Contacts of the helix formed by residues 224 - 242 (chain E) in PDB entry 3TJK
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 224 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131E PHE* 4.7 2.5 - - - -
223E ARG* 1.3 77.4 - - - +
225E VAL* 1.3 58.8 + - - +
226E ASP* 3.4 13.0 + - - +
227E GLU* 3.1 29.6 + - - +
228E THR* 2.9 32.4 + - - -
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Residues in contact with VAL 225 (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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130E ALA* 3.7 39.7 - - + +
131E PHE* 3.8 25.4 - - + +
134E ARG* 3.8 36.1 - - + +
138E PHE* 3.6 30.1 - - + -
223E ARG 4.2 1.5 + - - +
224E SER* 1.3 68.5 + - - +
226E ASP* 1.3 65.6 + - - +
228E THR* 3.2 1.4 + - - -
229E LEU* 2.9 24.7 + - + +
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Residues in contact with ASP 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E ARG* 2.9 32.6 + - - +
224E SER* 3.3 9.5 + - - +
225E VAL* 1.3 78.4 - - - +
227E GLU* 1.3 57.5 + - - +
229E LEU* 3.5 6.7 - - - +
230E ARG* 3.1 27.4 + - - +
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Residues in contact with GLU 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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224E SER* 3.1 22.9 + - - +
226E ASP* 1.3 77.0 - - - +
228E THR* 1.3 65.9 + - - +
230E ARG* 2.7 47.4 + - - -
231E LEU* 3.1 38.4 + - + +
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Residues in contact with THR 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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112E VAL* 3.8 41.1 - - + -
131E PHE* 3.6 13.5 - - + -
138E PHE* 4.0 4.0 - - + -
202E LEU* 3.5 22.5 - - + +
204E ILE* 4.4 9.9 - - + -
223E ARG* 5.6 0.2 - - - +
224E SER 2.9 18.0 + - - -
225E VAL 3.2 4.0 + - - -
227E GLU* 1.3 78.2 - - - +
229E LEU* 1.3 57.5 + - - +
231E LEU* 3.2 12.0 + - - +
232E VAL* 2.9 28.9 + - - +
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Residues in contact with LEU 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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134E ARG* 3.5 18.8 - - - +
137E GLU* 3.5 42.2 - - + +
138E PHE* 3.3 37.2 - - + -
141E ILE* 3.9 22.2 - - + -
225E VAL* 2.9 16.7 + - + +
226E ASP* 3.5 5.8 - - - +
228E THR* 1.3 77.5 - - - +
230E ARG* 1.3 57.3 + - - +
232E VAL* 3.3 2.8 + - - +
233E GLN* 2.9 47.1 + - - +
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Residues in contact with ARG 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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226E ASP 3.1 14.9 + - - +
227E GLU* 2.7 42.4 + - - +
228E THR 3.3 0.2 - - - -
229E LEU* 1.3 77.5 - - - +
231E LEU* 1.3 75.7 + - - +
233E GLN* 3.6 13.4 + - - +
234E ALA* 3.0 33.4 + - - +
246E PRO 4.9 1.4 + - - -
248E GLY* 3.7 16.5 - - - +
249E TRP* 3.2 53.8 + - - +
250E LYS* 4.3 28.9 - - + +
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Residues in contact with LEU 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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202E LEU* 6.0 1.1 - - + -
204E ILE* 3.7 15.9 - - + -
213E GLN* 4.0 39.3 - - + +
215E THR* 4.9 3.6 - - - +
227E GLU* 3.1 41.0 + - + +
228E THR* 3.2 8.5 + - - +
230E ARG* 1.3 92.9 - - - +
232E VAL* 1.3 65.2 + - - +
234E ALA* 3.2 6.6 + - + +
235E PHE* 2.9 40.7 + - + -
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Residues in contact with VAL 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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110E TYR* 4.2 7.9 - - + -
112E VAL* 3.9 26.9 - - + -
138E PHE* 4.8 3.4 - - + -
141E ILE* 3.8 13.2 - - + -
143E THR* 3.3 29.4 - - + +
204E ILE* 4.1 18.4 - - + -
228E THR* 2.9 21.1 + - + +
229E LEU* 3.8 4.9 - - + +
231E LEU* 1.3 75.5 - - - +
233E GLN* 1.3 63.7 + - - +
235E PHE* 3.2 6.3 + - - +
236E GLN* 3.0 36.8 + - - +
