Contacts of the helix formed by residues 225 - 243 (chain B) in PDB entry 1F5Q
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 THR 225 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B CYS* 5.2 1.5 - - - -
223B TYR 5.0 2.7 - - - +
224B ILE* 1.3 82.1 - - - +
226B LYS* 1.3 63.8 + - - +
227B GLU* 3.5 13.5 + - - +
228B GLU* 2.9 48.4 + - + +
229B LEU* 3.3 10.7 + - - +
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Residues in contact with LYS 226 (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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216B ASP* 4.4 18.2 - - - +
219B CYS* 5.8 2.0 - - - +
224B ILE 4.1 0.2 + - - -
225B THR* 1.3 73.8 - - - +
227B GLU* 1.3 63.2 + - - +
229B LEU* 3.3 11.0 + - + +
230B HIS* 3.1 61.7 + - + +
38C ASP 4.1 7.7 + - - -
39C THR 5.0 5.5 + - - -
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Residues in contact with GLU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B THR* 3.6 12.3 + - - +
226B LYS* 1.3 80.5 - - - +
228B GLU* 1.3 63.5 + - - +
230B HIS* 3.4 6.9 + - - +
231B GLN* 3.0 46.4 + - + +
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Residues in contact with GLU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU* 4.0 15.9 - - + +
223B TYR 3.9 9.4 - - - +
224B ILE* 3.4 23.9 - - + +
225B THR* 2.9 44.6 + - - +
227B GLU* 1.3 78.3 - - - +
229B LEU* 1.3 63.8 + - - +
231B GLN* 3.3 13.8 + - - +
232B CYS* 3.0 24.8 + - - +
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Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU* 4.1 13.8 - - + +
197B LEU* 3.7 42.8 - - + +
198B ALA* 3.7 5.8 - - - +
201B HIS* 3.8 29.2 - - + +
211B TYR* 4.3 5.8 - - - +
215B ILE* 4.3 8.3 - - + -
219B CYS* 4.1 20.6 - - - -
224B ILE* 4.7 4.0 - - + -
225B THR 3.3 8.9 + - - +
226B LYS* 3.5 13.2 - - + +
227B GLU 3.3 0.2 - - - -
228B GLU* 1.3 78.8 - - - +
230B HIS* 1.3 64.6 + - + +
232B CYS* 3.2 5.2 + - - +
233B CYS* 3.0 29.6 + - - -
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Residues in contact with HIS 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B HIS* 4.0 20.2 - + - -
226B LYS* 3.1 55.2 + - + +
227B GLU* 3.8 5.5 - - - +
229B LEU* 1.3 80.6 - - + +
231B GLN* 1.3 67.1 + - + +
233B CYS* 3.4 3.8 + - - +
234B ASP* 3.2 13.4 + - - +
36C ARG* 2.8 30.9 + - - +
38C ASP* 3.4 34.8 + - - -
39C THR* 3.4 19.7 - - + +
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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
----------------------------------------------------------
227B GLU* 3.0 44.3 + - + +
228B GLU* 3.7 12.3 - - - +
230B HIS* 1.3 72.8 - - + +
232B CYS* 1.3 67.0 + - - +
234B ASP* 2.8 20.9 + - - +
235B LEU* 3.0 17.9 + - + +
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Residues in contact with CYS 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B SER* 5.7 1.1 - - - -
190B LYS* 4.5 9.2 - - - -
194B LEU* 3.6 47.8 - - + -
195B ILE* 4.2 14.8 - - - -
198B ALA* 3.8 10.8 - - + -
228B GLU 3.0 13.1 + - - +
229B LEU 3.2 9.6 + - - +
231B GLN* 1.3 77.4 - - - +
233B CYS* 1.3 62.5 + - - +
235B LEU* 2.8 24.6 + - - +
236B VAL* 2.9 20.7 + - - +
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Residues in contact with CYS 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ALA* 3.8 28.7 - - - -
201B HIS* 3.8 29.4 - - - -
202B LEU* 4.0 16.4 - - + +
229B LEU* 3.0 27.4 + - - -
230B HIS* 3.4 12.1 - - - +
231B GLN 3.1 0.2 - - - -
232B CYS* 1.3 75.5 - - - +
234B ASP* 1.3 57.5 + - - +
236B VAL* 3.5 5.4 + - - +
237B ASP* 3.1 34.0 + - - +
36C ARG* 4.2 11.4 - - - +
74C ASN* 4.7 0.9 - - - -
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Residues in contact with ASP 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B HIS 3.2 15.3 - - - +
231B GLN* 2.8 11.3 + - - +
233B CYS* 1.3 76.4 - - - +
235B LEU* 1.3 65.3 + - + +
237B ASP* 3.5 10.1 + - - +
238B ILE* 3.0 34.4 + - + +
34C LYS* 4.8 12.9 + - - +
36C ARG* 3.3 29.3 + - - +
75C LYS* 5.7 1.0 - - - +
