Contacts of the helix formed by residues 236 - 255 (chain F) in PDB entry 2FRV
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 PRO 236 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234F LEU 3.9 3.6 - - - +
235F ARG* 1.3 85.0 - - + +
237F GLU* 1.3 77.5 + - - +
239F ILE* 3.2 8.3 + - + +
240F ALA* 3.0 25.6 + - - +
433F GLU* 5.1 7.2 - - + +
436F VAL* 5.6 5.2 - - + -
437F LYS* 4.8 18.2 - - - +
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Residues in contact with GLU 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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235F ARG* 3.3 40.0 + - - +
236F PRO* 1.3 97.8 - - - +
238F ARG* 1.3 60.0 + - + +
240F ALA* 3.3 6.3 + - - +
241F GLU* 3.1 29.0 + - - +
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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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236E VAL* 3.1 30.1 + - - +
237E ASN* 3.6 22.4 - - - +
241E GLN* 4.0 9.0 + - - -
212F ILE* 3.4 42.7 - - + +
213F PHE* 5.3 0.2 - - - -
232F ASP* 3.6 13.0 + - - +
233F SER* 3.8 20.2 - - - +
235F ARG* 3.0 48.8 + - + +
237F GLU* 1.3 76.6 - - - +
239F ILE* 1.3 60.5 + - - +
241F GLU* 2.6 40.1 + - - +
242F PHE* 3.5 10.4 + - - +
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Residues in contact with ILE 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213F PHE* 4.6 9.6 - - + -
233F SER 3.5 18.8 - - - +
234F LEU* 4.3 13.9 - - + +
235F ARG 3.1 10.2 + - - +
236F PRO* 4.0 4.9 - - + +
238F ARG* 1.3 74.5 - - - +
240F ALA* 1.3 60.9 + - - +
242F PHE* 3.6 6.3 + - - +
243F ARG* 2.9 46.8 + - - +
429F LEU* 4.1 12.7 - - + +
432F LEU* 3.6 34.3 - - + +
433F GLU* 3.7 39.9 - - + +
436F VAL* 5.3 2.5 - - + -
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Residues in contact with ALA 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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236F PRO 3.0 16.8 + - - +
237F GLU* 3.4 8.3 - - - +
239F ILE* 1.3 79.3 - - - +
241F GLU* 1.3 55.9 + - - +
243F ARG* 3.3 10.9 + - - +
244F LYS* 3.0 28.9 + - - +
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Residues in contact with GLU 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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236E VAL* 3.2 27.0 - - - +
208F ARG* 5.5 0.5 - - - -
212F ILE* 3.8 11.3 - - + +
237F GLU* 3.1 8.7 + - - +
238F ARG* 2.6 46.2 + - - +
240F ALA* 1.3 75.3 - - - +
242F PHE* 1.3 64.2 - - - +
244F LYS* 3.4 9.5 + - - +
245F LEU* 3.3 29.7 + - + +
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Residues in contact with PHE 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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98F LEU* 4.2 10.1 - - + -
102F ALA* 4.8 10.8 - - + -
209F ALA* 3.2 39.3 - - + +
210F MET* 5.0 0.2 - - - -
212F ILE* 3.8 15.3 - - + -
213F PHE* 3.1 34.5 - + + -
238F ARG 3.5 15.4 + - - +
239F ILE* 3.7 5.2 - - - +
241F GLU* 1.3 76.4 - - - +
243F ARG* 1.3 71.0 + - - +
245F LEU* 3.4 4.8 + - - +
246F TYR* 2.9 39.3 + + + +
425F VAL* 3.9 28.9 - - + -
429F LEU* 3.9 24.2 - - + -
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Residues in contact with ARG 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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239F ILE* 2.9 29.5 + - - +
240F ALA* 3.3 9.6 + - - +
242F PHE* 1.3 81.2 - - - +
244F LYS* 1.3 55.6 + - - +
246F TYR* 3.3 5.5 - - + +
247F LYS* 3.1 53.8 + - + +
426F GLU* 3.4 18.8 + - - +
429F LEU* 3.4 28.7 - - + +
430F ASP* 2.9 26.6 + - - -
433F GLU* 3.0 34.6 + - - +
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Residues in contact with LYS 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 ALA 3.0 12.5 + - - +
241F GLU* 3.4 12.5 + - - +
243F ARG* 1.3 70.5 - - - +
245F LEU* 1.3 77.5 + - - +
247F LYS* 3.4 7.3 + - - +
248F GLU* 2.4 60.7 + - - +
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Residues in contact with LEU 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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205F LYS* 4.0 34.8 - - + +
208F ARG* 3.7 39.5 - - + +
209F ALA* 4.0 16.6 - - + +
212F ILE* 3.9 17.9 - - + -
241F GLU* 3.3 19.6 + - + +
242F PHE 3.8 4.3 - - - +
244F LYS* 1.3 83.4 - - - +
246F TYR* 1.3 65.7 + - - +
248F GLU* 3.2 16.6 + - - +
249F VAL* 2.9 30.0 + - - +
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Residues in contact with TYR 246 (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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105F MET* 4.0 22.4 - - + -
