Contacts of the helix formed by residues 250 - 265 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ASP* 4.0 7.9 - - - -
233C PHE* 3.4 5.3 - - - -
234C ASP* 6.0 1.6 - - + -
237C VAL* 4.5 13.0 - - + -
248C GLY 5.0 2.9 - - - +
249C LEU* 1.3 78.1 - - - +
251C TYR* 1.3 67.1 + - - +
252C ALA* 3.4 7.7 + - - +
253C GLN* 3.0 43.4 + - - +
254C GLY 3.2 12.1 + - - -
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Residues in contact with TYR 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A PRO* 3.5 32.5 - - + -
247A ASP* 3.2 22.2 + - - +
233C PHE* 3.8 15.9 - + - -
237C VAL* 4.4 16.8 - - + +
238C ILE* 5.7 1.8 - - + -
250C THR* 1.3 74.4 - - - +
252C ALA* 1.3 65.8 + - - +
254C GLY* 3.4 0.9 + - - -
255C MET* 3.0 28.5 + - + +
288C LEU* 3.2 34.1 - - + -
289C MET* 6.0 1.8 - - - -
291C ARG* 3.0 28.9 + - - +
292C LEU* 3.3 31.0 - - + +
295C GLU* 2.8 28.8 + - - -
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Residues in contact with ALA 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ASP* 3.1 30.1 + - + +
250C THR* 3.1 6.0 - - - +
251C TYR* 1.3 78.9 - - - +
253C GLN* 1.3 56.9 + - + +
255C MET* 3.4 4.5 + - - +
256C LYS* 2.9 53.6 + - - +
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Residues in contact with GLN 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C MET* 3.7 11.2 - - - +
207C VAL* 3.9 30.4 + - + +
208C THR* 4.7 5.5 + - - +
211C LEU* 4.8 11.9 - - + +
248C GLY 4.1 1.0 - - - +
249C LEU* 3.5 18.1 - - + -
250C THR* 3.0 45.9 + - - +
252C ALA* 1.3 74.3 - - + +
254C GLY* 1.3 66.9 + - - +
256C LYS* 3.2 12.7 + - + +
257C ILE* 3.1 28.5 + - - +
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Residues in contact with GLY 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C LEU* 4.0 9.2 - - - +
233C PHE* 3.8 20.0 - - - -
249C LEU* 4.1 17.3 - - - +
250C THR 3.2 8.1 + - - -
253C GLN* 1.3 78.4 - - - +
255C MET* 1.3 61.2 + - - +
257C ILE* 3.2 7.0 + - - +
258C LEU* 3.1 27.9 + - - +
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Residues in contact with MET 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C TYR* 3.0 26.7 + - + +
252C ALA* 3.7 5.4 - - - +
254C GLY* 1.3 77.0 - - - +
256C LYS* 1.3 56.3 + - - +
258C LEU* 3.3 9.1 + - + -
259C ALA* 2.8 34.2 + - + +
292C LEU* 3.5 24.7 - - + +
295C GLU* 3.4 42.0 - - + +
296C THR* 3.6 37.7 - - - +
299C GLU* 3.9 21.1 - - + +
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Residues in contact with LYS 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A ASP* 6.0 0.4 + - - -
211C LEU* 4.3 30.5 - - + -
215C LEU* 4.0 7.5 - - + +
252C ALA* 2.9 47.5 + - - +
253C GLN* 3.2 9.7 + - + +
255C MET* 1.3 76.1 - - - +
257C ILE* 1.3 58.8 + - - +
259C ALA* 3.5 6.0 + - - +
260C ALA* 2.9 30.5 + - - +
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Residues in contact with ILE 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C VAL* 4.7 7.0 - - + -
142C LEU* 4.1 21.1 - - + -
179C VAL* 3.8 31.2 - - + -
207C VAL* 4.6 2.2 - - + -
211C LEU* 4.3 12.1 - - + -
214C VAL* 4.6 3.8 - - + -
215C LEU* 3.9 21.1 - - + -
218C LEU* 3.5 27.3 - - + +
249C LEU* 4.2 16.8 - - + -
253C GLN 3.1 16.4 + - - +
254C GLY* 3.5 9.0 - - - +
256C LYS* 1.3 73.8 - - - +
258C LEU* 1.3 64.8 + - - +
260C ALA 3.4 0.7 + - - -
261C ALA* 3.0 23.0 + - - +
