Contacts of the helix formed by residues 230 - 245 (chain F) in PDB entry 1Z6Z
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 ASP 230 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199F ASP* 6.1 1.8 - - - -
228F LEU 3.5 4.4 + - - -
229F VAL* 1.3 77.4 - - - +
231F CYS* 1.3 76.6 + - - +
232F LYS* 3.3 22.8 + - - +
233F VAL* 3.1 21.2 + - + +
234F SER* 3.1 18.9 + - - -
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Residues in contact with CYS 231 (chain F).
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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15F GLY 4.3 1.8 - - - -
16F PHE* 3.9 21.9 - - + -
19F THR* 3.5 26.5 - - + +
198F LEU* 4.0 21.1 - - - -
199F ASP* 4.9 6.0 - - - +
200F THR* 3.8 29.2 - - - -
229F VAL 3.4 4.0 + - - -
230F ASP* 1.3 76.1 + - - +
232F LYS* 1.3 57.4 + - - +
234F SER* 3.4 1.7 + - - -
235F ALA* 2.8 31.7 + - - +
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Residues in contact with LYS 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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19F THR* 3.5 21.7 - - + +
23F LEU* 4.1 14.3 - - + +
230F ASP* 3.3 15.5 + - - +
231F CYS* 1.3 78.2 - - - +
233F VAL* 1.3 58.1 + - + +
235F ALA* 3.3 4.1 + - - +
236F GLN* 2.9 43.0 + - - +
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Residues in contact with VAL 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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229F VAL* 4.9 0.9 - - + -
230F ASP* 3.1 30.8 + - + +
232F LYS* 1.3 76.5 - - + +
234F SER* 1.3 63.4 + - - +
236F GLN* 3.3 16.1 + - - +
237F LYS* 3.1 20.3 + - - +
255F PHE* 3.8 24.5 - - + -
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Residues in contact with SER 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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16F PHE* 3.8 4.9 - - - -
193F TYR* 3.1 18.9 + - - -
195F PRO* 2.7 39.3 + - - +
198F LEU* 3.8 18.8 - - - -
229F VAL* 3.9 5.6 - - - +
230F ASP 3.1 9.4 + - - -
231F CYS 3.9 2.0 - - - -
233F VAL* 1.3 77.8 - - - +
235F ALA* 1.3 60.5 + - - +
237F LYS 3.1 1.6 + - - -
238F LEU* 3.0 20.4 + - - +
255F PHE* 3.8 10.9 - - - -
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Residues in contact with ALA 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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16F PHE* 3.6 17.0 - - + -
19F THR* 4.6 2.2 - - + -
20F LEU* 3.8 24.5 - - + +
23F LEU* 3.7 19.3 - - + -
231F CYS 2.8 22.6 + - - +
232F LYS* 3.6 4.5 - - - +
234F SER* 1.3 71.6 - - - +
236F GLN* 1.3 58.2 + - - +
238F LEU* 3.2 4.3 + - - +
239F LEU* 3.0 33.8 + - - +
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Residues in contact with GLN 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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23F LEU* 4.3 18.6 - - + +
232F LYS* 2.9 32.0 + - - +
233F VAL* 3.6 13.9 - - - +
235F ALA* 1.3 72.7 - - - +
237F LYS* 1.3 60.5 + - - +
239F LEU* 3.8 8.7 - - + +
240F SER* 3.0 30.3 + - - -
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Residues in contact with LYS 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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193F TYR* 3.5 18.4 - - + +
233F VAL 3.1 12.9 + - - +
234F SER 3.1 9.4 + - - +
236F GLN* 1.3 74.5 - - - +
238F LEU* 1.3 65.0 + - - +
240F SER* 3.2 12.6 + - - +
241F LEU* 3.0 43.6 + - + +
253F VAL* 5.2 2.6 - - - +
254F ASP 4.0 10.7 + - - -
255F PHE* 3.5 36.8 + - + +
257F ASP* 4.3 11.7 + - - +
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Residues in contact with LEU 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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16F PHE* 4.2 7.9 - - + -