209F ALA* 4.8 4.6 - - + +
242F PHE* 2.9 32.2 + + + +
243F ARG* 3.3 14.4 - - + +
245F LEU* 1.3 76.4 - - - +
247F LYS* 1.3 66.3 + - + +
249F VAL* 3.3 5.1 + - - +
250F ARG* 2.7 56.9 + - + +
422F ALA 2.6 30.5 + - - -
425F VAL* 3.7 22.9 - - + -
426F GLU* 2.9 44.7 + - - +
429F LEU* 4.9 4.3 - - + -
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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
----------------------------------------------------------
243F ARG* 3.1 32.1 + - + +
244F LYS* 3.9 6.5 - - - +
245F LEU 3.3 0.2 - - - -
246F TYR* 1.3 82.3 - - + +
248F GLU* 1.3 66.4 + - - +
250F ARG* 3.1 6.9 + - - +
251F GLU* 3.0 41.1 + - - +
426F GLU* 3.9 25.9 + - - -
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Residues in contact with GLU 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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202F VAL* 5.1 1.5 - - - +
205F LYS* 2.7 45.2 + - + +
244F LYS* 2.4 52.9 + - - +
245F LEU* 3.2 9.5 + - - +
247F LYS* 1.3 75.7 - - - +
249F VAL* 1.3 66.7 + - + +
251F GLU* 3.6 10.3 + - - +
252F PHE* 3.3 19.4 + - - +
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Residues in contact with VAL 249 (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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105F MET* 3.4 24.0 - - + -
109F LEU* 4.8 4.0 - - + -
202F VAL* 3.9 22.9 - - + -
205F LYS* 3.8 27.6 - - + -
206F ALA* 4.0 27.6 - - + +
209F ALA* 6.1 0.2 - - + -
245F LEU 2.9 18.9 + - - +
246F TYR* 3.9 3.6 - - - +
248F GLU* 1.3 77.1 - - + +
250F ARG* 1.3 64.7 + - - +
252F PHE* 3.2 4.7 + - - +
253F ILE* 3.1 28.7 + - + +
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Residues in contact with ARG 250 (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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105F MET* 3.7 10.4 - - + +
246F TYR* 2.7 52.3 + - + +
247F LYS* 3.6 7.6 - - - +
249F VAL* 1.3 73.1 - - - +
251F GLU* 1.3 63.2 + - + +
253F ILE* 3.1 13.9 + - - +
254F GLU* 2.9 52.2 + - + +
422F ALA* 4.0 21.1 + - + +
423F GLN* 3.5 34.4 + - - +
426F GLU* 4.0 13.5 + - - +
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Residues in contact with GLU 251 (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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247F LYS* 3.0 33.3 + - - +
248F GLU* 3.8 9.3 - - - +
250F ARG* 1.3 77.2 - - + +
252F PHE* 1.3 51.0 + - - +
254F GLU* 3.3 10.6 + - - +
255F GLN* 2.7 62.7 + - - +
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Residues in contact with PHE 252 (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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109F LEU* 3.4 33.4 - - + -
113F TYR* 3.9 10.1 - + - -
144F LYS* 4.0 3.6 - - - +
195F HIS 4.2 6.3 - - - -
198F GLU* 3.7 30.1 - - + -
199F ALA* 4.1 20.4 - - + -
202F VAL* 3.7 32.3 - - + -
248F GLU 3.3 10.5 + - - +
249F VAL 3.2 8.0 + - - +
251F GLU* 1.3 79.4 - - - +
253F ILE* 1.3 56.8 + - - +
255F GLN* 5.0 0.2 - - - -
256F VAL* 3.0 62.2 + - + -
257F TYR 3.0 9.8 + - - -
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Residues in contact with ILE 253 (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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105F MET* 3.4 41.7 - - + +
109F LEU* 4.3 17.5 - - + -
249F VAL* 3.1 21.4 + - + +
250F ARG* 3.1 6.0 + - - +
252F PHE* 1.3 77.2 - - + +
254F GLU* 1.3 54.0 + - - +
257F TYR* 3.8 13.0 - - + -
258F ILE* 2.8 55.0 + - + +
418F CYS* 4.0 33.0 - - - -
419F LEU* 4.5 18.8 - - + -
422F ALA* 4.7 4.9 - - + -
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Residues in contact with GLU 254 (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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250F ARG* 2.9 57.3 + - + +
251F GLU* 3.6 12.1 - - - +
253F ILE* 1.3 79.3 - - + +
255F GLN* 1.3 67.8 + - + +
258F ILE* 4.1 10.3 - - - +
259F THR* 3.6 15.3 - - - +
419F LEU* 3.5 27.3 - - + +
423F GLN* 4.6 1.7 - - - +
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Residues in contact with GLN 255 (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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142F SER* 3.0 23.7 + - - -
143F PRO* 4.0 27.5 - - + +
144F LYS* 3.6 26.3 - - + +
251F GLU* 2.7 44.9 + - - +
254F GLU* 1.3 81.5 + - + +
256F VAL* 1.3 62.3 + - + +
259F THR* 2.9 18.1 + - - -
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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