Contacts of the helix formed by residues 221 - 239 (chain F) in PDB entry 6O81
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 GLY 221 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220F SER* 1.3 80.5 + - - +
222F SER* 1.3 60.7 + - - -
223F ASN 3.4 2.0 - - - -
224F ALA* 3.5 12.8 + - - +
225F ARG* 2.8 32.2 + - - +
338F CYS* 5.0 15.6 - - - -
339F SER* 6.0 2.7 - - - -
368F GLU* 6.0 0.2 - - - -
406F HIS* 5.5 1.1 - - - -
417F ARG* 4.8 2.5 - - - -
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Residues in contact with SER 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220F SER 3.8 1.6 + - - -
221F GLY* 1.3 70.7 - - - -
223F ASN* 1.3 65.0 + - - +
225F ARG* 3.3 8.9 + - - +
226F CYS* 2.9 23.9 + - - +
270F SER* 4.7 9.0 - - - -
272F SER* 3.6 23.3 + - - -
406F HIS* 4.4 32.5 + - - -
441F TYR* 4.9 0.4 - - - -
442F LYS* 3.5 29.4 + - - +
489F TYR* 5.6 1.3 - - - -
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Residues in contact with ASN 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221F GLY 3.4 0.4 - - - -
222F SER* 1.3 82.1 + - - +
224F ALA* 1.3 60.2 + - - +
226F CYS* 3.4 1.7 + - - +
227F ILE* 2.9 38.8 + - + +
312F ILE* 4.3 12.7 - - + +
339F SER* 5.9 2.0 - - - -
340F SER* 3.9 25.4 + - - +
341F LEU* 4.5 9.9 - - - +
439F GLU* 3.5 22.2 + - - -
441F TYR* 2.4 36.5 + - - +
442F LYS* 3.6 17.3 - - - +
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Residues in contact with ALA 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219F VAL* 3.7 15.5 - - + +
221F GLY* 3.5 16.4 + - - +
222F SER 3.3 0.4 - - - -
223F ASN* 1.3 75.0 - - - +
225F ARG* 1.3 59.5 + - - +
227F ILE* 3.9 8.4 - - - +
228F ALA* 2.9 32.1 + - - +
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Residues in contact with ARG 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214F TYR* 2.4 48.5 + - + +
219F VAL* 3.6 23.6 - - + +
220F SER 4.4 4.9 - - - -
221F GLY 2.8 21.6 + - - +
222F SER* 3.6 9.4 - - - +
223F ASN 3.3 0.2 - - - -
224F ALA* 1.3 77.3 - - - +
226F CYS* 1.3 57.3 + - - +
229F LEU* 2.9 17.2 + - - +
267F ARG* 3.1 37.4 - - - +
268F PRO 3.4 21.8 + - - -
269F LEU* 3.5 12.1 - - - +
270F SER* 3.4 24.5 - - - +
273F MET* 3.3 33.8 - - + -
456F GLU* 4.8 0.4 + - - -
489F TYR* 3.8 10.9 + - - -
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Residues in contact with CYS 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222F SER 2.9 17.1 + - - +
223F ASN 3.8 3.8 - - - +
225F ARG* 1.3 73.0 - - - +
227F ILE* 1.3 61.9 + - + +
229F LEU* 3.4 7.4 + - - +
230F LEU* 2.9 46.4 + - - +
272F SER* 4.0 11.9 - - - +
273F MET* 4.8 2.4 - - - +
276F ALA* 3.9 27.4 - - - -
307F TYR* 5.5 1.1 - - - -
308F VAL* 5.9 1.1 - - - -
312F ILE* 5.8 1.6 - - + -
441F TYR* 3.6 34.5 - - + +
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Residues in contact with ILE 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223F ASN* 2.9 25.8 + - + +
224F ALA* 3.9 7.0 - - - +
226F CYS* 1.3 76.6 - - + +
228F ALA* 1.3 58.4 + - + +
230F LEU* 3.3 5.9 + - - +
231F ARG* 2.9 47.7 + - + +
308F VAL* 4.0 21.1 - - + -
312F ILE* 4.3 27.6 - - + -
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Residues in contact with ALA 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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210F LEU* 3.5 24.2 - - + +
213F GLN* 3.9 13.2 + - - +
214F TYR* 4.4 4.9 - - + +
219F VAL* 4.8 6.1 - - + -
224F ALA 2.9 17.9 + - - +
225F ARG 4.0 2.2 - - - +
227F ILE* 1.3 79.7 - - + +
229F LEU* 1.3 58.0 + - - +
231F ARG* 3.4 8.1 + - - +
232F ALA* 2.9 23.4 + - - +
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Residues in contact with LEU 229 (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 MET* 4.9 0.9 - - - -
210F LEU* 3.7 23.1 - - + -
214F TYR* 3.5 7.3 + - - +
225F ARG 2.9 18.2 + - - +
226F CYS* 3.7 6.1 - - - +
228F ALA* 1.3 77.2 - - - +
230F LEU* 1.3 58.2 + - + +
232F ALA* 3.3 2.1 + - - +
233F LEU* 2.9 52.3 + - + +
260F MET* 4.5 9.2 - - + -
263F LEU* 3.8 18.4 - - + -
273F MET* 3.8 44.2 - - + +
276F ALA* 4.1 15.3 - - + -
277F ILE* 4.9 4.9 - - + -
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Residues in contact with LEU 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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226F CYS* 2.9 32.4 + - - +
227F ILE* 3.8 4.3 - - - +
229F LEU* 1.3 74.4 - - + +
