Contacts of the helix formed by residues 226 - 241 (chain F) in PDB entry 3IFS
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 ASN 226 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64F GLN* 5.6 0.2 + - - -
224F GLY 3.9 0.8 + - - -
225F LEU* 1.3 68.4 - - - +
227F ILE* 1.3 62.3 + - - +
228F GLU* 2.8 27.5 + - - +
229F GLU* 3.0 30.2 + - + +
230F MSE 3.2 14.0 + - - -
391F GLU* 2.7 31.7 + - - +
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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
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60F PHE* 3.6 27.6 - - + -
63F ILE* 4.1 23.1 - - + -
64F GLN* 3.9 27.1 - - + +
217F LEU* 3.7 38.1 - - + +
220F ILE* 3.8 23.6 - - + -
221F ALA* 4.1 14.6 - - + +
225F LEU 3.3 2.5 + - - +
226F ASN* 1.3 68.9 + - - +
228F GLU* 1.3 65.8 + - - +
230F MSE 3.6 8.3 - - - +
231F MSE 3.1 27.2 + - - +
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Residues in contact with GLU 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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60F PHE* 3.8 17.8 - - + -
64F GLN* 2.8 36.3 + - - +
226F ASN* 2.8 11.9 + - - +
227F ILE* 1.3 73.9 - - - +
229F GLU* 1.3 68.1 + - + +
231F MSE 3.3 4.8 + - - +
232F LYS* 3.0 36.3 + - - +
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Residues in contact with GLU 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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226F ASN* 3.0 37.7 + - + +
228F GLU* 1.3 77.4 - - - +
230F MSE 1.3 62.3 + - - +
232F LYS* 3.1 39.6 + - - +
233F GLY 2.9 19.1 + - - -
391F GLU* 4.3 10.8 - - + +
392F TYR* 3.5 31.5 - - + +
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Residues in contact with MSE 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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92F ALA* 4.5 0.7 - - + -
96F LEU* 4.0 20.9 - - + -
212F LEU* 4.1 18.2 - - + -
217F LEU* 4.3 10.3 - - + -
220F ILE* 3.7 41.7 - - + -
226F ASN 3.2 11.2 + - - +
227F ILE* 3.6 11.2 - - + +
228F GLU 3.2 0.6 - - - -
229F GLU* 1.3 76.5 - - - +
231F MSE 1.3 62.1 + - - +
233F GLY* 3.2 2.3 + - - -
234F ALA* 3.1 18.2 + - - +
391F GLU* 3.3 27.3 - - + +
394F PHE* 3.6 31.4 - - + -
395F GLY* 3.6 17.4 - - - -
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Residues in contact with MSE 231 (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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51F LEU* 4.1 2.0 - - + +
52F PRO* 3.0 50.6 - - + +
55F TYR* 3.7 28.0 - - + +
60F PHE* 3.7 22.0 - - + -
212F LEU* 4.2 37.9 - - + +
217F LEU* 4.8 9.4 - - + -
227F ILE 3.1 19.8 + - - +
228F GLU* 3.3 5.1 + - - +
230F MSE 1.3 72.4 - - - +
232F LYS* 1.3 61.5 + - - +
234F ALA* 3.2 5.0 + - + +
235F ALA* 2.8 30.8 + - - +
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Residues in contact with LYS 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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228F GLU* 3.0 26.1 + - - +
229F GLU* 3.1 39.7 + - - +
231F MSE 1.3 75.0 - - + +
233F GLY* 1.3 62.4 + - - +
235F ALA* 3.3 7.9 + - - +
236F ALA* 3.0 22.7 + - - +
392F TYR* 3.7 13.5 - - + -
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Residues in contact with GLY 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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229F GLU 2.9 11.5 + - - -
230F MSE 3.2 1.5 + - - -
232F LYS* 1.3 78.7 - - - +
234F ALA* 1.3 59.9 + - - +
236F ALA 3.1 1.6 + - - -
237F GLY 3.0 18.4 + - - -
392F TYR* 3.3 39.9 - - - -
396F TYR* 3.4 17.9 - - - -
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Residues in contact with ALA 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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52F PRO* 3.8 16.2 - - + +