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Residues in contact with LEU 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C VAL* 5.0 3.6 - - + +
142C LEU* 4.0 22.9 - - + -
226C PHE* 3.7 39.6 - - + -
228C VAL* 4.1 17.3 - - + -
254C GLY 3.1 19.9 + - - +
255C MET* 3.8 12.1 - - + +
257C ILE* 1.3 75.7 - - - +
259C ALA* 1.3 58.1 + - - +
261C ALA* 3.4 0.9 + - - -
262C ALA* 2.9 32.2 + - - +
270C LEU* 5.4 0.7 - - + -
292C LEU* 4.1 27.8 - - + -
296C THR* 3.3 28.7 - - + +
299C GLU* 5.4 0.2 - - - -
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Residues in contact with ALA 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C MET* 2.8 21.0 + - + +
256C LYS* 3.7 7.0 - - - +
258C LEU* 1.3 77.5 - - - +
260C ALA* 1.3 62.9 + - - +
262C ALA* 3.3 2.8 + - - +
263C ALA* 3.0 23.9 + - - +
299C GLU* 3.7 41.9 - - + +
303C HIS* 5.7 0.2 - - - -
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Residues in contact with ALA 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C LEU* 4.1 22.7 - - + +
218C LEU* 3.9 15.0 - - + -
256C LYS 2.9 17.9 + - - +
257C ILE 3.7 3.8 - - - +
259C ALA* 1.3 76.5 - - - +
261C ALA* 1.3 62.4 + - - +
263C ALA* 3.1 11.7 + - - +
264C ASN* 2.9 29.8 + - - +
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Residues in contact with ALA 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C VAL* 4.5 13.7 - - + -
218C LEU* 4.1 15.6 - - + +
219C PRO* 5.2 0.4 - - + -
224C VAL* 5.3 0.7 - - + -
226C PHE* 3.6 28.0 - - + -
257C ILE 3.0 17.2 + - - +
260C ALA* 1.3 76.5 - - - +
262C ALA* 1.3 62.8 + - - +
263C ALA 3.3 0.3 + - - -
264C ASN* 3.3 0.6 + - - +
265C ASN* 2.9 43.4 + - - +
267C VAL* 4.9 0.3 - - - +
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Residues in contact with ALA 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C PHE* 3.9 3.3 - - + -
258C LEU 2.9 18.4 + - - +
259C ALA 3.7 4.5 - - - +
260C ALA 3.3 0.2 - - - -
261C ALA* 1.3 76.4 - - - +
263C ALA* 1.3 60.2 + - - +
264C ASN 3.4 0.2 - - - -
265C ASN 3.7 11.2 - - - +
267C VAL* 4.0 13.9 - - + +
296C THR* 5.0 0.7 - - + +
299C GLU* 4.2 10.9 - - + +
300C VAL* 3.8 40.1 - - + +
303C HIS* 3.8 15.6 - - - +
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Residues in contact with ALA 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C ALA 3.0 16.5 + - - +
260C ALA* 3.1 8.7 + - - +
262C ALA* 1.3 79.3 - - - +
264C ASN* 1.3 66.5 + - - +
265C ASN 3.7 0.4 - - - -
303C HIS* 3.8 42.5 - - + +
305C LEU* 6.0 1.2 - - - +
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Residues in contact with ASN 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C PRO 4.2 7.6 - - - +
220C ARG* 4.5 19.3 + - + +
221C GLY* 2.6 34.7 + - - -
260C ALA* 2.9 27.8 + - - +
261C ALA 3.3 2.2 + - - -
263C ALA* 1.3 87.1 - - - +
265C ASN* 1.3 61.3 + - - +
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Residues in contact with ASN 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C PRO* 2.8 32.3 + - - +
220C ARG 3.3 4.3 - - - -
221C GLY* 3.0 8.7 + - - -
222C GLN* 2.8 37.2 + - - +
224C VAL* 3.5 21.6 - - + +
261C ALA* 2.9 32.8 + - - +
262C ALA 3.7 13.3 - - - +
263C ALA 3.7 0.7 - - - -
264C ASN* 1.3 79.7 - - - +
266C THR* 1.3 64.3 + - - +
267C VAL* 3.6 5.1 + - + +
303C HIS 4.9 5.9 - - - +
305C LEU* 5.5 4.6 - - - +
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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