231F ARG* 1.3 66.6 + - - +
233F LEU* 3.7 19.6 - - + +
234F GLN* 2.9 34.2 + - - +
276F ALA* 4.5 16.2 - - + +
279F PHE* 6.4 0.7 - - + -
280F LEU* 5.4 2.9 - - + -
304F ILE* 3.9 29.3 - - + +
307F TYR* 4.1 25.1 - - + -
308F VAL* 3.8 32.5 - - + -
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Residues in contact with ARG 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227F ILE* 2.9 38.7 + - + +
228F ALA* 3.7 8.1 - - - +
230F LEU* 1.3 77.8 - - - +
232F ALA* 1.3 59.2 + - - +
234F GLN* 3.3 35.5 + - - +
235F GLN* 3.0 34.2 + - + +
305F ASP* 4.2 6.5 + - - -
308F VAL* 3.9 26.9 - - - +
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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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206F ALA* 3.9 30.0 - - + +
207F MET* 4.7 6.3 - - - -
210F LEU* 3.9 22.9 - - + -
228F ALA 2.9 16.7 + - - +
229F LEU 3.6 4.7 - - - +
231F ARG* 1.3 75.7 - - - +
233F LEU* 1.3 58.4 + - - +
235F GLN* 3.3 4.4 + - - +
236F VAL* 2.9 32.6 + - - +
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Residues in contact with LEU 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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207F MET* 4.0 6.7 - - + -
229F LEU* 2.9 45.4 + - + +
230F LEU* 3.8 18.4 - - + +
231F ARG 3.3 0.4 - - - -
232F ALA* 1.3 73.6 - - - +
234F GLN* 1.3 60.7 + - - +
236F VAL* 3.2 5.6 + - + +
237F ILE* 2.9 35.4 + - + +
256F LEU* 3.7 30.5 - - + -
260F MET* 3.9 16.2 - - + -
276F ALA* 5.6 2.9 - - + +
277F ILE* 5.8 4.3 - - + -
280F LEU* 3.7 33.7 - - + -
304F ILE* 4.7 4.5 - - + -
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Residues in contact with GLN 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 LEU 2.9 18.3 + - - +
231F ARG* 3.3 34.7 + - - +
233F LEU* 1.3 76.2 - - - +
235F GLN* 1.3 58.8 + - + +
237F ILE* 3.4 6.2 + - - +
238F GLN* 2.9 24.3 + - - +
301F ARG* 2.9 40.9 + - + +
304F ILE* 3.4 31.3 - - + +
305F ASP* 2.5 40.0 + - - +
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Residues in contact with GLN 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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204F HIS* 3.5 7.7 - - + -
206F ALA* 3.7 20.2 - - + -
231F ARG* 3.0 20.0 + - + +
232F ALA* 3.6 8.3 - - - +
234F GLN* 1.3 75.5 - - - +
236F VAL* 1.3 63.6 + - - +
238F GLN* 3.7 22.7 + - - +
239F ASP* 3.3 33.8 + - - +
301F ARG* 5.2 3.8 - - - +
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Residues in contact with VAL 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204F HIS* 3.5 36.9 + - + +
207F MET* 3.7 24.5 - - + +
232F ALA 2.9 17.9 + - - +
233F LEU* 3.5 10.8 - - - +
234F GLN 3.2 0.4 - - - -
235F GLN* 1.3 76.8 - - - +
237F ILE* 1.3 68.5 + - + +
239F ASP 3.3 5.7 + - - +
240F TYR* 3.3 21.0 + - + +
252F LEU* 5.2 8.7 - - + -
255F LYS* 5.3 6.4 + - - +
256F LEU* 4.4 13.0 - - + -
259F TYR* 4.3 18.2 - - + -
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Residues in contact with ILE 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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233F LEU* 2.9 20.7 + - + +
234F GLN* 3.4 5.4 + - - +
236F VAL* 1.3 80.8 - - + +
238F GLN* 1.3 62.9 + - - +
240F TYR* 3.3 17.8 + - + +
252F LEU* 4.8 17.0 - - + -
256F LEU* 6.5 1.1 - - + -
280F LEU* 4.7 12.8 - - + -
297F LYS* 3.4 50.3 - - + +
300F LEU* 4.1 25.4 - - + -
301F ARG* 4.1 8.3 - - + +
304F ILE* 3.8 26.7 - - + -
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Residues in contact with GLN 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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234F GLN 2.9 16.7 + - - +
235F GLN* 3.7 27.2 + - - +
236F VAL 3.3 0.2 - - - -
237F ILE* 1.3 79.0 - - - +
239F ASP* 1.3 63.4 + - - +
240F TYR 3.3 2.5 + - - -
297F LYS* 3.9 17.0 + - - +
301F ARG* 3.6 33.0 + - - +
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Residues in contact with ASP 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204F HIS* 3.6 29.2 + - - +
235F GLN* 3.3 20.9 + - - +
236F VAL 3.3 7.6 + - - +
238F GLN* 1.3 84.1 - - - +
240F TYR* 1.3 58.9 + - - +
241F THR* 4.1 2.4 + - - +
255F LYS* 5.1 3.8 + - - -
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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
------------------------------------------------------------
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