Contacts of the helix formed by residues 226 - 241 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B GLN* 5.6 0.3 + - - -
224B GLY 4.0 0.8 + - - -
225B LEU* 1.3 69.1 - - - +
227B ILE* 1.3 63.1 + - - +
228B GLU* 3.0 28.6 + - - +
229B GLU* 3.1 26.7 + - + +
230B MSE 3.4 14.3 + - - +
391B GLU* 2.8 31.3 + - - +
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Residues in contact with ILE 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B PHE* 3.6 28.3 - - + -
63B ILE* 3.9 24.2 - - + -
64B GLN* 3.9 28.4 - - + +
217B LEU* 3.8 37.6 - - + +
220B ILE* 3.8 23.8 - - + -
221B ALA* 4.0 14.4 - - + +
225B LEU 3.4 2.7 + - - +
226B ASN* 1.3 70.0 - - - +
228B GLU* 1.3 65.7 + - - +
229B GLU 3.3 0.2 - - - -
230B MSE 3.3 7.6 + - - +
231B MSE 3.1 27.4 + - - +
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Residues in contact with GLU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B TYR* 6.0 0.4 - - - -
60B PHE* 3.8 15.9 - - + -
64B GLN* 3.1 32.7 + - - +
226B ASN* 3.0 13.7 + - - +
227B ILE* 1.3 78.0 - - - +
229B GLU* 1.3 63.4 + - + +
231B MSE 3.3 5.2 + - - +
232B LYS* 3.1 41.1 + - - +
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Residues in contact with GLU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B ASN* 3.1 32.7 + - + +
227B ILE 3.3 0.4 - - - -
228B GLU* 1.3 73.3 - - + +
230B MSE 1.3 67.3 + - - +
232B LYS* 3.3 26.5 + - - +
233B GLY 3.0 18.9 + - - -
391B GLU* 4.1 12.3 - - + -
392B TYR* 3.4 34.8 - - + +
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Residues in contact with MSE 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ALA* 4.5 0.4 - - + -
96B LEU* 3.9 21.1 - - + -
212B LEU* 4.0 22.7 - - + -
217B LEU* 4.4 8.7 - - + -
220B ILE* 3.7 47.3 - - + -
226B ASN 3.4 8.2 + - - +
227B ILE* 3.3 11.6 + - + +
228B GLU 3.2 0.2 - - - -
229B GLU* 1.3 80.2 - - - +
231B MSE 1.3 61.7 + - + +
233B GLY 3.4 1.0 + - - -
234B ALA* 3.1 19.2 + - - +
391B GLU* 3.4 27.3 - - + +
394B PHE* 3.7 25.8 - - + -
395B GLY* 3.5 13.9 - - - -
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Residues in contact with MSE 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU 3.8 3.6 - - - +
52B PRO* 3.2 40.0 - - + +
55B TYR* 3.4 36.1 - - + +
60B PHE* 3.6 20.6 - - + -
212B LEU* 4.0 44.0 - - + +
217B LEU* 4.4 10.3 - - + -
227B ILE 3.1 16.2 + - - +
228B GLU* 3.8 6.3 - - - +
230B MSE 1.3 72.8 - - - +
232B LYS* 1.3 62.2 + - + +
234B ALA* 3.2 3.8 + - + +
235B ALA* 2.8 30.4 + - - +
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Residues in contact with LYS 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B GLU* 3.1 28.5 + - - +
229B GLU* 3.3 29.7 + - - +
231B MSE 1.3 77.9 - - + +
233B GLY* 1.3 61.6 + - - +
235B ALA* 3.4 7.4 + - - +
236B ALA* 3.0 23.0 + - - +
392B TYR* 3.9 14.3 - - + -
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Residues in contact with GLY 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B GLU 3.0 11.1 + - - -
230B MSE 3.8 0.9 - - - -
231B MSE 3.2 0.2 - - - -
232B LYS* 1.3 75.6 - - - +
234B ALA* 1.3 61.8 + - - +
236B ALA 3.2 2.1 + - - -
237B GLY 3.0 16.8 + - - -
392B TYR* 3.2 41.4 - - - -
396B TYR* 3.2 20.1 - - - -
