Contacts of the helix formed by residues 225 - 239 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222B PHE* 4.1 3.4 - - - -
224B GLY* 1.3 73.3 - - - -
226B THR* 1.3 54.7 + - - +
227B PRO* 3.5 11.5 - - - +
228B ILE* 3.2 27.9 + - - +
229B ALA* 2.7 34.3 + - - +
247B GLY* 4.0 1.6 - - - -
248B GLY* 4.6 3.4 - - - +
382B GLU* 5.8 2.9 - - - -
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Residues in contact with THR 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B SER* 1.3 70.0 - - - +
227B PRO* 1.3 64.4 - - - +
228B ILE 3.0 0.3 + - - -
229B ALA* 3.4 1.8 - - - +
230B GLU* 2.8 35.6 + - - +
247B GLY* 3.8 7.9 - - - -
248B GLY* 2.7 29.1 + - - +
407B GLU* 4.6 0.4 - - - +
408B TYR* 2.9 27.7 + - + -
454B ARG* 3.5 53.1 + - - +
457B PHE* 4.2 6.3 - - + -
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Residues in contact with PRO 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B SER* 3.4 15.3 - - - +
226B THR* 1.3 96.0 - - + +
228B ILE* 1.3 64.3 + - + +
230B GLU* 3.6 12.6 - - + +
231B TYR* 3.4 18.4 + - - +
408B TYR* 5.3 2.7 - - - +
454B ARG* 5.8 1.8 - - - +
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Residues in contact with ILE 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B PHE* 3.5 28.9 - - + -
225B SER* 3.1 20.5 + - - +
227B PRO* 1.3 78.9 - - + +
229B ALA* 1.3 68.6 - - - +
230B GLU 3.1 1.1 - - - -
231B TYR* 2.9 12.2 + - + +
232B ILE* 2.8 33.9 + - + +
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Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B PHE* 3.4 18.6 - - + -
225B SER 2.7 21.6 + - - +
226B THR 3.4 3.8 - - - +
228B ILE* 1.3 71.9 - - - +
230B GLU* 1.3 57.4 + - - +
232B ILE* 3.3 0.7 + - - +
233B TYR* 2.9 26.0 + - - +
245B ALA* 3.5 18.1 - - + +
246B LEU 3.6 27.1 - - - +
247B GLY* 4.1 2.2 - - - -
457B PHE* 4.0 12.1 - - + -
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Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A SER 5.6 0.5 - - - +
238A ALA 4.7 5.3 - - - +
240A GLY* 5.8 1.9 + - - -
226B THR 2.8 19.2 + - - +
227B PRO* 3.6 10.9 - - - +
229B ALA* 1.3 72.7 - - - +
231B TYR* 1.3 57.8 + - - +
233B TYR* 3.5 3.9 + - - +
234B ARG* 3.0 59.2 + - - +
454B ARG* 3.1 36.8 + - - -
457B PHE* 3.9 22.7 - - + -
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Residues in contact with TYR 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B LYS* 3.5 25.7 + - + -
208B VAL* 5.1 1.3 - - + -
209B ASP* 2.6 36.6 + - - -
212B LEU* 4.0 11.9 - - + -
213B HIS* 4.9 2.3 - - - -
227B PRO 3.4 10.8 + - - +
228B ILE* 2.9 16.8 + - + +
230B GLU* 1.3 76.4 - - - +
232B ILE* 1.3 75.3 + - + +
234B ARG* 3.4 17.6 + - - +
235B THR* 2.9 59.5 + - - +
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Residues in contact with ILE 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B ILE* 4.3 4.7 - - + -
208B VAL* 3.4 33.9 - - + -
212B LEU* 3.8 13.8 - - + +
220B VAL* 3.9 21.3 - - + -
222B PHE* 3.7 40.8 - - + -
228B ILE* 2.8 32.4 + - + +
229B ALA 3.6 3.8 - - - +
231B TYR* 1.3 82.4 - - + +
233B TYR* 1.3 53.6 + - - +
