Contacts of the helix formed by residues 226 - 241 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224E GLY 3.9 1.6 + - - -
225E LEU* 1.3 69.1 - - - +
227E ILE* 1.3 60.7 + - - +
228E GLU* 2.8 27.6 + - - +
229E GLU* 3.0 29.1 + - + +
230E MSE 3.2 16.2 + - - +
391E GLU* 2.8 30.9 + - - +
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Residues in contact with ILE 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E PHE* 3.5 29.4 - - + -
63E ILE* 4.1 24.5 - - + -
64E GLN* 4.0 25.4 - - + +
217E LEU* 3.7 42.6 - - + +
220E ILE* 3.9 18.4 - - + -
221E ALA* 3.9 16.4 - - + -
225E LEU 3.3 2.9 + - - +
226E ASN* 1.3 69.9 + - - +
228E GLU* 1.3 64.4 + - - +
229E GLU 3.4 0.2 - - - -
230E MSE 3.7 7.4 - - - +
231E MSE 3.1 28.2 + - - +
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Residues in contact with GLU 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E PHE* 3.7 17.6 - - + -
64E GLN* 2.9 34.0 + - - +
226E ASN* 2.8 13.8 + - - +
227E ILE* 1.3 76.3 - - - +
229E GLU* 1.3 64.9 + - + +
231E MSE 3.2 5.4 + - - +
232E LYS* 3.0 35.8 + - - +
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Residues in contact with GLU 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E ASN* 3.0 36.4 + - + +
228E GLU* 1.3 75.0 - - + +
230E MSE 1.3 65.9 + - - +
232E LYS* 2.9 38.6 + - - +
233E GLY 3.0 18.5 + - - -
391E GLU* 4.2 11.2 - - + +
392E TYR* 3.5 30.2 - - + +
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Residues in contact with MSE 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E ALA* 4.5 1.8 - - + -
96E LEU* 4.3 7.4 - - + -
212E LEU* 4.0 23.6 - - + -
217E LEU* 4.2 11.4 - - + -
220E ILE* 3.8 42.6 - - + -
226E ASN 3.2 11.7 + - - +
227E ILE* 3.7 9.6 - - - +
228E GLU 3.2 0.2 - - - -
229E GLU* 1.3 77.7 - - - +
231E MSE 1.3 62.0 + - + +
233E GLY 3.2 0.7 + - - -
234E ALA* 3.1 18.7 + - - +
391E GLU* 3.4 40.3 - - + +
394E PHE* 3.7 28.5 - - + -
395E GLY* 3.6 13.1 - - - -
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Residues in contact with MSE 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E LEU* 3.6 5.4 - - + +
52E PRO* 3.0 50.8 - - + +
55E TYR* 3.2 32.1 - - + +
60E PHE* 3.7 21.5 - - + -
212E LEU* 4.1 39.3 - - + +
217E LEU* 4.5 8.5 - - + -
227E ILE 3.1 20.9 + - - +
228E GLU* 3.8 5.4 - - - +
230E MSE 1.3 76.5 - - - +
232E LYS* 1.3 58.2 + - + +
234E ALA* 3.3 2.9 + - - +
235E ALA* 2.9 28.8 + - - +
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Residues in contact with LYS 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228E GLU* 3.0 25.0 + - - +
229E GLU* 2.9 38.4 + - - +
231E MSE 1.3 76.2 - - + +
233E GLY* 1.3 57.8 + - - +
235E ALA* 3.3 7.3 + - - +
236E ALA* 3.0 27.9 + - - +
392E TYR* 3.9 14.4 - - + -
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Residues in contact with GLY 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E GLU 3.0 10.3 + - - -
230E MSE 3.2 1.1 + - - -
232E LYS* 1.3 77.1 - - - +
234E ALA* 1.3 56.5 + - - +
236E ALA 3.2 1.6 + - - -
237E GLY 2.9 24.1 + - - -
392E TYR* 3.3 41.4 - - - -
396E TYR* 3.4 18.7 - - - -
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Residues in contact with ALA 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E PRO* 3.7 17.0 - - + +
