Contacts of the helix formed by residues 225 - 239 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224D GLY* 1.3 74.4 - - - -
226D THR* 1.3 59.0 + - - +
227D PRO* 3.9 10.6 - - - +
228D ILE* 3.4 16.5 + - - +
229D ALA* 2.8 28.8 + - - +
247D GLY* 3.8 1.1 - - - -
248D GLY* 4.2 1.3 - - - +
501D NAD 2.6 53.6 + - - -
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Residues in contact with THR 226 (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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225D SER* 1.3 69.3 - - - +
227D PRO* 1.3 76.5 - - + +
229D ALA* 4.0 6.3 - - - -
230D GLU* 2.7 23.6 + - - +
247D GLY* 3.7 1.5 - - - -
248D GLY* 3.0 19.8 + - - +
407D GLU* 4.4 2.7 - - - +
408D TYR* 3.1 16.4 + - - -
454D ARG* 2.8 66.4 + - + +
457D PHE* 4.0 8.1 - - + -
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Residues in contact with PRO 227 (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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225D SER* 3.6 12.8 - - - +
226D THR* 1.3 98.4 - - + +
228D ILE* 1.3 68.2 + - + +
230D GLU* 3.6 8.9 - - + +
231D TYR* 3.2 17.8 + - - +
408D TYR* 5.0 5.4 - - - +
454D ARG* 5.6 3.4 - - - +
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Residues in contact with ILE 228 (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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222D PHE* 3.5 21.1 - - + -
225D SER* 3.4 16.0 + - - +
226D THR 3.2 0.4 - - - -
227D PRO* 1.3 78.5 - - + +
229D ALA* 1.3 56.0 + - - +
230D GLU 3.1 1.1 - - - -
231D TYR* 2.9 10.7 + - + +
232D ILE* 2.7 41.7 + - + +
501D NAD 3.5 79.0 - - + +
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Residues in contact with ALA 229 (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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222D PHE* 3.4 16.3 - - + -
225D SER 2.8 19.5 + - - +
226D THR* 3.5 7.0 - - - +
228D ILE* 1.3 75.2 - - - +
230D GLU* 1.3 56.2 + - - +
232D ILE* 3.8 0.8 - - - +
233D TYR* 2.9 32.2 + - - +
245D ALA* 3.6 7.7 - - + +
246D LEU 3.5 22.4 - - - +
457D PHE* 3.8 20.6 - - + -
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Residues in contact with GLU 230 (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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237C SER 5.6 0.2 - - - +
238C ALA 4.6 5.8 - - - +
239C ASN 6.1 0.2 - - - -
240C GLY* 5.9 3.0 + - - +
226D THR 2.7 20.5 + - - +
227D PRO* 3.6 8.1 - - - +
229D ALA* 1.3 73.2 - - - +
231D TYR* 1.3 62.5 - - - +
233D TYR* 3.9 2.4 - - - +
234D ARG* 2.8 51.3 + - + +
454D ARG* 2.6 36.0 + - - -
457D PHE* 3.7 24.4 - - + -
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Residues in contact with TYR 231 (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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205D LYS* 3.4 25.6 + - - -
209D ASP* 2.8 31.8 + - - -
212D LEU* 4.2 10.8 - - + -
213D HIS* 5.0 2.3 - - - -
227D PRO 3.2 10.4 + - - +
228D ILE* 2.9 14.0 + - + +
230D GLU* 1.3 76.5 - - - +
232D ILE* 1.3 67.7 + - + +
234D ARG* 3.3 20.9 + - - +
235D THR* 2.7 65.2 + - + +
501D NAD 4.1 17.3 - + - -
205E LYS* 4.8 11.2 - - + -
206E GLU* 5.9 9.0 - - + -
209E ASP* 4.3 6.0 + - - -
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Residues in contact with ILE 232 (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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145D ILE* 4.3 2.2 - - + -
208D VAL* 3.4 33.2 - - + -
212D LEU* 4.0 22.7 - - + +
220D VAL* 4.0 17.3 - - + -
222D PHE* 3.6 42.2 - - + -
228D ILE* 2.7 29.2 + - + +
229D ALA 3.8 3.4 - - - +
231D TYR* 1.3 83.3 - - + +
233D TYR* 1.3 58.2 + - - +
