Contacts of the helix formed by residues 225 - 239 (chain E) in PDB entry 4ZZ7
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 225 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224E GLY* 1.3 74.0 - - - -
226E THR* 1.3 53.6 + - - +
227E PRO* 3.8 11.4 - - - +
228E ILE* 3.3 14.6 + - - +
229E ALA* 2.8 33.8 + - - +
247E GLY* 4.0 0.9 - - - -
248E GLY 4.4 0.4 - - - +
501E NAD 2.6 56.8 + - - -
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Residues in contact with THR 226 (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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225E SER* 1.3 69.1 - - - +
227E PRO* 1.3 66.3 - - - +
229E ALA* 3.1 6.9 + - - -
230E GLU* 2.7 33.4 + - - +
247E GLY* 4.0 1.8 - - - -
248E GLY* 3.0 15.3 + - - +
407E GLU* 4.3 3.1 - - - +
408E TYR* 2.9 31.6 + - - -
454E ARG* 3.3 57.2 + - + +
457E PHE* 4.0 6.3 - - + -
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Residues in contact with PRO 227 (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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225E SER* 3.6 13.5 - - - +
226E THR* 1.3 95.1 - - + +
228E ILE* 1.3 62.4 - - + +
230E GLU* 3.7 11.4 - - + +
231E TYR* 3.3 22.0 + - - +
408E TYR* 5.0 5.2 - - - +
454E ARG* 5.4 4.5 - - - +
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Residues in contact with ILE 228 (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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222E PHE* 3.6 20.9 - - + -
225E SER* 3.3 17.8 + - - +
226E THR 3.1 0.4 - - - -
227E PRO* 1.3 79.8 - - + +
229E ALA* 1.3 58.3 + - - +
230E GLU 3.2 0.2 - - - -
231E TYR* 3.1 7.0 + - + +
232E ILE* 2.8 43.6 + - + +
501E NAD 3.3 80.1 - - + +
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Residues in contact with ALA 229 (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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222E PHE* 3.6 16.3 - - + -
225E SER 2.8 18.5 + - - +
226E THR* 3.3 7.9 - - - +
228E ILE* 1.3 75.7 - - - +
230E GLU* 1.3 53.0 + - - +
232E ILE* 3.0 4.9 + - - +
233E TYR* 2.8 35.2 + - - +
245E ALA* 3.7 7.8 - - + +
246E LEU 3.8 21.5 - - - +
457E PHE* 3.9 19.7 - - + -
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Residues in contact with GLU 230 (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 THR 2.7 18.8 + - - +
227E PRO* 3.7 8.9 - - - +
229E ALA* 1.3 71.9 - - - +
231E TYR* 1.3 63.4 + - - +
233E TYR* 4.0 4.7 - - + +
234E ARG* 3.1 48.8 + - + +
454E ARG* 2.7 36.7 + - - -
457E PHE* 4.0 21.7 - - + -
238F ALA 4.7 7.9 - - - +
239F ASN 5.6 1.6 - - - -
240F GLY* 5.6 3.4 - - - -
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Residues in contact with TYR 231 (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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205D LYS* 4.0 24.8 - - + +
209D ASP* 5.0 1.0 + - - -
205E LYS* 3.6 20.8 - - - -
209E ASP* 2.9 29.6 + - - -
212E LEU* 4.2 11.0 - - + -
213E HIS* 4.9 3.3 - - - -
227E PRO 3.3 11.5 + - - +
228E ILE* 3.1 12.2 + - + +
230E GLU* 1.3 79.3 - - - +
232E ILE* 1.3 63.8 + - + +
234E ARG* 3.7 19.7 - - - +
235E THR* 2.7 64.6 + - + +
501E NAD 4.0 21.1 - + - +
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Residues in contact with ILE 232 (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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145E ILE* 4.3 1.1 - - + -
208E VAL* 3.4 33.0 - - + -
212E LEU* 3.9 13.2 - - + +
220E VAL* 3.9 27.4 - - + -
222E PHE* 3.7 36.6 - - + -
228E ILE* 2.8 25.1 + - + +
229E ALA 3.5 5.6 - - - +
231E TYR* 1.3 84.4 - - + +