235B THR* 3.3 2.7 + - - -
236B ALA* 2.8 34.0 + - - +
243B CYS* 4.2 7.4 - - - -
245B ALA* 5.1 0.2 - - + -
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Residues in contact with TYR 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A TYR* 4.8 9.3 + - - -
237A SER* 3.6 41.9 + - - -
240A GLY 4.8 8.3 - - - -
241A LYS 4.8 1.6 - - - -
242A ARG* 4.3 14.4 - - - +
243A CYS 5.0 1.6 + - - -
229B ALA 2.9 16.7 + - - +
230B GLU* 3.8 4.5 - - - +
232B ILE* 1.3 76.4 - - - +
234B ARG* 1.3 55.5 + - - +
236B ALA* 4.2 0.2 - - - +
237B SER* 2.5 44.8 + - - -
243B CYS* 3.4 45.3 - - + -
245B ALA* 4.3 2.2 - - + +
457B PHE* 3.5 42.8 - + + -
458B GLY* 3.5 17.9 + - - -
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Residues in contact with ARG 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A ARG* 5.4 5.0 - - + +
237A SER* 4.7 11.2 + - - +
238A ALA* 4.1 38.0 + - + +
230B GLU* 3.0 52.9 + - + +
231B TYR* 3.8 27.5 - - - +
233B TYR* 1.3 76.3 - - - +
235B THR* 1.3 59.9 + - - +
237B SER* 3.8 4.6 - - - -
238B ALA* 3.0 31.7 + - + +
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Residues in contact with THR 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B LEU* 3.8 24.7 - - + -
213B HIS* 3.6 35.0 - - + +
231B TYR* 2.9 46.8 + - - +
232B ILE 3.9 2.2 - - - -
234B ARG* 1.3 81.6 - - - +
236B ALA* 1.3 59.4 + - - +
238B ALA* 3.4 4.0 + - - +
239B ASN* 2.9 31.9 + - - +
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Residues in contact with ALA 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B LEU* 4.4 8.9 - - + +
220B VAL* 4.4 10.5 - - + -
232B ILE 2.8 21.2 + - - +
235B THR* 1.3 72.4 - - - +
237B SER* 1.3 66.1 + - - +
239B ASN* 3.2 12.3 + - - -
240B GLY 3.2 6.2 + - - -
241B LYS* 3.2 37.1 + - + +
243B CYS* 4.0 24.0 - - + -
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Residues in contact with SER 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLU* 5.9 1.9 - - - +
233A TYR* 3.7 31.5 + - - -
234A ARG* 5.1 4.8 - - - +
237A SER* 3.2 36.2 + - - -
457A PHE* 5.3 0.7 - - - -
233B TYR* 2.5 35.3 + - - -
234B ARG 3.8 3.1 - - - -
236B ALA* 1.3 75.7 - - - +
238B ALA* 1.3 62.3 + - - +
240B GLY* 3.0 15.4 + - - -
241B LYS 4.0 3.8 + - - -
243B CYS* 5.0 1.9 - - - +
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Residues in contact with ALA 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLU* 4.3 6.1 - - - +
234A ARG* 3.8 46.2 + - + +
234B ARG* 3.0 21.1 + - + +
235B THR* 3.5 7.6 - - - +
236B ALA 3.3 0.2 - - - -
237B SER* 1.3 77.8 - - - +
239B ASN* 1.3 63.5 + - - +
240B GLY 3.7 0.2 + - - -
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Residues in contact with ASN 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLU* 5.9 0.9 - - - -
212B LEU 3.4 22.4 - - - +
213B HIS* 3.2 44.7 + - - +
235B THR* 2.9 24.1 + - - +
236B ALA 3.2 8.1 + - - +
237B SER 3.2 0.6 - - - -
238B ALA* 1.3 81.4 - - - +
240B GLY* 1.3 57.7 + - - +
241B LYS* 3.4 14.5 + - - -
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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