Contacts of the helix formed by residues 245 - 256 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113E GLU* 2.4 41.4 + - - -
243E HIS 3.8 1.0 + - - -
244E THR* 1.3 87.1 - - - +
246E GLU* 1.3 62.2 - - - +
247E LEU* 3.4 12.6 + - - +
248E ALA* 2.8 20.8 + - - +
249E LYS* 3.2 5.7 + - - +
274E TRP* 3.6 0.9 + - - -
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Residues in contact with GLU 246 (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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244E THR 5.4 0.2 - - - +
245E SER* 1.3 70.4 - - - +
247E LEU* 1.3 61.1 + - - +
249E LYS* 3.0 38.5 + - - +
250E ASP* 2.8 32.1 + - - +
253E ARG* 4.5 11.8 + - - +
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Residues in contact with LEU 247 (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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245E SER* 3.6 11.2 - - - +
246E GLU* 1.3 81.1 - - - +
248E ALA* 1.3 64.4 + - - +
250E ASP* 3.4 5.9 - - + +
251E PHE 3.2 12.8 + - - -
272E HIS* 3.3 15.5 - - + +
273E PRO* 3.7 19.1 - - + +
274E TRP* 3.2 44.3 - - + +
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Residues in contact with ALA 248 (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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113E GLU* 3.6 2.9 - - - +
211E LEU* 3.7 13.5 - - + -
244E THR* 3.4 16.4 - - + -
245E SER* 2.8 23.1 + - - +
247E LEU* 1.3 75.7 - - - +
249E LYS* 1.3 65.8 + - - +
251E PHE* 2.7 24.3 + - - +
252E ILE* 3.2 8.4 + - - +
274E TRP* 3.4 28.2 - - + +
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Residues in contact with LYS 249 (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* 6.0 0.2 - - - -
236E PHE* 3.4 31.3 - - + -
238E GLU* 5.1 4.1 + - - -
241E PHE* 3.9 29.8 + - + -
244E THR* 3.3 34.6 + - + +
245E SER 3.5 5.6 - - - +
246E GLU* 3.0 41.7 + - - +
248E ALA* 1.3 78.5 - - - +
250E ASP* 1.3 57.4 + - - +
252E ILE* 2.9 14.7 - - - +
253E ARG* 2.8 47.2 + - - +
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Residues in contact with ASP 250 (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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246E GLU 2.8 21.7 + - - +
247E LEU* 3.4 11.2 - - + +
248E ALA 2.8 2.6 + - - -
249E LYS* 1.3 68.4 - - - +
251E PHE* 1.3 66.5 + - - +
253E ARG* 2.8 27.8 + - - +
254E LYS* 2.7 48.5 + - - +
272E HIS* 3.0 18.5 + - - +
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Residues in contact with PHE 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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120E ILE* 4.1 20.9 - - + -
124E LEU* 4.3 10.8 - - + -
203E ILE* 4.8 3.8 - - + -
207E THR* 4.1 15.3 - - + -
247E LEU 3.2 7.8 + - - +
248E ALA 2.7 15.5 + - - +
250E ASP* 1.3 76.6 + - - +
252E ILE* 1.3 65.8 + - - +
254E LYS* 3.2 10.6 + - - +
255E LEU* 3.3 37.6 + - + +
264E LEU* 4.6 2.9 - - + -
269E ALA* 3.3 38.6 - - + -
272E HIS* 3.6 31.1 + + + -
274E TRP* 3.6 24.9 - + + -
275E ILE* 3.9 15.5 - - + -
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Residues in contact with ILE 252 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204E GLY* 4.0 4.9 - - - +
207E THR* 3.5 40.4 - - + +
208E TYR* 3.6 21.1 - - + +
211E LEU* 5.0 5.4 - - + -
234E TYR* 4.4 0.2 - - + -
236E PHE* 3.6 24.2 - - + -
241E PHE* 5.7 1.8 - - + -
248E ALA 3.6 11.0 - - - +
249E LYS* 2.9 18.6 - - - +
251E PHE* 1.3 75.3 - - + +
253E ARG* 1.3 56.2 + - - +
255E LEU* 2.8 30.5 + - - +
256E LEU* 2.9 39.8 + - + +
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Residues in contact with ARG 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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234E TYR* 3.6 15.0 + - - +
236E PHE* 3.6 33.4 - - + -
246E GLU* 4.5 14.5 + - - -
249E LYS* 2.8 43.7 + - - +
250E ASP* 2.8 22.7 + - - +
252E ILE* 1.3 72.1 - - - +
254E LYS* 1.3 63.0 + - + +
255E LEU 3.4 0.3 + - - -
256E LEU 3.6 6.4 - - - +
257E VAL* 3.2 17.7 - - - +
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Residues in contact with LYS 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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250E ASP* 2.7 48.4 + - - +
251E PHE 3.7 4.3 - - - +
252E ILE 3.0 0.4 + - - -
253E ARG* 1.3 77.3 - - + +
255E LEU* 1.3 57.4 + - - +
257E VAL* 3.6 14.5 - - - +
262E LYS 4.6 1.0 - - - +
263E ARG* 3.7 1.0 - - - +
264E LEU* 3.2 61.5 + - + +
272E HIS* 4.4 8.3 - - + -
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Residues in contact with LEU 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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200E MET* 3.8 48.5 - - + +
201E TRP* 3.9 7.2 - - - -
203E ILE* 4.1 7.2 - - + -
204E GLY* 3.6 30.5 - - - +
251E PHE* 3.3 43.3 + - + +
252E ILE 2.8 6.3 + - - +
254E LYS* 1.3 79.5 - - - +
256E LEU* 1.3 61.9 + - - +
257E VAL 2.9 9.0 + - - -
263E ARG* 3.1 22.3 + - - -
264E LEU* 3.9 22.4 - - + +
269E ALA* 4.4 1.8 - - + -
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Residues in contact with LEU 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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201E TRP* 3.6 36.8 - - + +
204E GLY* 4.0 4.9 - - - -
205E VAL* 3.7 22.9 - - + +
208E TYR* 4.5 2.0 - - + -
216E PRO* 4.5 13.7 - - + -
217E PHE* 4.4 13.2 - - + -
232E VAL* 4.3 10.2 - - - +
234E TYR* 3.7 41.8 + - + +
252E ILE* 2.9 41.9 + - + +
253E ARG 3.6 4.7 - - - +
255E LEU* 1.3 73.7 - - - +
257E VAL* 1.3 62.7 + - - +
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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