Contacts of the helix formed by residues 245 - 256 (chain F) in PDB entry 1ZWS
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 245 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113F GLU* 2.5 35.5 + - - -
243F HIS 3.7 1.7 + - - -
244F THR* 1.3 90.0 - - - +
246F GLU* 1.3 62.4 + - - +
247F LEU* 3.4 11.7 + - - +
248F ALA 2.8 18.0 + - - -
249F LYS* 3.2 9.6 + - - +
274F TRP* 3.7 0.7 + - - -
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Residues in contact with GLU 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245F SER* 1.3 71.1 - - - +
247F LEU* 1.3 56.4 + - - +
249F LYS* 3.1 38.8 + - - +
250F ASP* 2.7 36.0 + - - +
253F ARG* 4.5 10.4 + - - +
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Residues in contact with LEU 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245F SER* 3.5 11.6 - - - +
246F GLU* 1.3 82.5 - - - +
248F ALA* 1.3 64.9 + - - +
250F ASP* 3.3 5.6 - - + +
251F PHE 3.1 14.2 + - - -
272F HIS* 3.4 15.1 - - + +
273F PRO* 3.7 17.9 - - + +
274F TRP* 3.3 42.9 - - + +
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Residues in contact with ALA 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F GLU* 3.7 2.9 - - - +
207F THR* 6.4 0.2 - - - -
211F LEU* 3.7 14.4 - - + -
244F THR* 3.5 14.8 - - + -
245F SER* 2.8 24.0 + - - +
247F LEU* 1.3 72.9 - - - +
249F LYS* 1.3 68.6 + - - +
251F PHE* 2.7 25.2 + - - +
252F ILE* 3.1 8.0 + - - +
274F TRP* 3.4 30.7 - - + +
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Residues in contact with LYS 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236F PHE* 3.7 30.6 - - + -
238F GLU* 4.9 5.9 + - - -
241F PHE* 3.8 27.2 + - + -
244F THR* 3.1 37.9 + - + +
245F SER 3.2 5.8 + - - +
246F GLU* 3.1 41.0 + - - +
248F ALA* 1.3 76.4 - - - +
250F ASP* 1.3 63.6 + - - +
252F ILE* 2.9 15.0 - - - +
253F ARG* 2.8 44.4 + - - +
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Residues in contact with ASP 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246F GLU 2.7 21.9 + - - +
247F LEU* 3.3 10.5 - - + +
248F ALA 2.8 2.6 + - - -
249F LYS* 1.3 67.5 - - - +
251F PHE* 1.3 68.8 + - - +
253F ARG* 2.8 28.4 + - - +
254F LYS* 2.6 45.9 + - - +
272F HIS* 2.9 24.2 + - - +
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Residues in contact with PHE 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F ILE* 4.1 14.8 - - + -
124F LEU* 4.4 11.2 - - + -
203F ILE* 4.8 1.3 - - + -
207F THR* 4.1 14.6 - - + -
247F LEU 3.1 3.7 + - - +
248F ALA 2.7 16.1 + - - +
250F ASP* 1.3 75.7 + - - +
252F ILE* 1.3 66.6 + - - +
254F LYS* 3.2 10.7 + - - +
255F LEU* 3.4 35.4 + - + +
264F LEU* 4.5 4.0 - - + -
269F ALA* 3.4 39.9 - - + -
272F HIS* 3.6 34.1 + + + -
274F TRP* 3.6 33.2 - + + -
275F ILE* 4.0 14.6 - - + -
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Residues in contact with ILE 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204F GLY* 3.9 5.2 - - - +
207F THR* 3.4 35.9 - - + -
208F TYR* 3.5 26.2 - - + +
211F LEU* 4.9 5.8 - - + -
234F TYR* 4.3 0.4 - - + -
236F PHE* 3.6 24.7 - - + -
241F PHE* 5.7 1.6 - - + -
248F ALA 3.6 10.8 - - - +
249F LYS* 2.9 18.8 - - - +
250F ASP 2.9 0.2 + - - -
251F PHE* 1.3 77.2 - - + +
253F ARG* 1.3 55.1 + - - +
255F LEU* 2.8 29.2 + - - +
256F LEU* 3.0 42.1 + - + +
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Residues in contact with ARG 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234F TYR* 3.5 16.1 + - - +
236F PHE* 3.5 34.6 - - + -
246F GLU* 4.5 12.3 + - - +
249F LYS* 2.8 40.2 + - - +
250F ASP* 2.8 20.5 + - - +
252F ILE* 1.3 72.4 - - - +
254F LYS* 1.3 59.4 + - + +
255F LEU 3.4 0.3 + - - -
256F LEU 3.6 6.2 - - - +
257F VAL* 3.1 21.5 - - - +
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Residues in contact with LYS 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250F ASP* 2.6 51.0 + - - +
251F PHE 3.7 4.5 - - - +
252F ILE 3.0 0.2 + - - -
253F ARG* 1.3 78.3 - - + +
255F LEU* 1.3 57.1 + - - +
257F VAL* 3.4 15.4 - - - +
262F LYS 4.6 0.9 - - - +
263F ARG* 3.6 1.7 - - - +
264F LEU* 3.3 60.4 + - + +
272F HIS* 4.3 8.7 - - + -
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Residues in contact with LEU 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200F MET* 3.7 44.4 - - + +
201F TRP* 4.0 5.9 - - - -
203F ILE* 3.9 15.5 - - + -
204F GLY* 3.4 37.2 - - - +
251F PHE* 3.7 33.2 - - + +
252F ILE* 2.8 6.0 + - - +
254F LYS* 1.3 75.1 - - - +
256F LEU* 1.3 57.4 + - + +
257F VAL 2.6 19.1 + - - -
263F ARG* 2.9 24.2 + - - -
264F LEU* 4.0 22.4 - - + +
269F ALA* 4.4 2.7 - - + -
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Residues in contact with LEU 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201F TRP* 3.7 41.3 - - + +
204F GLY* 3.9 4.9 - - - -
205F VAL* 3.7 23.1 - - + +
208F TYR* 4.5 1.8 - - + -
216F PRO* 4.5 8.3 - - + -
217F PHE* 4.4 13.9 - - + -
232F VAL* 4.3 11.1 - - - +
234F TYR* 3.6 43.0 + - + +
252F ILE* 3.0 36.8 + - + +
253F ARG 3.6 4.0 - - - +
255F LEU* 1.3 71.1 - - - +
257F VAL* 1.3 63.9 + - - +
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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