Contacts of the helix formed by residues 231 - 247 (chain F) in PDB entry 5IC4
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 GLU 231 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F LEU* 1.3 76.0 - - - +
232F PHE* 1.3 77.6 + - - +
233F MET* 2.9 38.9 + - - +
234F HIS* 3.0 21.7 + - - +
235F ILE* 3.0 9.9 + - - +
269F LEU* 5.6 1.0 - - - +
271F LYS 4.7 0.9 - - - +
272F GLU* 3.7 9.5 - - + +
273F LEU* 2.9 40.9 + - - +
274F TYR* 3.5 29.4 - - + +
234H HIS* 2.9 38.1 + - + +
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Residues in contact with PHE 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E PHE* 6.1 1.8 - + - -
157E LEU* 3.9 19.1 - - + -
159E ILE* 5.1 13.5 - - + -
194F LEU* 3.7 22.9 - - + -
219F LEU* 4.7 6.7 - - + -
223F LEU* 4.1 19.5 - - + -
230F LEU 3.9 0.6 + - - -
231F GLU* 1.3 74.3 - - - +
233F MET* 1.3 62.0 + - + +
235F ILE* 3.2 15.3 + - + -
236F LEU* 2.8 65.4 + - + +
269F LEU* 5.4 1.6 - - + -
273F LEU* 2.9 48.9 + - + +
275F PHE* 3.7 19.5 - + + -
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Residues in contact with MET 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194F LEU* 4.2 15.7 - - - -
231F GLU* 2.9 27.0 + - - +
232F PHE* 1.3 79.7 - - + +
234F HIS* 1.3 54.1 + - + +
236F LEU* 3.4 9.5 + - - +
237F THR* 2.5 38.0 + - - +
265F ILE* 3.6 26.4 - - + +
267F SER* 3.6 27.6 - - - +
269F LEU* 4.8 7.9 - - + -
233H MET* 3.5 43.7 - - + +
234H HIS* 4.9 0.9 - - + +
237H THR* 5.1 12.1 - - - +
265H ILE* 5.4 1.6 - - + -
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Residues in contact with HIS 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230F LEU* 4.2 19.7 - - + +
231F GLU* 3.0 15.8 + - - +
233F MET* 1.3 79.5 - - + +
235F ILE* 1.3 65.2 + - - +
237F THR* 3.4 8.8 + - - -
238F ARG* 3.1 28.1 + - - +
231H GLU* 3.1 40.9 + - + +
233H MET* 5.2 0.7 - - + -
234H HIS* 3.3 36.0 + + - -
272H GLU* 3.6 36.4 + - + +
274H TYR* 4.3 4.0 - - - -
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Residues in contact with ILE 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219F LEU* 5.3 0.2 - - + -
222F MET* 3.9 30.3 - - + +
223F LEU* 4.0 19.3 - - + +
226F TYR* 3.9 16.8 - - + +
227F ALA* 4.0 13.0 - - - -
230F LEU* 3.5 36.6 - - + +
231F GLU 3.0 7.5 + - - +
232F PHE* 3.3 28.3 - - + +
234F HIS* 1.3 77.8 - - - +
236F LEU* 1.3 58.7 + - + +
238F ARG* 3.2 8.4 + - - +
239F VAL* 3.0 31.2 + - + +
275F PHE* 4.5 5.6 - - + -
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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
----------------------------------------------------------
194F LEU* 3.8 16.8 - - + -
196F ALA* 4.5 14.4 - - + -
215F PHE* 5.3 3.1 - - + -
219F LEU* 3.7 30.3 - - + -
232F PHE* 2.8 53.3 + - + +
233F MET* 3.7 7.6 - - - +
235F ILE* 1.3 73.8 - - - +
237F THR* 1.3 60.5 + - - +
239F VAL* 3.2 9.7 + - + +
240F ASN* 3.0 31.0 + - - +
265F ILE* 3.6 35.0 - - + -
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Residues in contact with THR 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233F MET* 2.5 26.7 + - - +
234F HIS* 3.6 12.8 - - - -
235F ILE 3.2 0.4 - - - -
236F LEU* 1.3 77.0 - - - +
238F ARG* 1.3 60.8 + - + +
240F ASN* 3.1 20.3 + - - +
241F ARG 3.3 5.0 + - - -
265F ILE* 4.0 11.3 - - - +
231H GLU* 5.7 0.2 + - - -
233H MET* 5.0 10.6 - - - +
267H SER* 5.3 2.5 + - - +
269H LEU* 3.9 10.5 - - + +
270H THR 3.6 7.1 - - - +
271H LYS* 3.5 42.2 - - - +
272H GLU* 4.2 6.9 - - + +
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Residues in contact with ARG 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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222F MET* 4.0 17.1 - - + +
226F TYR* 3.3 44.4 + - - -
230F LEU* 3.2 33.2 - - - +
234F HIS 3.1 10.4 + - - +
235F ILE* 3.5 8.5 - - - +
237F THR* 1.3 75.3 - - + +
239F VAL* 1.3 64.1 + - - +
241F ARG* 3.4 36.9 + - - +
242F LYS* 3.1 23.7 + - - +
272H GLU* 4.3 14.4 + - - +
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Residues in contact with VAL 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215F PHE* 3.8 34.5 - - + -
