Contacts of the helix formed by residues 225 - 241 (chain E) in PDB entry 6F0X
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 SER 225 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216E SER* 4.9 9.2 - - - -
220E LYS* 4.6 18.5 - - - -
221E TRP 3.7 12.0 + - - -
223E SER* 3.4 1.7 + - - -
224E GLU* 1.3 77.9 - - - +
226E GLY* 1.3 71.2 + - - -
228E LEU* 3.3 6.3 + - - +
229E VAL* 2.9 28.7 + - - +
257E LEU* 5.9 2.7 - - - -
272E ASP* 4.7 6.2 + - - +
276E VAL* 3.1 31.3 - - - +
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Residues in contact with GLY 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D HIS* 5.6 6.1 - - - -
218D PHE* 6.4 0.7 - - - -
223E SER* 3.3 8.5 + - - +
225E SER* 1.3 78.7 + - - +
227E LYS* 1.3 58.5 + - - +
229E VAL* 2.7 30.0 + - - +
230E THR* 3.0 15.9 + - - +
275E ARG* 5.7 3.6 - - - -
276E VAL* 4.8 11.9 - - - -
279E ALA* 5.2 4.4 - - - +
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Residues in contact with LYS 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D ASN* 6.1 3.1 - - - +
119D ILE* 5.4 11.1 - - - +
120D ILE* 5.1 16.2 - - + -
215D HIS 5.6 1.8 + - - -
220D LYS* 5.1 9.9 - - - +
223E SER* 3.1 31.2 + - - +
226E GLY* 1.3 71.2 - - - +
228E LEU* 1.3 57.9 + - - +
230E THR* 2.2 34.5 + - + +
231E LYS* 2.9 59.5 + - - +
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Residues in contact with LEU 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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120E ILE* 3.6 36.1 - - + +
212E ILE* 3.5 28.2 - - + +
216E SER* 3.1 36.3 - - - +
217E LEU* 5.9 1.6 - - + -
223E SER 3.5 2.7 + - - +
224E GLU* 3.8 14.4 - - - +
225E SER* 3.3 9.4 + - - +
226E GLY 3.0 0.8 - - - -
227E LYS* 1.3 78.6 - - - +
229E VAL* 1.3 66.4 + - + +
231E LYS* 3.2 15.3 + - + +
232E MET* 2.9 25.2 + - - +
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Residues in contact with VAL 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E SER* 2.9 22.0 + - - +
226E GLY* 2.7 14.8 + - - +
228E LEU* 1.3 77.1 - - + +
230E THR* 1.3 63.5 + - - +
232E MET* 3.2 7.2 + - + +
233E PHE* 3.0 49.1 + - + -
257E LEU* 5.0 9.0 - - + -
276E VAL* 4.8 10.1 - - + -
279E ALA* 3.9 25.4 - - + -
280E VAL* 4.3 17.5 - - + +
283E GLN* 4.8 1.6 - - + -
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Residues in contact with THR 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D ILE* 5.1 14.2 - - - +
120D ILE* 5.6 7.2 - - + +
121D ALA* 5.8 5.8 - - + -
215D HIS* 4.7 25.4 - - + +
216D SER* 5.6 1.1 - - - +
226E GLY 3.0 13.7 + - - +
227E LYS* 2.2 42.6 + - + +
229E VAL* 1.3 76.7 - - + +
231E LYS* 1.3 58.5 + - - +
233E PHE* 3.5 3.3 + - - +
234E GLN* 2.9 28.8 + - - +
279E ALA* 5.3 3.4 - - + -
283E GLN* 5.4 11.6 - - - +
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Residues in contact with LYS 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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119D ILE* 5.5 7.0 - - + -
111E ASN 5.7 1.3 - - - +
112E LEU* 2.8 41.0 - - + +
114E GLU* 6.2 1.2 - - - +
120E ILE* 5.6 3.2 - - + +
227E LYS* 2.9 43.4 + - - +
228E LEU* 3.5 17.3 - - + +
230E THR* 1.3 82.7 + - - +
232E MET* 1.3 62.9 + - - +
234E GLN* 3.1 9.5 + - - +
235E LYS* 3.0 31.5 + - - +
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Residues in contact with MET 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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122E ALA* 5.6 2.0 - - + -
210E ILE* 4.7 13.5 - - + -
212E ILE* 3.4 52.3 - - + -
228E LEU* 2.9 16.0 + - + +
229E VAL* 3.6 7.9 - - + +
231E LYS* 1.3 76.4 - - - +
233E PHE* 1.3 100.5 + - + +
235E LYS* 3.0 13.9 + - + +
236E ILE* 2.9 44.5 + - + +
249E VAL* 5.0 1.8 - - + -
251E ILE* 4.3 17.0 - - + -
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Residues in contact with PHE 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 VAL* 3.0 40.3 + - + +
230E THR 4.2 1.1 - - - +
232E MET* 1.3 98.7 - - + +
234E GLN* 1.3 60.6 + - - +
