Contacts of the helix formed by residues 232 - 248 (chain F) in PDB entry 1RFU
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 232 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18F TYR 3.8 5.8 - - - -
19F VAL* 3.3 20.6 - - - -
23F ALA* 4.1 3.3 - - - +
231F VAL* 1.3 75.6 - - - +
233F THR* 1.3 66.0 + - - +
234F GLY 3.3 2.2 - - - -
235F ASP* 3.2 7.3 + - - +
236F LEU* 3.0 21.8 + - - +
291F LEU* 4.3 6.3 - - - -
5401F PLP 2.9 18.8 + - - -
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Residues in contact with THR 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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230F PHE* 3.7 28.6 + - + -
231F VAL 3.3 1.4 + - - -
232F GLY* 1.3 75.9 + - - +
234F GLY* 1.3 63.3 + - - +
236F LEU* 2.9 12.9 + - - -
237F PHE* 2.9 10.6 + - - +
263F MET* 3.1 19.1 - - + +
267F LEU* 3.8 16.8 - - + -
291F LEU* 4.2 8.6 - - + +
5401F PLP 3.9 1.7 + - - -
5402F ADP 2.6 66.4 + - + +
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Residues in contact with GLY 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F ASP* 4.1 7.7 - - - +
148F THR* 5.3 0.5 + - - -
186F THR* 5.5 3.6 - - - -
233F THR* 1.3 72.5 + - - +
235F ASP* 1.3 58.4 + - - +
237F PHE* 2.8 26.6 + - - +
238F ALA* 3.0 8.1 + - - +
5401F PLP 3.2 1.2 + - - -
5402F ADP 2.8 47.9 + - - -
5403F ZN 3.7 1.6 - - - -
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Residues in contact with ASP 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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11F GLN* 3.1 25.2 + - - +
20F GLY* 3.8 27.0 + - - +
23F ALA* 4.4 3.6 - - + -
24F ALA* 4.2 4.6 - - + +
81F LEU* 5.6 0.2 - - - +
83F GLY* 5.0 0.5 - - - -
84F TYR 4.9 2.6 + - - -
113F ASP* 3.7 16.5 + - - +
115F VAL* 4.2 8.8 - - - +
232F GLY* 3.5 10.6 - - - +
234F GLY* 1.3 73.5 - - - +
236F LEU* 1.3 62.7 + - - +
238F ALA* 3.5 3.8 + - - +
239F ALA* 3.2 23.9 + - - +
5401F PLP 2.3 43.2 + - - +
5403F ZN 4.6 0.2 - - - -
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Residues in contact with LEU 236 (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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23F ALA* 3.5 13.1 - - + +
27F PRO* 3.2 36.3 - - + -
232F GLY 3.0 10.6 + - - +
233F THR 2.9 9.4 + - - +
235F ASP* 1.3 75.2 - - - +
237F PHE* 1.3 63.4 + - - +
239F ALA* 3.4 2.2 + - - +
240F MET* 3.0 41.7 + - + +
263F MET* 3.6 19.5 - - + -
266F VAL* 4.2 24.2 - - + -
291F LEU* 4.0 21.5 - - + -
293F MET* 4.2 10.3 - - + -
300F ILE* 4.7 2.5 - - + -
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Residues in contact with PHE 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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148F THR* 4.4 7.2 - - - -
184F VAL* 4.0 24.0 - - + -
186F THR* 3.3 31.9 - - + -
221F MET* 6.3 0.7 - - + -
233F THR 2.9 10.0 + - - +
234F GLY* 2.8 14.4 - - - +
236F LEU* 1.3 73.0 - - - +
238F ALA* 1.3 61.0 + - - +
240F MET* 3.0 4.2 + - - +
241F LEU* 2.5 57.2 + - + +
256F CYS* 5.7 4.3 - - - -
259F THR* 3.3 29.8 - - + +
260F VAL* 3.9 21.1 - - + -
263F MET* 3.9 19.2 - - + +
5402F ADP 4.3 16.8 - - - -
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Residues in contact with ALA 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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81F LEU* 4.1 19.5 - - + -
111F VAL* 4.5 3.0 - - + +
113F ASP* 4.5 10.3 - - + +
148F THR* 4.0 25.6 - - + +
234F GLY 3.0 8.0 + - - +
235F ASP* 3.9 7.9 - - - +
237F PHE* 1.3 81.2 - - - +
239F ALA* 1.3 54.3 + - - +
241F LEU* 2.9 8.4 + - - +
242F LEU* 2.6 38.2 + - - +
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Residues in contact with ALA 239 (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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24F ALA* 3.7 36.8 - - + +
27F PRO* 4.6 5.4 - - + -
28F LEU* 2.9 28.4 - - + +
81F LEU* 3.8 14.5 - - + +
235F ASP 3.2 11.5 + - - +
236F LEU* 3.4 9.4 - - - +
238F ALA* 1.3 80.9 - - - +
240F MET* 1.3 62.2 + - - +
242F LEU* 3.1 8.8 + - - +
243F ALA 3.2 1.0 + - - -
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Residues in contact with MET 240 (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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27F PRO* 4.2 18.2 - - + -
31F LEU* 4.6 9.0 - - + -
236F LEU* 3.0 31.1 + - + +
237F PHE 3.6 4.0 - - - +
239F ALA* 1.3 72.7 - - - +
241F LEU* 1.3 59.1 + - - +
