Contacts of the helix formed by residues 219 - 235 (chain F) in PDB entry 3FZ7
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 PHE 219 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209F PHE* 4.7 0.7 - + - -
217F TYR* 3.9 33.4 - + + -
218F GLU* 1.3 71.2 - - - +
220F PRO* 1.3 69.5 - - - +
221F GLN* 3.3 1.9 + - + +
222F PRO* 3.3 26.4 - - + +
223F LEU* 3.6 14.9 - - - +
258F ILE* 3.9 32.8 - - + -
372F ASP 3.3 26.7 - - - -
373F GLU* 4.2 11.7 - - + -
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Residues in contact with PRO 220 (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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207F PRO* 4.3 8.5 - - + -
209F PHE* 4.0 8.3 - - + -
218F GLU 3.2 10.8 - - - +
219F PHE* 1.3 85.7 - - + +
221F GLN* 1.3 53.0 + - - +
223F LEU* 3.2 13.0 + - + +
224F HIS* 2.6 36.6 + - - +
240F MET* 3.7 4.5 - - + +
242F ILE* 3.7 25.6 - - + -
258F ILE* 5.5 0.2 - - + -
259F VAL 4.5 1.1 - - - +
260F TRP* 3.7 34.5 - - + +
264F LEU* 3.7 20.4 - - + -
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Residues in contact with GLN 221 (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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219F PHE* 4.4 1.3 - - + +
220F PRO* 1.3 78.0 - - - +
222F PRO* 1.3 76.5 - - + +
224F HIS* 2.9 11.1 + - - +
225F ASP* 2.8 36.5 + - - +
259F VAL* 3.8 38.3 + - - +
264F LEU* 3.6 23.9 - - + +
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Residues in contact with PRO 222 (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 PRO* 4.3 21.8 - - + +
219F PHE* 3.3 27.8 - - + +
221F GLN* 1.3 96.7 - - + +
223F LEU* 1.3 60.9 + - + +
225F ASP* 3.1 16.1 + - + +
226F ALA* 3.0 21.3 + - - +
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Residues in contact with LEU 223 (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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189F MET* 3.7 44.2 - - + +
190F ASP 3.8 2.9 - - - +
191F PRO* 3.6 31.6 - - + -
194F MET* 3.4 27.2 - - - +
207F PRO* 3.9 23.6 - - + -
218F GLU* 5.1 4.3 - - + -
219F PHE 3.6 19.5 - - - +
220F PRO* 3.5 4.7 - - + +
221F GLN 3.2 0.4 - - - -
222F PRO* 1.3 76.6 - - + +
224F HIS* 1.3 63.9 + - - +
226F ALA* 3.0 4.1 + - - -
227F LEU* 2.9 20.4 + - - +
240F MET* 3.5 11.2 - - + -
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Residues in contact with HIS 224 (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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220F PRO 2.6 17.9 + - - +
221F GLN* 2.9 10.2 + - - +
223F LEU* 1.3 72.1 - - - +
225F ASP* 1.3 64.9 + - - +
227F LEU* 3.1 6.0 + - - +
228F ASP* 3.1 45.7 + - - +
240F MET* 3.4 14.3 - - + +
264F LEU* 3.5 34.4 - - + +
265F PRO* 3.4 27.1 - - + -
266F ARG* 3.0 45.6 + - + +
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Residues in contact with ASP 225 (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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221F GLN* 2.8 34.7 + - - +
222F PRO* 3.1 15.1 + - + +
224F HIS* 1.3 74.6 + - - +
226F ALA* 1.3 63.3 + - - +
228F ASP* 3.2 20.3 + - - +
229F LYS* 3.2 13.9 + - - +
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Residues in contact with ALA 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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191F PRO* 4.1 15.5 - - + -
194F MET* 3.7 16.2 - - + -
195F ILE* 3.7 17.5 - - + +
222F PRO 3.0 12.2 + - - +
223F LEU 3.0 7.4 + - - +
225F ASP* 1.3 77.7 - - - +
227F LEU* 1.3 57.2 + - - +
229F LYS* 3.5 11.6 + - + +
230F PHE* 2.9 28.8 + - - +
