Contacts of the helix formed by residues 266 - 278 (chain D) in PDB entry 1WLZ
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 SER 266 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265D ILE* 1.3 76.1 - - - +
267D ARG* 1.3 58.5 + - - +
268D GLU* 3.6 14.5 + - - +
269D GLU* 2.9 44.2 + - - +
270D PHE* 2.9 28.2 + - - +
290D TRP* 4.4 1.6 - - - -
300D ARG* 3.6 24.1 - - - +
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Residues in contact with ARG 267 (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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266D SER* 1.3 72.9 - - - +
268D GLU* 1.3 91.7 + - - +
270D PHE* 3.2 2.6 + - - +
271D ARG* 3.0 25.3 + - - +
286D PHE* 3.4 30.7 - - + -
287D ASP* 4.9 10.1 + - - -
290D TRP* 3.3 58.9 - - + +
299D GLY 4.4 7.0 + - - +
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Residues in contact with GLU 268 (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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266D SER* 3.7 15.8 + - - +
267D ARG* 1.3 115.0 + - - +
269D GLU* 1.3 66.1 + - + +
271D ARG* 3.3 9.9 + - - +
272D ALA* 3.0 22.9 + - - +
286D PHE* 5.7 0.4 - - - -
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Residues in contact with GLU 269 (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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257D PHE* 3.6 52.0 - - + +
265D ILE* 3.4 15.6 - - + +
266D SER* 2.9 46.5 + - - +
268D GLU* 1.3 77.6 - - + +
270D PHE* 1.3 62.4 + - - +
272D ALA* 3.2 10.4 + - - +
273D ILE* 3.2 24.1 + - - +
300D ARG* 4.5 4.9 + - - -
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Residues in contact with PHE 270 (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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239D LEU* 4.4 6.7 - - + -
254D PHE* 4.6 6.3 - + - -
265D ILE* 3.7 14.8 - - + +
266D SER 2.9 13.6 + - - +
267D ARG 3.2 6.9 + - - +
269D GLU* 1.3 78.9 - - - +
271D ARG* 1.3 60.9 + - - +
273D ILE* 3.1 10.7 + - + +
274D CYS* 2.9 44.3 + - - -
286D PHE* 3.8 9.4 - + - -
289D LEU* 4.2 9.9 - - + -
290D TRP* 3.6 26.9 - + + -
293D MET* 3.8 35.2 - - + -
301D LEU* 3.5 25.1 - - + -
306D PHE* 3.9 23.1 - + - -
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Residues in contact with ARG 271 (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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267D ARG* 3.0 11.2 + - - +
268D GLU* 3.6 11.4 - - - +
270D PHE* 1.3 76.0 - - - +
272D ALA* 1.3 63.2 + - - +
274D CYS* 3.2 4.9 + - + +
275D ASN* 2.9 37.7 + - - +
281D LEU* 3.0 29.9 + - + +
282D THR* 3.4 0.8 - - - +
283D ASP* 2.9 43.0 + - - +
286D PHE* 3.4 55.2 - - + +
287D ASP* 5.6 1.0 + - - -
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Residues in contact with ALA 272 (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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253D GLU* 5.4 0.2 - - - -
257D PHE* 4.4 13.9 - - + -
268D GLU 3.0 13.0 + - - +
269D GLU* 3.3 13.5 - - - +
270D PHE 3.2 0.4 - - - -
271D ARG* 1.3 78.1 - - - +
273D ILE* 1.3 60.9 + - - +
275D ASN* 3.4 25.6 + - - +
276D ARG* 3.5 16.4 + - - +
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Residues in contact with ILE 273 (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 ILE* 4.5 15.0 - - + +
253D GLU* 3.6 44.4 - - + +
254D PHE* 3.5 37.2 - - + -
257D PHE* 3.9 17.0 - - + -
265D ILE* 4.0 12.1 - - + -
269D GLU 3.2 9.1 + - - +
270D PHE* 3.1 14.0 + - + +
272D ALA* 1.3 75.0 - - - +
274D CYS* 1.3 65.8 + - - +
276D ARG* 3.0 3.9 + - - +
277D ARG* 2.9 31.8 + - + +
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Residues in contact with CYS 274 (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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239D LEU* 4.6 1.6 - - - -
270D PHE* 2.9 52.9 + - - -
271D ARG* 3.2 12.1 + - + +
273D ILE* 1.3 77.6 - - - +
275D ASN* 1.3 60.6 + - - +
278D VAL* 2.8 46.6 + - + -
279D GLN 2.9 16.8 + - - +
281D LEU* 4.5 9.9 - - + -
286D PHE* 4.6 1.3 - - + -
289D LEU* 4.0 15.9 - - - -
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Residues in contact with ASN 275 (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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271D ARG* 2.9 32.7 + - - +
272D ALA* 3.4 16.9 - - - +
274D CYS* 1.3 77.3 - - - +
276D ARG* 1.3 62.8 + - + +
279D GLN* 3.7 12.4 + - - +
280D ILE* 3.5 48.8 - - + +
281D LEU 4.1 3.8 + - - -
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Residues in contact with ARG 276 (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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253D GLU* 3.3 24.7 + - - +
272D ALA* 3.5 11.9 + - - +
273D ILE 3.0 7.0 + - - +
275D ASN* 1.3 83.2 - - + +
277D ARG* 1.3 91.8 + - + +
278D VAL 5.5 0.2 - - - -
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Residues in contact with ARG 277 (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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242D ALA* 3.3 29.1 - - + +
246D HIS* 4.3 29.3 + - + -
249D ALA* 3.2 36.5 + - - +
250D ILE* 3.9 24.6 - - + +
253D GLU* 3.3 23.6 + - - +
273D ILE* 2.9 24.3 + - + +
276D ARG* 1.3 104.6 + - - +
278D VAL* 1.3 63.0 + - + +
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Residues in contact with VAL 278 (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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235D ILE* 4.1 15.3 - - + +
238D ARG* 3.6 31.7 - - + +
239D LEU* 3.5 39.9 - - + +
242D ALA* 4.3 5.4 - - + -
274D CYS* 2.8 31.7 + - + +
275D ASN 5.2 0.2 - - - -
276D ARG 5.5 0.2 - - - -
277D ARG* 1.3 80.9 - - + +
279D GLN* 1.3 76.9 + - + +
281D LEU* 5.5 2.0 - - + -
289D LEU* 5.9 0.9 - - + -
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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