235D THR* 4.0 3.3 - - - -
236D ALA* 2.9 28.9 + - - +
243D CYS* 4.3 5.6 - - - -
245D ALA* 4.9 0.2 - - + -
501D NAD 4.5 0.9 - - + +
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Residues in contact with TYR 233 (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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233C TYR* 4.8 8.5 + - - -
237C SER* 3.5 42.7 + - - -
240C GLY 4.0 13.0 - - - -
241C LYS 4.8 0.4 - - - -
242C ARG* 4.5 13.5 - - - +
243C CYS 5.1 1.7 + - - -
229D ALA 2.9 17.5 + - - +
230D GLU 3.9 4.0 - - - +
232D ILE* 1.3 75.3 - - - +
234D ARG* 1.3 63.0 + - - +
236D ALA* 3.8 0.9 - - - +
237D SER* 2.7 38.2 + - - -
243D CYS* 3.5 39.9 + - + -
245D ALA* 4.3 2.0 - - + -
457D PHE* 3.5 45.5 - + + -
458D GLY* 3.7 16.9 + - - -
459D ASP* 6.1 0.2 - - - -
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Residues in contact with ARG 234 (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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234C ARG* 5.6 2.9 - - + +
237C SER* 4.3 10.7 - - - +
238C ALA* 4.0 26.8 + - + -
230D GLU* 2.8 53.0 + - - +
231D TYR* 3.6 29.2 - - - +
233D TYR* 1.3 79.2 - - - +
235D THR* 1.3 62.4 + - - +
237D SER* 3.4 4.0 + - - -
238D ALA* 2.9 29.8 + - + +
18E ARG* 3.7 49.2 - - - +
204E ASP* 5.0 2.4 + - - -
206E GLU* 4.2 14.1 - - - +
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Residues in contact with THR 235 (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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212D LEU* 3.7 29.8 - - + -
213D HIS* 4.0 23.8 - - + +
231D TYR* 2.7 49.9 + - + +
232D ILE 4.0 0.2 - - - -
234D ARG* 1.3 81.6 - - - +
236D ALA* 1.3 59.5 + - - +
238D ALA* 3.4 5.5 + - - +
239D ASN* 2.9 35.3 + - - +
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Residues in contact with ALA 236 (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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212D LEU* 4.3 15.2 - - + +
220D VAL* 4.6 2.9 - - + -
232D ILE 2.9 19.7 + - - +
233D TYR 3.8 2.5 - - - +
235D THR* 1.3 72.7 - - - +
237D SER* 1.3 60.7 + - - +
239D ASN* 3.0 20.3 + - - -
240D GLY 3.3 8.1 + - - -
241D LYS* 3.3 31.5 - - + +
243D CYS* 3.8 24.5 - - + -
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Residues in contact with SER 237 (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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233C TYR* 3.9 30.1 + - - -
234C ARG* 4.7 6.7 - - - +
237C SER* 3.3 36.6 + - - -
457C PHE* 5.7 0.5 - - - -
233D TYR* 2.7 34.0 + - - -
234D ARG 3.6 2.9 - - - -
236D ALA* 1.3 77.7 - - - +
238D ALA* 1.3 60.9 + - - +
240D GLY* 3.2 13.3 + - - -
241D LYS 4.0 5.4 + - - -
243D CYS* 4.9 2.3 - - - +
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Residues in contact with ALA 238 (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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230C GLU* 5.0 4.0 - - - +
234C ARG* 4.1 40.7 + - + +
234D ARG* 2.9 18.7 + - + +
235D THR* 3.6 9.4 - - - +
236D ALA 3.3 0.4 - - - -
237D SER* 1.3 75.8 - - - +
239D ASN* 1.3 65.5 + - - +
240D GLY 3.4 1.5 + - - -
206E GLU* 5.9 3.8 - - - +
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Residues in contact with ASN 239 (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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212D LEU 3.5 23.3 + - - +
213D HIS* 3.5 37.5 + - - +
215D ASP* 5.5 4.7 - - - +
235D THR* 2.9 23.7 + - - +
236D ALA 3.0 9.1 + - - +
238D ALA* 1.3 84.0 + - - +
240D GLY* 1.4 53.7 + - - +
241D LYS* 3.1 21.9 + - - -
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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