Contacts of the helix formed by residues 250 - 264 (chain D) in PDB entry 1WOH
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233D PHE* 3.4 4.6 - - - -
234D ASP* 5.3 2.0 - - + -
237D VAL* 4.6 13.2 - - + -
248D GLY 4.9 2.7 - - - +
249D LEU* 1.3 77.7 - - - +
251D TYR* 1.3 65.1 + - - +
252D ALA* 3.4 8.1 + - - +
253D GLN* 2.9 43.9 + - - +
254D GLY 3.1 15.9 + - - -
247E ASP* 4.0 8.5 - - - -
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Residues in contact with TYR 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D PHE* 3.9 11.6 - - - -
237D VAL* 4.5 15.5 - - + +
250D THR* 1.3 75.4 - - - +
252D ALA* 1.3 59.6 + - - +
254D GLY* 3.3 0.7 + - - -
255D MET* 2.9 35.5 + - + +
288D LEU* 3.3 29.2 - - + -
289D MET* 4.4 9.9 - - + -
291D ARG* 3.1 28.8 + - - +
292D LEU* 3.3 31.9 - - + +
295D GLU* 2.7 29.8 + - - -
246E PRO* 3.6 31.2 - - + -
247E ASP* 3.1 23.6 + - - +
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Residues in contact with ALA 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D THR* 3.2 5.6 - - - +
251D TYR* 1.3 83.4 - - - +
253D GLN* 1.3 58.0 + - + +
255D MET* 3.4 4.7 + - - +
256D LYS* 2.9 48.6 + - - +
247E ASP* 3.2 26.3 + - + +
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Residues in contact with GLN 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D MET* 3.6 14.5 - - - +
207D VAL* 4.0 25.0 + - + +
208D THR* 4.7 6.9 + - - +
211D LEU* 5.0 9.9 - - + +
248D GLY 3.9 1.6 - - - +
249D LEU* 3.5 19.2 - - + -
250D THR* 2.9 45.4 + - + +
252D ALA* 1.3 73.9 - - + +
254D GLY* 1.3 67.8 + - - +
256D LYS* 3.2 10.3 + - + +
257D ILE* 3.2 28.2 + - - +
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Residues in contact with GLY 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D LEU* 4.0 4.6 - - - +
233D PHE* 3.8 19.3 - - - -
249D LEU* 4.2 16.6 - - - +
250D THR 3.1 8.9 + - - -
251D TYR 3.8 1.6 - - - -
253D GLN* 1.3 78.8 - - - +
255D MET* 1.3 61.4 + - - +
257D ILE* 3.3 6.1 + - - +
258D LEU* 3.1 32.3 + - - +
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Residues in contact with MET 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D TYR* 2.9 25.6 + - + +
252D ALA* 3.7 5.8 - - - +
254D GLY* 1.3 77.9 - - - +
256D LYS* 1.3 52.6 + - + +
258D LEU* 3.3 10.0 + - + -
259D ALA* 2.7 39.6 + - + +
292D LEU* 3.8 22.7 - - + +
295D GLU* 3.4 43.1 - - + +
296D THR* 3.4 35.2 - - - +
299D GLU* 4.0 19.5 - - + +
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Residues in contact with LYS 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D LEU* 4.5 27.6 - - + -
215D LEU* 3.7 6.7 - - + +
252D ALA* 2.9 34.9 + - - +
253D GLN* 3.2 8.7 + - + +
255D MET* 1.3 75.6 - - - +
257D ILE* 1.3 57.2 + - - +
259D ALA* 3.8 6.2 - - - +
260D ALA* 3.0 30.0 + - - +
205E ASP* 5.9 1.4 + - - -
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Residues in contact with ILE 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D VAL* 4.7 8.1 - - + -
142D LEU* 4.0 22.0 - - + -
179D VAL* 3.6 30.5 - - + -
207D VAL* 4.7 0.7 - - + -
211D LEU* 4.4 13.0 - - + -
214D VAL* 4.6 7.2 - - + -