212E LEU* 3.5 32.1 - - + -
230E MSE 3.1 12.8 + - - +
231E MSE 3.7 9.6 - - - +
232E LYS 3.3 0.2 - - - -
233E GLY* 1.3 76.6 - - - +
235E ALA* 1.3 57.2 + - - +
237E GLY* 3.2 1.7 + - - -
238E ARG* 2.8 27.4 + - - +
395E GLY* 3.4 17.8 - - - +
396E TYR* 4.3 0.7 - - - +
399E TYR* 3.9 6.5 - - + -
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Residues in contact with ALA 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E PRO* 3.5 15.4 - - + +
53E LEU* 3.8 26.1 - - + +
231E MSE 2.9 17.5 + - - +
232E LYS* 3.6 7.9 - - - +
234E ALA* 1.3 74.7 - - - +
236E ALA* 1.3 65.7 + - - +
238E ARG* 3.1 8.2 + - - +
239E ASP* 3.1 21.3 + - - +
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Residues in contact with ALA 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E LYS 3.0 11.3 + - - +
233E GLY 3.2 7.8 + - - +
235E ALA* 1.3 75.0 - - - +
237E GLY* 1.3 58.8 + - - +
239E ASP* 3.2 7.0 + - - +
240E ASP* 2.9 34.4 + - - +
392E TYR* 3.2 27.8 - - - +
396E TYR* 3.7 12.8 - - + -
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Residues in contact with GLY 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E GLY 2.9 11.2 + - - -
234E ALA 3.5 4.5 - - - -
235E ALA 3.1 0.2 - - - -
236E ALA* 1.3 75.3 - - - +
238E ARG* 1.3 64.1 + - - +
241E PHE* 2.9 42.3 + - - +
396E TYR* 3.5 19.2 - - - -
399E TYR* 3.6 13.4 - - - -
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Residues in contact with ARG 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E HIS* 6.3 3.3 - - + -
49E VAL* 3.7 19.1 - - + +
50E ASP* 2.7 34.7 + - - +
52E PRO* 4.4 5.6 - - + -
53E LEU* 3.1 42.8 - - - +
234E ALA 2.8 13.7 + - - +
235E ALA* 3.1 11.9 + - - +
237E GLY* 1.3 75.4 - - - +
239E ASP* 1.3 72.0 + - - +
241E PHE 3.8 0.5 - - - -
242E GLY* 3.0 27.5 + - - -
399E TYR* 3.4 22.7 + - + +
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Residues in contact with ASP 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E ALA 3.1 11.8 + - - +
236E ALA* 3.5 10.1 - - - +
237E GLY 3.1 0.2 - - - -
238E ARG* 1.3 86.7 + - - +
240E ASP* 1.3 71.7 + - - +
242E GLY* 3.2 12.5 + - - -
243E THR* 4.1 5.2 + - - -
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Residues in contact with ASP 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E THR* 3.8 22.5 - - + +
4E HIS 4.4 0.9 + - - -
236E ALA* 2.9 17.1 + - - +
237E GLY 4.2 1.6 - - - +
239E ASP* 1.3 84.3 - - - +
241E PHE* 1.3 66.5 + - + +
242E GLY 3.4 0.4 - - - -
243E THR* 3.7 18.2 - - - +
248E GLU 4.2 6.8 - - - +
249E ASN* 4.4 0.2 - - - -
250E PRO* 4.7 0.9 - - - +
396E TYR* 2.5 39.1 + - + +
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Residues in contact with PHE 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E THR* 4.3 8.1 - - + -
5E VAL 4.4 5.8 - - - -
237E GLY* 2.9 30.4 + - - +
238E ARG 3.8 2.5 - - - -
240E ASP* 1.3 78.2 - - - +
242E GLY* 1.3 48.8 + - - +
249E ASN* 2.9 39.9 + - - +
250E PRO* 3.9 29.6 - - + -
251E ALA* 3.8 15.9 - - + -
396E TYR* 3.4 41.7 - + - -
399E TYR* 4.3 3.1 - + + -
400E PHE* 3.6 42.4 - + + -
403E LYS* 2.7 38.0 + - + +
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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