20F LEU* 4.1 26.5 - - + -
95F ILE* 4.8 6.7 - - + -
150F VAL* 4.2 10.8 - - + -
152F ILE* 4.1 23.3 - - + -
191F LEU* 3.8 27.8 - - + -
193F TYR* 3.7 30.7 + - + -
234F SER 3.0 7.6 + - - +
235F ALA* 3.2 8.9 + - - +
237F LYS* 1.3 77.6 - - - +
239F LEU* 1.3 57.5 + - + +
241F LEU* 3.1 9.8 + - - +
242F LEU* 3.0 42.7 + - + +
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Residues in contact with LEU 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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2F LEU* 4.9 5.8 - - + +
20F LEU* 4.1 15.3 - - + -
23F LEU* 3.8 32.5 - - + +
24F LEU* 3.8 28.9 - - + -
27F LEU* 4.0 29.0 - - + +
95F ILE* 5.8 0.7 - - + -
235F ALA 3.0 22.4 + - - +
236F GLN* 3.8 10.1 - - + +
237F LYS 3.3 0.2 - - - -
238F LEU* 1.3 76.3 - - + +
240F SER* 1.3 57.3 + - - +
242F LEU* 3.1 18.5 + - + +
243F GLU* 2.8 29.3 + - - +
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Residues in contact with SER 240 (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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236F GLN 3.0 15.6 + - - -
237F LYS* 3.2 17.8 + - - +
239F LEU* 1.3 73.6 - - - +
241F LEU* 1.3 63.5 + - - +
243F GLU* 3.9 6.7 - - - +
244F LYS* 2.9 47.2 + - - +
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Residues in contact with LEU 241 (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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191F LEU* 4.7 14.1 - - + -
193F TYR* 3.7 37.0 - - + -
237F LYS* 3.0 31.1 + - + +
238F LEU* 3.2 9.6 - - - +
240F SER* 1.3 78.6 + - - +
242F LEU* 1.3 56.6 + - - +
244F LYS* 4.0 18.5 + - - +
245F ASP* 3.0 25.5 + - - -
246F GLU 4.4 0.5 + - - -
247F PHE* 3.7 23.8 - - + +
253F VAL* 3.8 25.8 - - + -
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Residues in contact with LEU 242 (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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2F LEU* 4.6 7.4 - - + -
91F ARG* 3.8 25.1 + - - +
93F LEU* 4.1 29.4 - - + -
95F ILE* 4.9 4.0 - - + -
148F THR* 3.8 30.1 - - + -
150F VAL* 4.0 14.1 - - + -
191F LEU* 4.2 12.6 - - + -
238F LEU* 3.0 32.9 + - + +
239F LEU* 3.1 19.9 + - + +
241F LEU* 1.3 73.9 - - - +
243F GLU* 1.3 64.7 + - - +
245F ASP* 3.4 16.6 + - - +
247F PHE* 4.5 7.0 - - + -
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Residues in contact with GLU 243 (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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0F HIS* 4.3 31.0 - - + +
1F MET 5.4 4.3 - - - +
2F LEU* 4.7 12.5 - - + +
27F LEU* 6.4 2.0 - - + -
91F ARG* 4.8 4.8 + - - +
239F LEU 2.8 15.7 + - - +
240F SER* 3.9 7.9 - - - +
242F LEU* 1.3 79.0 - - - +
244F LYS* 1.3 64.5 + - + +
245F ASP* 3.4 4.0 + - - +
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Residues in contact with LYS 244 (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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240F SER* 2.9 30.0 + - - +
241F LEU* 4.0 24.8 + - - +
243F GLU* 1.3 79.5 - - + +
245F ASP* 1.3 67.9 + - - +
246F GLU* 3.2 37.6 + - + +
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Residues in contact with ASP 245 (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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91F ARG* 5.2 2.7 + - - +
146F ASN* 3.2 26.5 + - - -
148F THR* 4.9 2.3 + - - -
189F ARG* 2.8 46.2 + - - +
241F LEU 3.0 15.2 + - - -
242F LEU 3.4 11.9 + - - +
243F GLU 3.2 4.4 - - - +
244F LYS* 1.3 76.5 - - - +
246F GLU* 1.3 57.7 + - - +
247F PHE* 3.9 10.1 - - - -
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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