Contacts of the helix formed by residues 250 - 264 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233E PHE* 3.5 4.0 - - - -
234E ASP* 5.3 2.0 - - + -
237E VAL* 4.7 12.3 - - + -
248E GLY 5.0 2.7 - - - +
249E LEU* 1.3 77.8 - - - +
251E TYR* 1.3 63.7 + - - +
252E ALA* 3.5 7.3 + - - +
253E GLN* 2.9 44.4 + - - +
254E GLY 3.1 15.6 + - - -
247F ASP* 4.1 8.5 - - - -
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Residues in contact with TYR 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E PHE* 3.9 11.8 - - - -
237E VAL* 4.6 16.2 - - + +
250E THR* 1.3 73.6 - - - +
252E ALA* 1.3 66.0 + - - +
254E GLY* 3.3 0.9 + - - -
255E MET* 2.9 27.1 + - + +
288E LEU* 3.3 28.7 - - + -
289E MET* 4.3 11.2 - - + -
291E ARG* 3.2 26.7 + - - +
292E LEU* 3.3 37.0 - - + +
295E GLU* 2.8 29.8 + - - -
246F PRO* 3.6 28.3 - - + -
247F ASP* 3.2 23.1 + - - +
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Residues in contact with ALA 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250E THR* 3.2 5.4 - - - +
251E TYR* 1.3 82.2 - - - +
253E GLN* 1.3 58.1 + - + +
255E MET* 3.4 3.8 + - - +
256E LYS* 2.8 48.5 + - + +
247F ASP* 3.2 27.1 + - + +
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Residues in contact with GLN 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E MET* 3.5 14.6 - - - +
207E VAL* 3.7 27.0 + - + +
208E THR* 4.8 5.3 + - - +
211E LEU* 5.0 8.6 - - + +
248E GLY 3.9 1.9 - - - +
249E LEU* 3.4 18.4 - - + -
250E THR* 2.9 52.5 + - + +
252E ALA* 1.3 73.6 - - + +
254E GLY* 1.3 66.6 + - - +
256E LYS* 3.1 20.0 + - + +
257E ILE* 3.1 20.3 + - - +
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Residues in contact with GLY 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E LEU* 3.8 8.8 - - - +
233E PHE* 3.8 21.3 - - - -
249E LEU* 4.0 17.1 - - - +
250E THR 3.1 8.7 + - - -
253E GLN* 1.3 80.1 - - - +
255E MET* 1.3 60.8 + - - +
257E ILE* 3.2 7.2 + - - +
258E LEU* 3.1 26.0 + - - +
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Residues in contact with MET 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E TYR* 2.9 23.1 + - + +
252E ALA* 3.7 5.2 - - - +
254E GLY* 1.3 73.9 - - - +
256E LYS* 1.3 60.5 + - - +
258E LEU* 3.9 11.2 - - + -
259E ALA* 2.8 35.0 + - + +
292E LEU* 3.6 26.1 - - + +
295E GLU* 3.4 44.4 - - + +
296E THR* 3.3 38.1 - - - +
299E GLU* 4.0 16.8 - - + +
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Residues in contact with LYS 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211E LEU* 4.5 26.7 - - + -
215E LEU* 4.1 6.6 - - + +
252E ALA* 2.8 35.1 + - - +
253E GLN* 3.5 11.4 - - + +
255E MET* 1.3 75.2 - - - +
257E ILE* 1.3 58.8 + - - +
259E ALA* 3.9 4.9 - - - +
260E ALA* 3.0 30.1 + - - +
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Residues in contact with ILE 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E VAL* 4.6 8.3 - - + -
142E LEU* 3.9 24.7 - - + -
179E VAL* 3.7 31.0 - - + -
207E VAL* 4.6 4.9 - - + -
211E LEU* 4.3 9.2 - - + -
214E VAL* 5.0 2.7 - - + -
215E LEU* 3.8 18.8 - - + -
218E LEU* 3.6 26.7 - - + +
249E LEU* 4.0 18.8 - - + -
