Contacts of the helix formed by residues 222 - 239 (chain B) in PDB entry 5FI6
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 222 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B ARG* 3.5 27.5 + - - +
220B ILE* 3.4 5.4 - - - +
221B PRO* 1.3 76.1 - - - +
223B PHE* 1.3 63.2 + - - +
224B MET* 3.8 7.6 + - - +
225B SER* 3.0 37.4 + - - -
226B PHE* 3.2 11.6 + - - +
541B PRO 5.0 0.6 + - - -
543B ARG 5.4 3.6 + - - +
544B GLU* 4.7 7.2 - - + +
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Residues in contact with PHE 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B SER 4.2 6.5 + - - +
165B THR* 3.9 7.2 - - - +
166B GLY* 3.4 22.0 - - - -
220B ILE* 3.6 17.5 + - + -
221B PRO 3.3 5.6 + - - +
222B ASP* 1.3 75.9 - - - +
224B MET* 1.3 63.8 + - + +
226B PHE* 4.1 17.5 - + - -
227B THR* 3.0 54.1 + - + +
264B VAL* 4.7 5.2 - - + -
266B THR* 3.7 21.8 - - + -
270B GLN* 3.5 42.8 - - + +
271B ARG 3.2 30.1 - - - -
272B HIS* 4.1 4.5 - - + -
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Residues in contact with MET 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LYS 4.0 7.0 - - - +
164B SER* 3.2 50.5 - - - +
166B GLY* 4.7 0.7 - - - -
222B ASP* 3.2 7.9 + - - +
223B PHE* 1.3 93.3 - - + +
225B SER* 1.3 60.9 + - - +
227B THR* 3.1 22.2 + - + +
228B SER* 3.5 10.0 + - - -
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Residues in contact with SER 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ASP* 3.0 34.4 + - - -
224B MET* 1.3 77.6 - - - +
226B PHE* 1.3 63.3 + - - +
228B SER* 2.5 25.6 + - - -
229B HIS* 3.4 19.1 + - - -
539B LEU* 6.0 0.7 - - - +
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Residues in contact with PHE 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ILE* 3.9 35.9 - - + -
222B ASP 3.2 5.1 + - - +
223B PHE* 3.4 17.7 + + - +
225B SER* 1.3 81.6 + - - +
227B THR* 1.3 64.8 + - + +
229B HIS* 3.1 18.0 + - + +
230B ILE* 3.0 50.8 + - + +
233B LEU* 6.2 0.4 - - + -
264B VAL* 4.4 9.0 - - + -
495B MET* 3.9 28.9 - - + -
520B LEU* 4.8 2.2 - - + -
523B LEU* 6.0 0.2 - - + -
524B CYS* 4.5 9.0 - - - -
526B PHE* 4.2 7.9 - + - -
539B LEU* 5.8 0.4 - - + -
541B PRO* 3.7 35.2 - - + -
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Residues in contact with THR 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B PHE* 3.0 43.6 + - + +
224B MET* 3.1 20.8 + - + +
226B PHE* 1.3 74.2 - - + +
228B SER* 1.3 70.1 + - - +
230B ILE* 3.1 5.8 + - - +
231B ASP* 2.8 28.1 + - - -
272B HIS* 3.5 43.9 - - + +
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Residues in contact with SER 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B MET 3.5 8.4 + - - -
225B SER* 2.5 26.0 + - - -
227B THR* 1.3 81.3 + - - +
229B HIS* 1.3 59.5 + - - +
231B ASP* 3.3 12.1 + - - +
232B GLU* 3.0 32.5 + - - +
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Residues in contact with HIS 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B SER* 3.7 20.5 + - - -
226B PHE* 3.1 19.2 + - + +
227B THR 3.0 0.8 - - - -
228B SER* 1.3 79.5 + - - +
230B ILE* 1.3 60.6 + - + +
231B ASP 3.1 1.3 - - - -
232B GLU* 3.0 27.4 + - - +
233B LEU* 2.8 36.1 + - + +
523B LEU* 3.7 31.4 - - + +
539B LEU* 3.4 34.3 - - + +
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Residues in contact with ILE 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B PHE* 3.0 47.2 + - + +
227B THR* 3.1 8.5 + - - +
229B HIS* 1.3 75.1 - - - +
231B ASP* 1.3 52.4 + - - +
233B LEU* 3.6 13.5 - - + +
234B TYR* 2.7 32.9 + - - +
262B VAL* 4.0 24.2 - - + -
264B VAL* 4.2 16.8 - - + -
272B HIS* 3.8 21.1 - - + -
274B THR* 4.3 5.6 - - + -
497B MET* 4.7 3.6 - - + -
516B PHE* 3.9 18.2 - - + -
520B LEU* 4.4 6.5 - - + -