212F LEU* 3.5 32.3 - - + -
230F MSE 3.1 12.0 + - - +
231F MSE 3.2 11.4 + - + +
233F GLY* 1.3 76.0 - - - +
235F ALA* 1.3 57.1 + - - +
237F GLY* 3.3 1.7 + - - -
238F ARG* 2.8 28.1 + - - +
395F GLY 3.5 17.1 - - - +
396F TYR* 4.3 0.4 - - - +
399F TYR* 4.0 5.4 - - + -
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Residues in contact with ALA 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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52F PRO* 3.7 14.7 - - - +
53F LEU* 4.1 25.1 - - + +
231F MSE 2.8 16.8 + - - +
232F LYS* 3.6 8.3 - - - +
234F ALA* 1.3 75.1 - - - +
236F ALA* 1.3 63.8 - - - +
238F ARG* 3.2 7.3 + - - +
239F ASP* 3.1 22.7 + - - +
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Residues in contact with ALA 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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232F LYS 3.0 10.7 + - - +
233F GLY 3.1 7.6 + - - +
235F ALA* 1.3 75.6 - - - +
237F GLY* 1.3 57.8 + - - +
239F ASP* 3.2 7.0 + - - +
240F ASP* 2.8 36.2 + - - +
392F TYR* 3.2 26.2 - - - +
396F TYR* 3.7 13.0 - - + -
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Residues in contact with GLY 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 GLY 3.0 11.6 + - - -
234F ALA 3.6 3.8 - - - -
236F ALA* 1.3 75.3 - - - +
238F ARG* 1.3 57.8 + - - +
240F ASP 4.4 0.2 - - - -
241F PHE* 2.8 47.9 + - - +
396F TYR* 3.3 20.8 - - - -
399F TYR* 3.6 12.1 - - - -
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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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36F HIS* 6.3 2.6 - - + -
49F VAL* 3.6 21.3 - - + +
50F ASP* 2.9 30.7 + - - +
52F PRO* 4.5 5.4 - - + -
53F LEU* 2.9 42.6 - - - +
234F ALA 2.8 16.9 + - - +
235F ALA* 3.2 11.3 + - - +
237F GLY* 1.3 73.8 - - - +
239F ASP* 1.3 77.0 + - - +
241F PHE 3.8 0.7 - - - -
242F GLY* 3.1 21.5 + - - -
399F TYR* 3.4 25.6 + - + +
451F SO4 4.7 15.6 + - - -
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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
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235F ALA 3.1 12.9 + - - +
236F ALA* 3.4 10.3 - - - +
238F ARG* 1.3 86.5 + - - +
240F ASP* 1.3 71.5 + - - +
242F GLY* 3.3 12.1 + - - -
243F THR* 4.2 3.6 + - - -
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Residues in contact with ASP 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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3F THR* 3.9 23.9 - - + +
4F HIS 4.5 1.0 + - - -
236F ALA* 2.8 22.5 + - - +
237F GLY 4.1 2.0 - - - +
239F ASP* 1.3 81.9 - - - +
241F PHE* 1.3 65.1 + - + +
242F GLY 3.3 0.2 - - - -
243F THR* 3.5 20.4 - - - +
248F GLU 4.3 5.2 - - - +
249F ASN* 4.5 0.2 - - - -
250F PRO* 4.9 1.2 - - - +
396F TYR* 2.6 38.6 + - + +
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Residues in contact with PHE 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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3F THR* 4.6 1.6 - - + -
5F VAL 4.5 4.7 - - - -
237F GLY* 2.8 32.5 + - - +
238F ARG 3.8 2.0 - - - -
240F ASP* 1.3 78.3 - - + +
242F GLY* 1.3 50.2 - - - +
243F THR 3.3 4.5 - - - -
249F ASN* 3.0 33.3 + - - +
250F PRO* 4.0 24.5 - - + -
251F ALA* 3.9 14.6 - - + -
396F TYR* 3.4 45.5 - + - -
399F TYR* 4.2 4.0 - + + -
400F PHE* 3.5 50.7 - + + -
403F LYS* 2.8 37.1 + - + +
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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
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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