243F ALA* 2.6 28.2 + - - +
244F TRP* 3.0 24.9 + - - +
259F THR* 3.9 17.0 - - + +
262F ALA* 3.3 34.5 - - + -
263F MET* 3.5 32.8 - - - +
266F VAL* 5.4 0.2 - - + -
300F ILE* 4.3 20.2 - - + +
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Residues in contact with LEU 241 (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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111F VAL* 5.5 2.2 - - + -
146F ILE* 4.1 17.9 - - + -
148F THR* 3.6 30.1 - - + -
182F THR* 5.9 0.4 - - + -
184F VAL* 4.4 12.1 - - + -
237F PHE* 2.5 38.6 + - + +
238F ALA* 3.2 6.1 - - - +
240F MET* 1.3 72.5 - - - +
242F LEU* 1.3 65.5 + - - +
243F ALA 2.9 1.4 + - - -
244F TRP 3.2 0.2 + - - -
245F THR* 3.1 49.4 + - + +
252F LEU* 5.3 1.3 - - + -
255F ALA* 4.8 4.9 - - + +
256F CYS* 4.7 19.5 - - - -
259F THR* 3.6 20.8 + - + +
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Residues in contact with LEU 242 (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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7F VAL* 3.8 28.7 - - + -
28F LEU* 4.0 13.5 - - + -
33F PHE* 4.1 20.9 - - + -
79F TYR* 3.8 30.7 - - + -
80F VAL 4.8 0.2 - - - +
81F LEU* 4.2 16.6 - - + -
111F VAL* 4.0 25.1 - - + +
146F ILE* 6.0 0.2 - - - -
238F ALA 2.6 15.4 + - - +
239F ALA* 3.1 11.9 - - - +
241F LEU* 1.3 74.6 - - - +
243F ALA* 1.3 66.3 + - - +
245F THR* 3.7 6.1 + - - -
246F HIS* 3.5 16.8 + - - +
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Residues in contact with ALA 243 (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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28F LEU* 4.3 2.0 - - + -
31F LEU* 3.6 27.6 - - + -
33F PHE* 3.5 32.9 - - + -
239F ALA 3.2 7.7 + - - +
240F MET 2.6 17.5 + - - +
242F LEU* 1.3 73.2 - - - +
244F TRP* 1.3 68.5 + - + +
246F HIS* 3.5 6.8 - - - +
247F LYS* 3.5 16.6 + - - +
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Residues in contact with TRP 244 (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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31F LEU* 4.2 19.6 - - + +
240F MET* 3.0 25.7 + - - +
241F LEU 4.2 1.1 - - - +
243F ALA* 1.3 77.1 - - + +
245F THR* 1.3 53.4 + - - +
246F HIS 3.1 1.6 - - - -
247F LYS* 2.7 37.1 + - + +
248F HIS* 2.6 36.8 + + + -
255F ALA* 3.7 24.2 - - + +
258F LYS* 3.6 39.4 - - + +
259F THR* 3.0 37.7 - - - +
300F ILE 4.1 9.8 + - - -
301F GLU 4.0 13.7 - - - -
302F SER* 5.5 0.7 - - - -
303F PRO* 4.1 23.4 - - + +
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Residues in contact with THR 245 (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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79F TYR* 5.3 3.1 + - - -
146F ILE* 4.0 24.5 - - + +
182F THR* 5.3 3.1 - - + -
205F GLN* 6.2 1.8 - - - +
241F LEU* 3.1 34.5 + - + +
242F LEU* 3.7 6.2 + - - -
244F TRP* 1.3 75.4 - - - +
246F HIS* 1.3 61.8 + - - +
248F HIS 3.7 11.7 - - - +
249F PRO* 2.8 36.5 - - - +
252F LEU* 5.0 10.3 - - + -
255F ALA* 3.7 18.1 - - + +
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Residues in contact with HIS 246 (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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1F MET* 4.4 4.4 - - + -
3F GLU* 2.9 34.9 + - - -
5F CYS* 3.4 28.3 - - - -
33F PHE* 3.9 19.7 - + + -
79F TYR* 2.6 37.1 + + + +
242F LEU 3.5 15.6 + - - +
243F ALA 3.5 5.6 - - - +
244F TRP 3.1 0.4 - - - -
245F THR* 1.3 83.4 + - - +
247F LYS* 1.3 68.1 + - + +
249F PRO* 4.1 6.2 - - - +
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Residues in contact with LYS 247 (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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1F MET* 6.1 5.6 - - + -
243F ALA 3.8 9.0 - - - +
244F TRP* 2.7 38.2 + - + +
246F HIS* 1.3 89.2 - - + +
248F HIS* 1.3 83.7 + - + +
249F PRO* 2.9 11.5 - - - +
258F LYS* 4.3 5.2 - - - +
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Residues in contact with HIS 248 (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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244F TRP* 2.6 21.2 + + - +
245F THR* 3.0 13.0 - - - +
247F LYS* 1.3 99.3 + - + +
249F PRO* 1.3 66.6 - - - +
250F ASN 3.0 4.2 + - - +
251F ASN* 3.1 40.5 + - + +
252F LEU 4.5 0.5 + - - -
254F VAL* 3.6 24.4 - - + +
255F ALA* 4.4 5.4 - - - +
258F LYS* 3.1 32.3 + - + -
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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