Contacts of the helix formed by residues 225 - 239 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222F PHE* 3.9 3.8 - - - -
224F GLY* 1.3 71.7 - - - -
226F THR* 1.3 55.3 + - - +
227F PRO* 3.9 9.3 - - - +
228F ILE* 3.0 28.9 + - - +
229F ALA* 2.7 34.5 + - - +
247F GLY* 3.9 2.0 - - - -
248F GLY* 4.3 4.9 - - - +
382F GLU* 5.6 3.4 - - - -
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Residues in contact with THR 226 (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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225F SER* 1.3 70.8 - - - +
227F PRO* 1.3 66.8 - - - +
229F ALA* 3.2 2.0 + - - +
230F GLU* 2.8 29.7 + - - +
247F GLY* 3.5 8.6 - - - -
248F GLY* 2.7 28.3 + - - +
408F TYR* 3.0 27.0 + - + -
454F ARG* 3.3 53.5 + - - +
457F PHE* 4.0 6.3 - - + -
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Residues in contact with PRO 227 (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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225F SER* 3.4 12.8 - - - +
226F THR* 1.3 96.0 - - + +
228F ILE* 1.3 65.3 - - + +
230F GLU* 3.6 11.2 - - + +
231F TYR* 3.3 20.8 + - - +
408F TYR* 5.1 4.7 - - - +
454F ARG* 5.6 4.0 - - - +
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Residues in contact with ILE 228 (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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222F PHE* 3.7 25.6 - - + -
225F SER* 3.0 23.4 + - - +
227F PRO* 1.3 80.6 - - + +
229F ALA* 1.3 59.5 + - - +
231F TYR* 3.2 14.2 + - + +
232F ILE* 2.9 43.3 + - + +
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Residues in contact with ALA 229 (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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222F PHE* 3.7 16.2 - - + -
225F SER 2.7 20.9 + - - +
226F THR* 3.4 7.9 - - - +
228F ILE* 1.3 72.5 - - - +
230F GLU* 1.3 53.3 + - - +
232F ILE* 3.0 4.0 + - - +
233F TYR* 2.7 35.9 + - - +
245F ALA* 3.8 15.6 - - + +
246F LEU 3.9 20.9 - - - +
457F PHE* 4.0 14.6 - - + -
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Residues in contact with GLU 230 (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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238E ALA 4.7 3.8 - - - +
239E ASN 5.9 0.7 - - - -
240E GLY* 5.7 2.8 + - - -
226F THR 2.8 18.5 + - - +
227F PRO* 3.6 9.9 - - - +
229F ALA* 1.3 70.7 - - - +
231F TYR* 1.3 57.9 + - - +
233F TYR* 3.8 4.7 - - - +
234F ARG* 2.9 67.1 + - + +
454F ARG* 2.6 38.8 + - - -
457F PHE* 4.0 20.5 - - + -
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Residues in contact with TYR 231 (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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16D ASN 4.3 3.6 + - - -
17D THR* 3.7 30.3 - - + -
205F LYS* 3.4 26.9 + - + -
208F VAL* 4.9 3.1 - - + -
209F ASP* 2.5 36.7 + - - -
212F LEU* 4.5 6.5 - - + +
227F PRO 3.3 10.3 + - - +
228F ILE* 3.2 18.9 + - + +
230F GLU* 1.3 78.7 - - - +
232F ILE* 1.3 76.8 + - + +
234F ARG* 3.9 14.3 - - - +
235F THR* 2.7 64.5 + - - +
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Residues in contact with ILE 232 (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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145F ILE* 4.1 7.6 - - + -
208F VAL* 3.6 31.6 - - + -
212F LEU* 4.0 14.0 - - + +
220F VAL* 3.9 28.7 - - + -
222F PHE* 3.7 35.9 - - + -
228F ILE* 2.9 26.9 + - + +
229F ALA 3.4 4.9 - - - +
231F TYR* 1.3 84.5 - - + +
233F TYR* 1.3 62.6 + - - +
235F THR* 3.9 0.7 - - - -
236F ALA* 2.9 33.8 + - - +
243F CYS* 4.2 4.5 - - - -
245F ALA* 4.9 0.2 - - + -