236E ILE* 3.4 23.9 - - + +
237E GLN* 2.8 31.7 + - - +
249E VAL* 4.9 5.6 - - + -
251E ILE* 4.3 15.5 - - + -
280E VAL* 4.9 14.1 - - + -
283E GLN* 3.2 55.3 - - + +
284E ILE* 4.8 7.6 - - + -
287E ILE* 4.3 26.2 - - + +
295E ILE* 5.2 1.8 - - + -
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Residues in contact with GLN 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D ILE* 3.2 39.1 - - + +
230E THR 2.9 15.8 + - - +
231E LYS* 3.1 12.3 - - - +
233E PHE* 1.3 77.0 - - - +
235E LYS* 1.3 67.7 + - + +
237E GLN* 3.3 9.7 + - - +
238E ASP* 3.0 54.6 + - - +
270P LYS* 5.2 4.6 - - - +
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Residues in contact with LYS 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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110E GLU* 3.1 18.0 - - + +
111E ASN* 2.4 54.7 + - - +
122E ALA* 5.4 0.6 - - - +
231E LYS* 3.0 22.0 + - - +
232E MET* 3.4 13.5 - - + +
234E GLN* 1.3 79.0 - - + +
236E ILE* 1.3 63.1 + - + +
238E ASP* 3.4 6.5 + - - +
239E LEU* 2.9 41.0 + - + +
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Residues in contact with ILE 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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210E ILE* 4.9 15.5 - - + -
232E MET* 2.9 44.5 + - + +
233E PHE* 3.4 37.5 - - + +
235E LYS* 1.3 75.3 - - + +
237E GLN* 1.3 64.3 - - - +
239E LEU* 2.8 20.1 + - - -
240E ILE* 2.9 33.2 + - + +
247E VAL* 4.8 5.2 - - + -
249E VAL* 3.8 31.6 - - + -
287E ILE* 5.1 5.6 - - + -
293E VAL* 5.9 0.2 - - + -
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Residues in contact with GLN 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 PHE 2.8 22.0 + - - +
234E GLN* 3.3 11.7 - - - +
236E ILE* 1.3 71.1 - - - +
238E ASP* 1.3 71.1 + - - +
240E ILE* 3.3 21.7 + - - +
241E ASP* 4.1 12.8 + - - +
283E GLN* 5.4 2.6 - - - +
286E GLN* 5.3 6.8 - - - +
287E ILE* 3.7 21.5 - - + +
290E HIS* 3.6 27.9 + - - -
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Residues in contact with ASP 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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234E GLN* 3.0 41.8 + - - +
235E LYS* 3.8 8.2 - - - +
237E GLN* 1.3 82.4 - - - +
239E LEU* 1.3 62.1 + - + +
240E ILE 2.8 7.3 + - - -
241E ASP* 3.7 9.6 + - - +
123P LYS* 3.5 37.8 + - - +
270P LYS* 3.9 17.7 + - - -
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Residues in contact with LEU 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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124E HIS* 5.2 10.1 - - + +
208E GLN* 5.4 14.7 - - + +
210E ILE* 4.7 19.5 - - + -
235E LYS* 2.9 30.6 + - + +
236E ILE* 2.8 11.6 + - - +
238E ASP* 1.3 74.1 - - + +
240E ILE* 1.3 61.9 + - - +
242E ASP* 4.6 7.6 + - - +
245E ALA* 5.5 2.4 - - - +
247E VAL* 4.1 10.0 - - + +
123P LYS* 6.2 2.5 - - - -
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Residues in contact with ILE 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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236E ILE* 2.9 41.7 + - + +
237E GLN* 3.4 21.1 - - - +
238E ASP 2.8 4.4 + - - -
239E LEU* 1.3 79.8 - - - +
241E ASP* 1.3 56.3 + - - +
242E ASP* 2.5 28.5 + - - +
245E ALA* 4.6 0.3 - - - +
247E VAL* 4.1 12.5 - - + +
287E ILE* 4.5 10.3 - - + -
290E HIS* 3.5 43.3 - - + +
292E ASN* 3.6 23.6 + - - +
293E VAL* 3.8 19.5 - - + -
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Residues in contact with ASP 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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237E GLN* 4.3 13.0 + - - +
238E ASP* 3.7 7.7 + - - +
240E ILE* 1.3 75.1 - - - +
242E ASP* 1.3 57.4 + - - +
243E LYS* 2.8 29.0 + - - +
290E HIS* 3.3 32.0 + - - -
292E ASN* 4.9 1.1 - - - +
123P LYS* 5.7 4.0 + - - +
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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
------------------------------------------------------------
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