Contacts of the helix formed by residues 219 - 235 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209B PHE* 4.9 0.9 - + - -
217B TYR* 3.8 31.6 - - + -
218B GLU* 1.3 69.1 - - - +
220B PRO* 1.3 72.1 - - + +
221B GLN* 3.3 1.9 + - + +
222B PRO* 3.4 25.4 - - + +
223B LEU* 3.4 16.2 - - - +
258B ILE* 3.9 35.4 - - + -
372B ASP 3.4 25.6 - - - -
373B GLU* 4.2 10.5 - - + -
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Residues in contact with PRO 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B PRO* 4.3 8.1 - - + -
209B PHE* 4.3 8.3 - - + -
218B GLU 3.2 11.9 - - - +
219B PHE* 1.3 86.5 - - + +
221B GLN* 1.3 51.6 + - - +
223B LEU* 3.2 13.3 + - + +
224B HIS* 2.7 35.0 + - - +
240B MET* 3.6 5.8 - - + +
242B ILE* 3.9 23.8 - - + -
258B ILE* 5.6 0.4 - - + -
259B VAL 4.7 1.3 - - - +
260B TRP* 3.7 36.1 - - + +
264B LEU* 3.8 20.6 - - + -
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Residues in contact with GLN 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B PHE* 3.3 1.3 - - + -
220B PRO* 1.3 79.6 - - - +
222B PRO* 1.4 67.1 - - + +
224B HIS* 3.0 9.5 + - - +
225B ASP* 2.9 42.1 + - - +
259B VAL* 3.7 39.4 + - - +
264B LEU* 3.7 23.3 - - + +
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Residues in contact with PRO 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B PRO* 4.2 18.8 - - + +
219B PHE* 3.4 26.7 - - + +
221B GLN* 1.4 91.2 - - + +
223B LEU* 1.3 64.9 + - + +
225B ASP* 3.3 13.5 + - + +
226B ALA* 3.0 21.5 + - - +
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Residues in contact with LEU 223 (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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189B MET* 3.7 40.8 - - + +
190B ASP 4.0 1.6 - - - -
191B PRO* 3.6 36.8 - - + -
194B MET* 3.4 26.2 - - + +
207B PRO* 4.0 22.2 - - + -
218B GLU* 5.0 5.2 - - + -
219B PHE 3.4 18.6 - - - +
220B PRO* 3.4 5.2 - - + +
221B GLN 3.2 0.4 - - - -
222B PRO* 1.3 78.2 - - + +
224B HIS* 1.4 61.9 + - - +
226B ALA* 3.0 11.8 + - - +
227B LEU* 3.1 11.4 + - - +
240B MET* 3.5 11.0 - - + -
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Residues in contact with HIS 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B PRO 2.7 18.9 + - - +
221B GLN* 3.0 14.3 + - - +
223B LEU* 1.4 69.5 - - - +
225B ASP* 1.3 68.5 + - - +
227B LEU* 3.1 7.1 + - - +
228B ASP* 3.0 40.0 + - - +
240B MET* 3.6 14.3 - - + +
264B LEU* 3.6 27.6 - - + +
265B PRO* 3.6 27.2 - - + -
266B ARG* 3.0 51.3 + - + +
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Residues in contact with ASP 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B GLN* 2.9 32.0 + - - +
222B PRO* 3.5 14.2 - - + +
224B HIS* 1.3 81.6 + - - +
226B ALA* 1.3 63.5 + - - +
228B ASP* 3.3 12.2 + - - +
229B LYS* 3.0 21.8 + - - +
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Residues in contact with ALA 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B PRO* 4.0 15.5 - - + -
194B MET* 3.8 6.5 - - + -
195B ILE* 3.4 26.4 - - + +
222B PRO 3.0 12.9 + - - +
223B LEU 3.0 8.5 + - - +
225B ASP* 1.3 78.9 - - - +
227B LEU* 1.3 55.6 + - - +
229B LYS* 3.4 12.2 + - - +
230B PHE* 3.0 25.8 + - - +
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Residues in contact with LEU 227 (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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194B MET* 3.6 20.0 - - + -
195B ILE* 3.6 12.3 - - + -
198B CYS* 4.3 15.5 - - - -
205B VAL* 4.2 7.2 - - + -
223B LEU 3.1 13.2 + - - +
224B HIS 3.1 6.5 + - - +
226B ALA* 1.3 74.3 - - - +
228B ASP* 1.3 59.5 + - - +
230B PHE* 3.4 6.9 - - + +
231B GLN* 2.8 30.0 + - - +
236B ILE 4.7 1.0 - - - +
238B ILE* 3.7 40.7 + - + +
240B MET* 4.1 31.9 - - + -
266B ARG* 3.7 21.0 + - - +
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Residues in contact with ASP 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B HIS* 3.0 31.6 + - - +
225B ASP* 3.5 15.1 - - - +
227B LEU* 1.3 75.5 - - - +
229B LYS* 1.3 62.6 + - - +
230B PHE 3.2 0.2 + - - -
231B GLN* 3.3 4.0 + - - +
232B ALA* 3.0 22.6 + - - +
266B ARG* 2.7 32.5 + - - +
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Residues in contact with LYS 229 (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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225B ASP 3.0 14.1 + - - +
226B ALA* 3.7 12.6 - - - +
228B ASP* 1.3 75.7 - - - +
230B PHE* 1.3 58.6 + - - +
232B ALA* 3.3 6.5 + - + +
233B ASP* 3.0 56.0 + - - +
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Residues in contact with PHE 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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195B ILE* 3.6 42.0 - - + -
198B CYS* 3.8 23.8 - - + -
199B ASP* 4.7 0.2 - - - -
226B ALA 3.0 17.8 + - - +
227B LEU* 3.4 9.0 - - + +
228B ASP 3.1 0.2 - - - -
229B LYS* 1.3 78.8 - - - +
231B GLN* 1.3 57.6 + - - +
233B ASP* 3.4 4.1 + - + -
234B THR* 2.9 54.2 + - + +
236B ILE* 3.9 41.1 - - + -
238B ILE* 4.0 22.9 - - + -
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Residues in contact with GLN 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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227B LEU 2.8 15.1 + - - +
228B ASP 3.6 4.5 - - - +
230B PHE* 1.3 74.9 - - - +
232B ALA* 1.3 61.8 + - - +
235B GLY* 2.8 33.1 + - - +
236B ILE 3.3 23.2 + - - +
237B ASP* 2.7 30.7 + - - +
266B ARG* 2.5 30.5 + - - +
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Residues in contact with ALA 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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228B ASP 3.0 13.6 + - - +
229B LYS* 3.3 12.5 + - + +
231B GLN* 1.3 76.4 - - - +
233B ASP* 1.3 65.2 + - - +
235B GLY 4.7 0.9 + - - -
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Residues in contact with ASP 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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229B LYS* 3.0 42.0 + - - +
230B PHE* 3.8 5.9 - - + +
232B ALA* 1.3 84.6 - - - +
234B THR* 1.3 66.9 + - + +
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Residues in contact with THR 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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230B PHE* 2.9 43.1 + - + +
233B ASP* 1.3 88.7 - - + +
235B GLY* 1.3 59.5 + - - +
236B ILE* 3.0 39.0 + - + +
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Residues in contact with GLY 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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231B GLN* 2.8 26.3 + - - +
232B ALA 4.7 0.8 + - - -
234B THR* 1.3 76.9 - - - +
236B ILE* 1.3 62.0 + - - +
237B ASP* 3.4 6.1 + - - +
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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