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Residues in contact with GLN 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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141E ILE* 4.1 25.7 - - + +
229E LEU* 2.9 36.6 + - - +
230E ARG* 3.7 12.0 + - - +
232E VAL* 1.3 77.3 - - - +
234E ALA* 1.3 56.9 + - - +
236E GLN* 3.4 8.6 + - - +
237E TYR* 2.9 29.8 + - - +
249E TRP* 3.9 12.9 - - + -
251E PRO* 3.5 30.6 - - + +
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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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230E ARG* 3.0 25.3 + - - +
231E LEU* 3.2 8.7 + - + +
233E GLN* 1.3 77.0 - - - +
235E PHE* 1.3 59.0 + - + +
237E TYR* 3.7 1.1 - - - +
238E THR* 2.9 36.5 + - - +
245E ALA* 4.2 15.3 - - + -
249E TRP* 3.6 25.1 - - + -
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Residues in contact with PHE 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 TYR* 3.3 24.5 - - + +
204E ILE* 4.7 7.9 - - + -
212E ARG* 3.3 60.8 - - + -
213E GLN* 3.8 28.3 - - + -
231E LEU* 2.9 41.4 + - + +
232E VAL 3.9 0.9 - - - +
234E ALA* 1.3 73.7 - - + +
236E GLN* 1.3 60.7 + - - +
238E THR* 3.3 7.2 + - - -
239E ASP* 2.8 35.5 + - - +
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Residues in contact with GLN 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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110E TYR* 3.6 33.1 - - + +
141E ILE* 2.7 43.9 + - - +
142E ASN* 4.5 6.1 + - - +
143E THR* 3.4 12.5 + - - -
232E VAL* 3.0 24.1 + - + +
233E GLN* 3.8 6.1 - - - +
235E PHE* 1.3 73.0 - - - +
237E TYR* 1.3 66.7 + - - +
239E ASP* 3.4 9.0 + - - +
240E LYS* 3.1 23.0 + - - +
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Residues in contact with TYR 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 GLN 2.9 18.4 + - - +
234E ALA* 3.7 4.3 - - - +
235E PHE 3.3 0.2 - - - -
236E GLN* 1.3 76.1 - - - +
238E THR* 1.3 66.7 + - + +
240E LYS* 2.9 18.8 + - - +
241E HIS* 3.0 59.7 + + + +
243E GLU* 5.4 4.4 + - + -
249E TRP* 3.8 28.0 - + + -
253E SER 5.4 2.7 + - - -
255E THR* 3.5 40.4 + - + +
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Residues in contact with THR 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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212E ARG* 5.1 2.9 + - - -
234E ALA 2.9 21.1 + - - +
235E PHE* 3.3 15.4 + - - -
237E TYR* 1.3 80.2 - - + +
239E ASP* 1.3 69.5 + - - +
241E HIS 5.3 0.2 - - - -
242E GLY* 3.1 22.6 + - - +
243E GLU 3.3 25.1 - - - +
244E VAL* 4.0 4.0 - - - -
245E ALA* 3.7 30.3 - - + +
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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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110E TYR* 2.6 30.6 + - - -
206E ASP* 4.6 1.4 - - - +
207E ASP* 4.1 7.3 - - - +
208E LYS* 6.4 0.4 - - - -
212E ARG* 2.8 28.5 + - - -
235E PHE 2.8 23.5 + - - +
236E GLN* 3.4 7.5 - - - +
238E THR* 1.3 79.3 + - - +
240E LYS* 1.3 60.7 + - + +
242E GLY* 4.3 2.4 + - - -
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Residues in contact with LYS 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 GLN 3.1 11.5 + - - +
237E TYR* 2.9 11.0 + - - +
239E ASP* 1.3 79.2 - - + +
241E HIS* 1.3 94.7 + - + +
242E GLY 3.6 0.2 - - - -
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Residues in contact with HIS 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 TYR* 3.0 69.7 + + + +
240E LYS* 1.3 111.2 + - + +
242E GLY* 1.3 65.7 - - - +
243E GLU* 3.0 23.4 + - + +
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Residues in contact with GLY 242 (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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238E THR 3.1 18.2 + - - -
239E ASP 4.3 1.7 + - - -
240E LYS 3.6 1.6 - - - -
241E HIS* 1.3 77.7 - - - +
243E GLU* 1.3 62.3 + - - +
244E VAL* 5.6 0.4 - - - -
258E PRO* 3.8 19.1 - - - +
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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