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Residues in contact with ASP 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B THR* 2.8 18.2 + - - +
228B SER* 3.5 12.1 - - - +
230B ILE* 1.3 74.5 - - - +
232B GLU* 1.3 59.9 + - + +
234B TYR* 3.3 6.8 + - - +
235B GLU* 2.9 36.8 + - + +
272B HIS* 2.9 29.3 + - - -
274B THR* 3.2 23.5 - - - +
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Residues in contact with GLU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B SER* 3.0 19.6 + - - +
229B HIS* 3.0 32.7 + - - +
231B ASP* 1.3 75.7 - - - +
233B LEU* 1.3 66.0 + - + +
235B GLU* 3.2 4.9 + - - +
236B SER* 2.9 25.6 + - - -
523B LEU* 5.8 0.2 - - - +
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Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B PHE* 6.2 0.4 - - + -
229B HIS* 2.8 24.1 + - + +
230B ILE* 3.6 8.3 - - + +
232B GLU* 1.3 73.3 - - + +
234B TYR* 1.3 63.6 + - - +
236B SER* 3.5 5.9 + - - -
237B ALA* 3.2 24.9 + - - +
516B PHE* 3.3 27.6 - - + -
519B ASP* 3.5 38.1 - - + +
520B LEU* 3.7 38.6 - - + -
523B LEU* 4.3 21.1 - - + -
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Residues in contact with TYR 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 ILE 2.7 23.6 + - - +
231B ASP* 3.3 5.6 - - + +
233B LEU* 1.3 75.0 - - - +
235B GLU* 1.3 84.4 + - + +
237B ALA 3.3 0.2 + - - -
238B LYS* 2.9 32.1 + - + +
260B TRP* 2.7 84.0 + + - +
261B GLY* 4.3 0.2 - - - -
262B VAL* 4.0 6.7 - - + -
274B THR* 3.4 44.2 - - + -
275B GLY* 3.1 15.1 - - - -
276B ASP* 4.8 2.1 + - - -
516B PHE* 3.6 9.1 - - + -
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Residues in contact with GLU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ASP* 2.9 26.3 + - + +
232B GLU* 4.1 3.6 - - - +
234B TYR* 1.3 84.0 - - + +
236B SER* 1.3 68.5 + - - +
238B LYS* 3.2 39.7 + - - +
239B LYS* 3.6 18.0 + - - +
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Residues in contact with SER 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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232B GLU 2.9 17.9 + - - -
233B LEU* 3.7 5.2 - - - -
235B GLU* 1.3 79.2 - - - +
237B ALA* 1.3 62.6 + - - +
238B LYS 3.1 0.3 + - - -
239B LYS* 3.3 22.6 + - - +
240B GLN* 4.2 6.1 - - - +
515B HIS* 3.4 10.7 + - - -
519B ASP* 3.2 22.9 + - - -
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Residues in contact with ALA 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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233B LEU 3.2 15.7 + - - +
236B SER* 1.3 77.4 + - - +
238B LYS* 1.3 63.7 - - - +
239B LYS 3.3 0.4 - - - -
240B GLN* 3.4 13.5 + - - +
260B TRP* 3.7 16.8 - - + -
512B LYS* 3.3 36.7 - - - +
515B HIS* 3.5 26.0 - - + -
516B PHE* 4.0 5.8 - - + +
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Residues in contact with LYS 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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234B TYR* 2.9 28.1 + - + +
235B GLU* 3.4 34.5 + - - +
236B SER 3.1 0.8 - - - -
237B ALA* 1.3 78.1 - - - +
239B LYS* 1.3 58.0 + - + +
240B GLN 3.0 7.0 + - - -
241B SER* 4.5 2.3 + - - -
258B ASP* 5.3 8.5 - - - +
260B TRP* 3.5 27.4 - - + -
512B LYS* 3.5 15.8 - - - -
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Residues in contact with LYS 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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235B GLU* 3.8 17.9 - - - +
236B SER* 3.6 11.8 - - - +
237B ALA 3.3 0.6 - - - -
238B LYS* 1.3 73.2 - - + +
240B GLN* 1.3 66.0 + - + +
241B SER* 3.6 7.4 + - - -
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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
------------------------------------------------------------
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