253E GLN 3.1 15.5 + - - +
254E GLY* 3.4 7.2 - - - +
256E LYS* 1.3 75.3 - - - +
258E LEU* 1.3 64.7 + - - +
260E ALA 3.4 1.0 + - - -
261E ALA* 3.2 20.1 + - - +
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Residues in contact with LEU 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E VAL* 5.1 3.4 - - + +
142E LEU* 3.9 22.0 - - + -
226E PHE* 3.6 41.6 - - + -
228E VAL* 4.1 18.8 - - + -
254E GLY 3.1 14.0 + - - +
255E MET* 3.7 13.7 - - + +
257E ILE* 1.3 80.0 - - - +
259E ALA* 1.3 61.8 + - - +
261E ALA 3.4 1.0 + - - -
262E ALA* 3.0 25.1 + - - +
270E LEU* 5.1 1.1 - - + -
292E LEU* 4.1 27.4 - - + -
296E THR* 3.5 24.9 - - + +
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Residues in contact with ALA 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255E MET* 2.8 24.6 + - + +
256E LYS* 3.9 5.4 - - - +
258E LEU* 1.3 74.1 - - - +
260E ALA* 1.3 63.3 + - - +
262E ALA* 3.4 2.3 + - - +
263E ALA* 3.1 23.6 + - - +
299E GLU* 3.6 43.2 - - + +
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Residues in contact with ALA 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E LEU* 4.0 20.0 - - + +
218E LEU* 3.9 15.0 - - + -
256E LYS 3.0 18.9 + - - +
257E ILE 3.7 4.7 - - - +
258E LEU 3.3 0.2 - - - -
259E ALA* 1.3 76.7 - - - +
261E ALA* 1.3 61.7 + - - +
263E ALA* 3.3 17.1 + - - +
264E ASN* 3.3 15.2 + - - +
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Residues in contact with ALA 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E VAL* 4.5 13.0 - - + -
218E LEU* 4.1 16.1 - - + +
219E PRO* 5.3 0.2 - - + -
224E VAL* 5.3 1.1 - - + -
226E PHE* 3.5 30.1 - - + -
257E ILE 3.2 12.2 + - - +
260E ALA* 1.3 79.0 - - - +
262E ALA* 1.3 61.4 + - - +
263E ALA 3.4 0.2 + - - -
264E ASN* 4.2 0.7 - - - -
265E ASN* 2.8 43.6 + - - +
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Residues in contact with ALA 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E PHE* 3.9 4.0 - - + -
258E LEU 3.0 16.9 + - - +
259E ALA 3.8 4.5 - - - +
261E ALA* 1.3 77.7 - - - +
263E ALA* 1.3 62.0 + - - +
264E ASN 3.4 0.4 + - - -
265E ASN 3.7 11.6 - - - +
267E VAL* 4.1 13.0 - - + +
296E THR* 4.8 1.1 - - + +
299E GLU* 4.1 11.2 - - + +
300E VAL* 3.9 39.8 - - + +
303E HIS* 3.8 12.5 - - - +
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Residues in contact with ALA 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259E ALA 3.1 16.4 + - - +
260E ALA* 3.6 9.0 - - - +
261E ALA 3.2 0.8 - - - -
262E ALA* 1.3 78.9 - - - +
264E ASN* 1.3 60.0 + - + +
265E ASN 3.8 0.2 - - - -
303E HIS* 3.4 50.2 - - + +
305E LEU* 6.0 0.9 - - - +
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Residues in contact with ASN 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E PRO 3.6 2.6 - - - +
220E ARG* 3.6 38.7 - - + +
221E GLY* 2.8 32.9 + - - +
260E ALA 3.3 14.0 + - - +
261E ALA* 4.2 0.5 - - - -
262E ALA 3.4 0.2 - - - -
263E ALA* 1.3 79.7 - - + +
265E ASN* 1.3 65.6 + - - +
305E LEU* 6.3 2.9 - - - -
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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