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Residues in contact with LEU 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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194F MET* 3.9 9.2 - - + -
195F ILE* 3.8 21.3 - - + -
198F CYS* 4.2 13.0 - - - -
205F VAL* 4.0 15.9 - - + -
223F LEU 2.9 14.2 + - - +
224F HIS 3.1 3.3 + - - +
226F ALA* 1.3 72.8 - - - +
228F ASP* 1.3 60.4 + - - +
230F PHE* 3.6 5.9 - - + +
231F GLN* 2.9 23.7 + - - +
236F ILE 4.7 1.4 - - - +
238F ILE* 3.7 38.3 + - + +
240F MET* 4.0 30.5 - - + -
266F ARG* 3.4 29.5 + - - +
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Residues in contact with ASP 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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224F HIS* 3.1 35.4 + - - +
225F ASP* 3.2 13.2 + - - +
227F LEU* 1.3 77.6 - - - +
229F LYS* 1.3 57.3 + - - +
231F GLN* 3.3 6.1 + - - +
232F ALA* 3.0 25.0 + - - +
266F ARG* 2.7 38.6 + - - +
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Residues in contact with LYS 229 (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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225F ASP 3.2 12.3 + - - +
226F ALA* 3.9 8.5 - - + +
228F ASP* 1.3 75.1 - - - +
230F PHE* 1.3 61.9 + - - +
232F ALA* 3.1 7.1 + - + +
233F ASP* 2.8 59.0 + - - +
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Residues in contact with PHE 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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195F ILE* 3.7 42.0 - - + -
198F CYS* 3.7 34.5 - - + -
199F ASP* 4.6 0.2 - - - -
226F ALA 2.9 18.6 + - - +
227F LEU* 3.6 8.3 - - + +
229F LYS* 1.3 78.8 - - - +
231F GLN* 1.3 52.6 + - - +
233F ASP* 4.6 4.3 - - + -
234F THR* 2.8 59.8 + - + +
236F ILE* 3.8 42.2 - - + -
238F ILE* 4.0 12.3 - - + -
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Residues in contact with GLN 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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227F LEU 2.9 13.1 + - - +
228F ASP 3.4 9.0 - - - +
229F LYS 3.2 0.2 - - - -
230F PHE* 1.3 73.5 - - - +
232F ALA* 1.3 61.2 + - - +
235F GLY* 2.8 32.7 + - - +
236F ILE 3.2 23.6 + - - +
237F ASP* 3.1 28.9 + - - +
266F ARG* 2.6 28.2 + - - +
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Residues in contact with ALA 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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228F ASP 3.0 13.9 + - - +
229F LYS* 3.1 10.1 + - + +
231F GLN* 1.3 77.4 - - - +
233F ASP* 1.3 67.6 + - - +
235F GLY 4.6 1.0 + - - -
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Residues in contact with ASP 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 LYS* 2.8 54.8 + - - +
230F PHE* 4.0 3.9 - - + +
232F ALA* 1.3 77.3 - - - +
234F THR* 1.3 70.7 + - + +
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Residues in contact with THR 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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230F PHE* 2.8 41.8 + - + +
233F ASP* 1.3 89.3 - - + +
235F GLY* 1.3 59.7 + - - +
236F ILE* 3.0 38.0 + - + +
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Residues in contact with GLY 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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231F GLN* 2.8 31.3 + - - +
232F ALA 4.6 1.4 + - - -
233F ASP 4.0 0.2 - - - -
234F THR* 1.3 71.8 - - - +
236F ILE* 1.3 62.0 + - - +
237F ASP* 3.4 5.7 + - - +
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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