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Residues in contact with TYR 233 (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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233E TYR* 4.9 8.4 + - - -
237E SER* 3.8 41.6 + - - -
240E GLY 4.3 9.4 - - - -
241E LYS 4.7 1.0 + - - -
242E ARG* 4.4 13.5 - - - +
243E CYS 5.0 1.6 + - - -
229F ALA 2.7 19.4 + - - +
230F GLU* 3.8 3.6 - - - +
232F ILE* 1.3 74.1 - - - +
234F ARG* 1.3 62.9 + - - +
236F ALA* 3.6 1.0 - - - +
237F SER* 2.9 36.3 + - - -
243F CYS* 3.5 38.8 - - + -
245F ALA* 4.3 2.7 - - + -
457F PHE* 3.4 49.8 - + + -
458F GLY* 3.4 17.6 + - - -
459F ASP* 5.9 0.9 - - - -
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Residues in contact with ARG 234 (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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17D THR* 5.5 14.2 - - - +
38D SER* 5.7 9.2 - - - -
206D GLU* 5.7 2.2 - - - -
234E ARG* 5.3 4.4 - - + +
237E SER* 4.7 8.0 - - - +
238E ALA* 3.8 43.6 + - + +
230F GLU* 2.9 65.6 + - + +
231F TYR* 3.9 15.9 - - - +
233F TYR* 1.3 74.4 - - - +
235F THR* 1.3 64.2 + - - +
237F SER* 3.4 5.1 + - - -
238F ALA* 3.0 26.6 + - + +
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Residues in contact with THR 235 (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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17D THR* 3.6 28.1 + - - +
212F LEU* 3.9 23.1 - - + -
213F HIS* 3.7 26.5 - - + +
231F TYR* 2.7 50.9 + - - +
232F ILE 4.0 2.5 - - - -
234F ARG* 1.3 73.8 - - - +
236F ALA* 1.3 60.2 + - - +
238F ALA* 3.5 3.9 + - - +
239F ASN* 2.9 31.2 + - - +
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Residues in contact with ALA 236 (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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212F LEU* 4.2 17.0 - - + +
220F VAL* 4.7 2.2 - - + -
232F ILE 2.9 22.2 + - - +
233F TYR 3.6 2.9 - - - +
235F THR* 1.3 72.5 - - - +
237F SER* 1.3 64.2 + - - +
239F ASN* 3.0 16.2 + - - +
240F GLY 3.2 8.7 + - - -
241F LYS* 3.4 27.0 + - + +
243F CYS* 3.8 25.6 - - + -
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Residues in contact with SER 237 (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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230E GLU* 6.1 1.2 - - - +
233E TYR* 3.6 37.1 + - - -
234E ARG* 4.7 5.4 - - - +
237E SER* 3.2 39.3 + - - -
233F TYR* 2.9 27.9 + - - -
234F ARG 3.7 2.9 - - - -
236F ALA* 1.3 76.6 - - - +
238F ALA* 1.3 63.1 + - - +
240F GLY* 3.0 11.6 + - - -
241F LYS 4.0 4.2 + - - -
243F CYS* 5.3 1.2 - - - +
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Residues in contact with ALA 238 (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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17D THR 5.2 0.4 - - - +
18D ARG* 4.0 30.9 - - + -
230E GLU* 4.7 7.4 - - - +
234E ARG* 4.0 36.3 + - + +
234F ARG* 3.0 15.0 + - + +
235F THR* 3.5 13.0 - - - +
237F SER* 1.3 77.9 - - - +
239F ASN* 1.3 63.4 + - - +
240F GLY* 3.5 0.5 + - - -
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Residues in contact with ASN 239 (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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17D THR 5.0 1.6 + - - -
18D ARG* 5.7 3.2 - - - +
230E GLU* 5.6 2.5 - - - -
212F LEU 3.6 12.1 + - - +
213F HIS* 3.5 39.8 + - - +
215F ASP* 5.2 8.6 - - - +
235F THR* 2.9 23.2 + - - +
236F ALA 3.0 9.3 + - - +
238F ALA* 1.3 81.4 - - - +
240F GLY* 1.3 55.2 + - - +
241F LYS* 3.4 25.8 + - - +
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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