233E TYR* 1.3 57.0 + - - +
235E THR* 3.9 3.0 - - - -
236E ALA* 2.9 31.0 + - - +
243E CYS* 4.3 5.4 - - - -
245E ALA* 5.1 0.2 - - + -
501E NAD 4.1 6.5 - - + +
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Residues in contact with TYR 233 (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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229E ALA 2.8 19.1 + - - +
230E GLU* 4.0 4.5 - - + +
232E ILE* 1.3 73.4 - - - +
234E ARG* 1.3 60.7 + - - +
236E ALA* 4.1 0.5 - - - +
237E SER* 2.7 42.5 + - - -
243E CYS* 3.6 40.1 - - + -
245E ALA* 4.2 2.7 - - + +
457E PHE* 3.5 45.1 - + + -
458E GLY* 3.8 17.0 - - - -
233F TYR* 4.9 8.7 + - - -
237F SER* 3.6 41.5 + - - -
240F GLY 4.4 10.5 - - - -
241F LYS 4.8 0.7 - - - -
242F ARG* 4.3 15.8 - - - +
243F CYS 5.0 1.4 + - - -
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Residues in contact with ARG 234 (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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18D ARG* 4.1 44.7 - - - +
204D ASP* 5.2 4.0 + - - -
206D GLU* 5.1 4.0 - - - +
230E GLU* 3.1 47.2 + - + +
231E TYR* 3.7 28.8 - - - +
233E TYR* 1.3 79.3 - - - +
235E THR* 1.3 61.3 + - - +
237E SER* 3.8 5.0 - - - -
238E ALA* 2.9 32.7 + - + +
234F ARG* 5.3 3.8 - - + +
237F SER 4.7 9.4 + - - +
238F ALA* 4.0 31.0 + - + +
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Residues in contact with THR 235 (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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212E LEU* 3.8 25.8 - - + -
213E HIS* 4.0 24.5 - - + +
231E TYR* 2.7 47.4 + - + +
232E ILE 3.9 2.2 - - - -
234E ARG* 1.3 77.2 - - - +
236E ALA* 1.3 63.8 + - - +
238E ALA* 3.2 6.5 + - + +
239E ASN* 2.8 38.5 + - - +
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Residues in contact with ALA 236 (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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212E LEU* 4.2 19.2 - - + +
220E VAL* 4.4 3.6 - - + -
232E ILE 2.9 17.8 + - - +
235E THR* 1.3 76.5 - - - +
237E SER* 1.3 62.4 + - - +
239E ASN* 3.3 10.9 + - - -
241E LYS* 3.1 42.6 + - + +
243E CYS* 3.8 26.7 - - + -
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Residues in contact with SER 237 (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 TYR* 2.7 35.3 + - - -
234E ARG 3.8 1.8 - - - -
236E ALA* 1.3 79.1 - - - +
238E ALA* 1.3 60.1 + - - +
240E GLY* 3.3 11.6 + - - -
241E LYS 4.1 4.1 + - - -
243E CYS* 5.0 1.9 - - - +
233F TYR* 3.8 33.1 + - - -
234F ARG* 4.7 6.2 + - - +
237F SER* 3.2 36.4 + - - -
457F PHE* 5.6 0.2 - - - -
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Residues in contact with ALA 238 (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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206D GLU* 5.3 9.6 - - - +
234E ARG* 2.9 22.0 + - + +
235E THR* 3.2 9.8 + - + +
237E SER* 1.3 76.8 - - - +
239E ASN* 1.3 61.2 + - - +
240E GLY 3.4 0.7 - - - -
230F GLU* 4.7 2.8 - - - +
234F ARG* 3.8 47.5 + - + +
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Residues in contact with ASN 239 (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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212E LEU 3.6 23.9 + - - +
213E HIS* 3.5 30.3 + - - +
215E ASP* 5.5 5.6 - - - +
235E THR* 2.8 35.7 + - - +
236E ALA 3.3 4.9 + - - +
237E SER 3.2 0.8 - - - -
238E ALA* 1.3 81.3 - - - +
240E GLY* 1.3 55.7 + - - +
241E LYS* 3.5 18.0 + - - +
230F GLU* 5.9 1.3 - - - -
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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