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Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B PRO* 3.8 15.1 - - + +
212B LEU* 3.6 32.1 - - + -
230B MSE 3.1 12.8 + - - +
231B MSE 3.2 9.6 + - - +
233B GLY* 1.3 77.4 - - - +
235B ALA* 1.3 55.5 + - - +
237B GLY* 3.1 2.9 + - - -
238B ARG* 2.8 26.3 + - - +
395B GLY 3.4 16.7 - - - +
396B TYR* 4.3 0.7 - - - +
399B TYR* 3.8 9.0 - - + -
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Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B PRO* 3.6 13.6 - - + +
53B LEU* 3.7 30.2 - - + +
231B MSE 2.8 17.0 + - - +
232B LYS* 3.6 8.5 - - - +
233B GLY 3.3 0.2 - - - -
234B ALA* 1.3 73.6 - - - +
236B ALA* 1.3 66.2 + - - +
238B ARG* 3.2 7.2 + - - +
239B ASP* 3.0 21.8 + - - +
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Residues in contact with ALA 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B LYS 3.0 12.4 + - - +
233B GLY 3.2 8.5 + - - +
235B ALA* 1.3 75.5 - - - +
237B GLY* 1.3 57.9 + - - +
239B ASP* 3.3 6.2 + - - +
240B ASP* 2.9 35.1 + - - +
392B TYR* 3.2 26.5 - - + +
396B TYR* 3.5 13.0 - - + -
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Residues in contact with GLY 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B GLY 3.0 10.7 + - - -
234B ALA 3.1 4.9 + - - -
236B ALA* 1.3 74.5 - - - +
238B ARG* 1.3 58.5 + - - +
241B PHE* 2.8 50.2 + - - +
396B TYR* 3.4 19.2 - - - -
399B TYR* 3.5 12.6 - - - -
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Residues in contact with ARG 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B HIS* 3.5 33.8 + - - -
49B VAL* 3.4 21.3 - - - +
50B ASP* 2.8 31.3 + - - +
52B PRO* 4.6 4.9 - - + -
53B LEU* 3.9 25.8 - - + +
234B ALA 2.8 13.6 + - - +
235B ALA* 3.2 14.1 + - - +
237B GLY* 1.3 76.7 - - - +
239B ASP* 1.3 66.5 + - - +
241B PHE 3.9 0.5 - - - -
242B GLY* 3.3 19.4 + - - -
399B TYR* 3.4 20.6 + - + +
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Residues in contact with ASP 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B ALA 3.0 13.2 + - - +
236B ALA* 3.5 10.1 - - - +
238B ARG* 1.3 82.2 - - - +
240B ASP* 1.3 69.7 + - - +
242B GLY* 3.1 15.6 + - - -
243B THR* 4.5 2.1 + - - +
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Residues in contact with ASP 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B HIS* 5.1 5.2 - - - +
236B ALA* 2.9 21.4 + - - +
237B GLY 4.1 2.0 - - - +
239B ASP* 1.3 81.7 - - - +
241B PHE* 1.3 70.5 + - + +
242B GLY 3.4 1.2 + - - -
243B THR* 3.8 6.4 - - - +
248B GLU 3.8 18.5 - - - +
249B ASN* 4.5 0.2 - - - -
250B PRO* 4.6 1.4 - - + +
396B TYR* 2.3 41.0 + - + +
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Residues in contact with PHE 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B VAL 4.9 3.8 - - - -
237B GLY* 2.8 43.0 + - - +
238B ARG 3.9 2.7 - - - -
240B ASP* 1.3 79.8 - - + +
242B GLY* 1.3 54.9 + - - +
243B THR 3.4 0.2 - - - -
249B ASN* 2.9 36.8 + - - +
250B PRO* 3.7 31.0 - - + -
251B ALA* 3.8 13.7 - - + -
396B TYR* 3.5 33.0 - + - -
399B TYR* 4.0 6.1 - + + -
400B PHE* 3.6 44.2 - + + -
403B LYS* 2.9 33.1 + - + +
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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