215D LEU* 3.7 17.0 - - + -
218D LEU* 3.4 29.1 - - + +
249D LEU* 4.1 18.2 - - + -
253D GLN 3.2 14.7 + - - +
254D GLY* 3.6 7.0 - - - +
255D MET 3.2 0.2 - - - -
256D LYS* 1.3 77.3 - - - +
258D LEU* 1.3 63.3 + - + +
261D ALA* 3.1 20.8 + - - +
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Residues in contact with LEU 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D VAL* 5.2 2.9 - - + +
142D LEU* 3.9 28.9 - - + -
226D PHE* 3.6 41.1 - - + -
228D VAL* 4.2 14.1 - - + -
254D GLY 3.1 17.7 + - - +
255D MET* 3.7 13.7 - - + +
257D ILE* 1.3 77.2 - - - +
259D ALA* 1.3 56.3 + - - +
261D ALA 3.5 0.2 + - - -
262D ALA* 2.9 32.7 + - - +
270D LEU* 5.1 0.7 - - + -
292D LEU* 4.1 25.1 - - + -
296D THR* 3.6 24.2 - - + +
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Residues in contact with ALA 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D MET* 2.7 24.5 + - + +
256D LYS* 3.8 6.7 - - - +
258D LEU* 1.3 73.8 - - - +
260D ALA* 1.3 62.7 + - - +
262D ALA* 3.2 2.9 + - - +
263D ALA* 3.0 25.3 + - - +
299D GLU* 3.8 40.3 - - + +
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Residues in contact with ALA 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D LEU* 3.7 30.1 - - + +
218D LEU* 4.0 6.7 - - + -
256D LYS 3.0 18.6 + - - +
257D ILE 3.8 2.0 - - - +
259D ALA* 1.3 76.5 - - - +
261D ALA* 1.3 61.3 + - - +
263D ALA* 3.3 10.2 + - - +
264D ASN* 3.0 30.3 + - - +
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Residues in contact with ALA 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D VAL* 4.4 12.1 - - + -
218D LEU* 3.9 16.6 - - + +
219D PRO* 5.2 0.7 - - + -
224D VAL* 5.3 0.4 - - + -
226D PHE* 3.5 30.3 - - + -
257D ILE 3.1 15.1 + - - +
260D ALA* 1.3 76.6 - - - +
262D ALA* 1.3 61.0 + - - +
265D ASN* 2.8 44.7 + - - +
267D VAL* 4.8 0.2 - - - +
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Residues in contact with ALA 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D PHE* 3.8 6.5 - - + -
258D LEU 2.9 19.8 + - - +
259D ALA 3.6 4.5 - - - +
261D ALA* 1.3 77.3 - - - +
263D ALA* 1.3 60.5 + - - +
264D ASN 3.4 0.4 - - - -
265D ASN 3.7 12.6 - - - +
267D VAL* 4.0 13.5 - - - +
296D THR* 4.8 1.1 - - + +
299D GLU* 4.1 8.7 - - + -
300D VAL* 3.9 40.8 - - + +
303D HIS* 4.0 11.9 - - - +
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Residues in contact with ALA 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D ALA 3.0 15.7 + - - +
260D ALA* 3.9 5.8 - - - +
261D ALA 3.3 0.4 - - - -
262D ALA* 1.3 78.1 - - - +
264D ASN* 1.3 68.1 + - - +
265D ASN 3.6 1.1 - - - -
299D GLU* 5.7 0.2 - - - +
303D HIS* 3.4 47.7 - - + +
305D LEU* 6.2 0.2 - - - +
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Residues in contact with ASN 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D PRO 4.5 1.3 + - - +
220D ARG* 4.3 32.8 - - + +
221D GLY* 2.6 35.0 + - - -
260D ALA* 3.0 29.0 + - - +
261D ALA 3.6 0.4 + - - -
263D ALA* 1.3 87.7 - - - +
265D ASN* 1.3 61.1 + - - +
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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