218F SER* 4.0 5.4 - - - +
219F LEU* 3.7 42.4 - - + +
222F MET* 3.7 17.0 - - + -
235F ILE* 3.0 16.2 + - + +
236F LEU* 3.3 16.2 - - + +
238F ARG* 1.3 78.4 - - - +
240F ASN* 1.3 62.7 + - - +
242F LYS* 3.3 3.8 + - - +
243F VAL* 3.1 24.8 + - + +
263F PRO* 4.7 1.3 - - + -
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Residues in contact with ASN 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215F PHE* 5.4 0.2 - - - -
236F LEU 3.0 18.0 + - - +
237F THR 3.1 5.4 + - - +
239F VAL* 1.3 77.8 - - - +
241F ARG* 1.3 57.9 + - - +
244F ALA* 3.0 29.7 + - - +
262F ILE* 3.7 10.5 - - + +
263F PRO* 3.2 36.1 + - - +
265F ILE* 3.5 17.6 - - - +
267H SER 3.4 23.8 + - - -
268H MET* 3.9 4.9 - - - +
269H LEU 2.9 32.0 + - - +
270H THR* 4.3 0.4 - - - -
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Residues in contact with ARG 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237F THR 3.3 3.9 + - - +
238F ARG* 3.4 49.3 + - - +
239F VAL 3.3 0.2 - - - -
240F ASN* 1.3 76.0 - - - +
242F LYS* 1.3 54.7 + - - +
244F ALA* 4.1 1.1 - - - -
245F THR* 2.4 58.2 + - + +
36G SER 4.6 8.5 - - - +
270H THR* 3.3 40.1 + - - +
271H LYS* 3.8 32.1 - - - +
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Residues in contact with LYS 242 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217F GLN* 5.3 1.1 - - - -
218F SER* 3.6 32.8 - - - +
221F ALA* 4.4 9.1 - - - +
222F MET* 3.8 30.8 - - + +
238F ARG 3.1 16.9 + - - +
239F VAL* 3.7 4.5 - - - +
240F ASN 3.3 0.2 - - - -
241F ARG* 1.3 78.0 - - - +
243F VAL* 1.3 57.2 + - - +
245F THR* 4.0 3.4 - - - -
246F GLU* 2.8 76.9 + - - +
247F PHE* 3.4 10.7 - - + -
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Residues in contact with VAL 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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214F TRP* 3.9 19.5 - - + +
215F PHE* 4.0 8.5 - - - -
218F SER* 3.4 21.5 - - - +
239F VAL* 3.1 19.3 + - + +
242F LYS* 1.3 76.7 - - - +
244F ALA* 1.3 61.4 + - - +
247F PHE* 3.6 27.5 + - - +
260F LYS* 4.1 0.7 + - - -
261F GLN* 3.3 47.5 + - + +
263F PRO* 3.8 21.1 - - + -
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Residues in contact with ALA 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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240F ASN 3.0 19.8 + - - +
241F ARG* 3.8 6.5 - - - +
243F VAL* 1.3 79.3 - - - +
245F THR* 1.3 61.9 + - + +
260F LYS* 2.3 29.2 + - - +
261F GLN 3.6 8.5 - - - -
262F ILE* 4.0 11.4 - - + -
186H LYS 3.4 6.4 - - - +
187H ILE* 3.9 3.0 - - + -
188H PRO* 3.5 25.0 - - + +
191H ALA* 5.0 0.4 - - + -
270H THR* 4.3 8.1 - - + -
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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
----------------------------------------------------------
241F ARG* 2.4 55.8 + - + +
242F LYS* 3.8 1.6 + - - -
244F ALA* 1.3 80.1 - - + +
246F GLU* 1.3 72.2 + - - +
247F PHE 3.5 1.5 + - - -
260F LYS* 5.0 1.3 - - - -
185H HIS* 5.3 7.6 + - - -
186H LYS 4.4 8.7 + - - +
187H ILE* 4.3 17.0 - - + -
270H THR* 6.1 0.7 - - + -
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Residues in contact with GLU 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242F LYS* 2.8 58.3 + - - +
245F THR* 1.3 86.9 + - - +
247F PHE* 1.3 72.7 + - + +
248F GLU 4.3 0.5 + - - -
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Residues in contact with PHE 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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208F ASN* 6.3 0.2 - - + -
214F TRP* 3.4 65.2 - + + -
217F GLN* 3.9 28.0 - - + -
218F SER* 3.4 25.1 - - - -
242F LYS* 3.4 26.9 - - + -
243F VAL* 3.6 15.5 + - - +
245F THR 3.5 1.2 - - - -
246F GLU* 1.3 93.3 - - + +
248F GLU* 1.3 60.9 + - - +
260F LYS* 3.2 28.8 + - - +
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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
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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