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Residues in contact with LEU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ASP* 4.9 1.4 - - - +
186B ARG* 3.2 39.0 - - + +
187B SER* 3.9 15.5 - - - -
190B LYS* 3.4 34.5 - - + -
231B GLN* 3.0 17.3 + - + +
232B CYS* 2.8 14.9 + - - +
234B ASP* 1.3 76.5 - - - +
236B VAL* 1.3 58.5 - - + +
238B ILE* 3.2 19.1 + - + +
239B ALA* 2.8 27.2 + - - +
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LYS* 4.0 23.1 - - + +
181B ALA* 4.6 12.6 - - + -
187B SER* 4.8 2.7 - - - -
195B ILE* 5.0 4.5 - - + +
198B ALA* 4.2 15.7 - - + -
199B CYS* 4.2 10.1 - - - -
202B LEU* 3.9 20.4 - - + -
232B CYS* 2.9 27.9 + - - +
233B CYS 3.7 4.7 - - - +
235B LEU* 1.3 77.7 - - + +
237B ASP* 1.3 57.6 + - - +
239B ALA* 3.0 8.0 + - - +
240B ILE* 2.8 41.1 + - + +
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Residues in contact with ASP 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LYS* 4.8 0.5 + - - -
202B LEU* 3.8 15.0 - - - +
233B CYS* 3.1 23.1 + - - +
234B ASP* 4.0 11.8 - - - +
235B LEU 3.3 0.4 - - - -
236B VAL* 1.3 75.5 - - - +
238B ILE* 1.3 61.5 + - + +
240B ILE* 3.8 18.4 - - - +
241B VAL* 3.2 28.5 + - + +
19C TYR* 5.1 2.5 + - - +
34C LYS* 4.8 11.6 + - - +
36C ARG* 6.0 0.2 + - - -
73C GLU* 4.2 8.5 - - - +
74C ASN* 4.9 0.3 - - - +
75C LYS* 2.8 40.4 + - - +
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Residues in contact with ILE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ASP* 4.6 10.8 - - - +
186B ARG* 6.3 4.0 - - + -
234B ASP* 3.0 29.9 + - + +
235B LEU* 3.3 20.0 - - + +
236B VAL 3.1 0.2 - - - -
237B ASP* 1.3 74.3 - - + +
239B ALA* 1.3 62.9 + - - +
241B VAL* 3.1 6.2 + - - +
242B SER* 2.8 42.4 + - - +
19C TYR* 5.8 3.8 - - - +
34C LYS* 6.1 2.7 - - - +
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Residues in contact with ALA 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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180B CYS* 3.4 27.0 - - + +
181B ALA* 3.7 7.9 - - - +
184B ASP* 3.6 23.4 - - + +
187B SER* 3.6 8.3 - - - +
235B LEU 2.8 13.9 + - - +
236B VAL* 3.3 9.6 - - - +
238B ILE* 1.3 78.3 - - - +
240B ILE* 1.3 60.6 + - - +
242B SER* 3.7 3.5 + - - -
243B PHE* 3.3 24.8 + - - +
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Residues in contact with ILE 240 (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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176B PRO 5.6 0.2 - - - -
177B LYS* 3.6 44.9 - - + +
180B CYS* 3.9 27.3 - - + -
236B VAL* 2.8 28.4 + - + +
237B ASP* 3.8 17.5 - - - +
238B ILE 3.2 0.2 - - - -
239B ALA* 1.3 79.8 - - - +
241B VAL* 1.3 64.2 + - + +
243B PHE* 3.7 12.1 + - - +
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Residues in contact with VAL 241 (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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237B ASP 3.2 17.1 + - - +
238B ILE* 3.1 7.4 + - - +
240B ILE* 1.3 82.5 - - + +
242B SER* 1.3 61.4 + - - +
243B PHE 3.6 3.6 + - - +
6C LYS 3.3 27.5 + - - +
7C VAL* 4.4 12.8 - - + -
19C TYR* 4.3 24.5 - - + +
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Residues in contact with SER 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ASP* 3.5 18.9 + - - -
238B ILE* 2.8 27.0 + - - +
239B ALA 3.7 2.4 + - - -
241B VAL* 1.3 77.6 - - - +
243B PHE* 1.3 63.7 + - - +
244B ASP* 3.5 6.5 + - - +
247B TYR* 6.1 0.9 - - - -
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Residues in contact with PHE 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B THR* 4.7 10.8 - - + -
57B PHE* 3.8 41.7 - + - -
179B PHE* 5.6 0.4 - - + -
180B CYS* 3.9 27.4 - - - -
183B CYS* 3.5 38.4 - - + -
239B ALA 3.3 17.1 + - - +
240B ILE 3.8 10.1 - - - +
241B VAL 3.4 5.8 - - - +
242B SER* 1.3 76.5 - - - +
244B ASP* 1.3 64.3 + - - +
245B GLU* 4.1 24.7 - - + -
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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
------------------------------------------------------------
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