 3.2 0.2 - - - -
258B LEU* 1.3 74.1 - - - +
260B ALA* 1.3 60.3 + - - +
262B ALA* 3.5 1.9 + - - +
263B ALA* 3.2 24.6 + - - +
299B GLU* 3.9 38.1 - - + +
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Residues in contact with ALA 260 (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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215B LEU* 4.0 19.5 - - + +
218B LEU* 4.0 14.8 - - + -
256B LYS 3.0 17.9 + - - +
257B ILE 3.7 4.3 - - - +
259B ALA* 1.3 77.6 - - - +
261B ALA* 1.3 61.1 + - - +
263B ALA* 3.4 4.4 + - - +
264B ASN* 3.2 37.8 + - - +
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Residues in contact with ALA 261 (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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140B VAL* 4.4 14.8 - - + -
218B LEU* 4.2 13.8 - - + +
219B PRO* 5.1 2.0 - - + -
224B VAL* 5.2 0.8 - - + +
226B PHE* 3.5 29.6 - - + -
257B ILE 3.1 12.0 + - - +
260B ALA* 1.3 79.7 - - - +
262B ALA* 1.3 63.4 + - - +
264B ASN* 5.0 0.4 - - - +
265B ASN* 2.9 43.7 + - - +
267B VAL* 4.8 0.5 - - - +
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Residues in contact with ALA 262 (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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226B PHE* 3.6 9.8 - - + -
258B LEU 2.9 20.8 + - - +
259B ALA 3.7 5.2 - - - +
261B ALA* 1.3 78.7 - - - +
263B ALA* 1.3 59.2 + - - +
265B ASN 3.5 14.2 - - - +
267B VAL* 4.0 9.9 - - - +
296B THR* 4.6 2.0 - - + +
299B GLU* 3.8 24.1 - - + +
300B VAL* 3.9 28.8 - - + +
303B HIS* 4.6 4.5 - - - +
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Residues in contact with ALA 263 (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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259B ALA 3.2 16.5 + - - +
260B ALA* 4.0 4.3 - - - +
261B ALA 3.3 0.2 - - - -
262B ALA* 1.3 76.7 - - - +
264B ASN* 1.3 68.4 + - - +
265B ASN 3.6 1.3 - - - +
299B GLU* 5.4 0.2 - - - +
303B HIS* 3.4 54.4 + - + +
305B LEU* 6.1 0.2 - - - +
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Residues in contact with ASN 264 (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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215B LEU 5.9 0.6 + - - -
218B LEU* 6.2 1.6 - - - +
219B PRO 4.2 7.7 + - - +
220B ARG* 4.4 24.8 - - + +
221B GLY* 2.6 34.3 + - - -
260B ALA* 3.2 27.1 + - - +
261B ALA 3.3 0.2 + - - -
263B ALA* 1.3 89.1 - - - +
265B ASN* 1.3 60.7 + - - +
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Residues in contact with ASN 265 (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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219B PRO* 2.8 31.4 + - - +
220B ARG 3.3 3.8 - - - -
221B GLY* 3.1 8.6 + - - +
222B GLN* 2.7 38.5 + - - +
224B VAL* 3.6 22.0 - - + +
261B ALA* 2.9 33.9 + - - +
262B ALA 3.5 13.8 - - - +
263B ALA 3.6 1.3 + - - +
264B ASN* 1.3 79.2 - - - +
266B THR* 1.3 63.4 + - - +
267B VAL* 3.7 4.0 + - + +
303B HIS 5.4 1.9 - - - +
305B LEU* 5.3 8.3 - - - +
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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