Contacts of the helix formed by residues 243 - 255 (chain E) in PDB entry 2X86
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 PHE 243 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169E ASN* 5.1 2.7 - - - -
184E VAL* 3.6 36.2 - - + +
188E LEU* 5.7 0.2 - - - +
200E LEU* 3.9 18.7 - - + +
204E SER* 4.2 10.3 + - - -
207E PHE* 3.4 38.0 + - + -
209E ARG* 3.7 37.5 - - + -
211E PHE* 3.8 21.3 - + - -
242E SER* 1.3 72.2 - - - +
244E GLN* 1.3 63.5 + - - +
246E VAL* 3.1 7.5 + - + +
247E ALA* 3.0 22.0 + - - +
272E TYR* 3.7 17.9 - - - -
401E ADP 3.7 23.8 - + - -
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Residues in contact with GLN 244 (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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200E LEU* 4.2 12.0 - - + +
204E SER 4.5 7.8 + - - +
205E GLU* 5.5 5.6 - - - -
242E SER* 3.1 12.7 + - - +
243E PHE* 1.3 78.9 - - - +
245E ALA* 1.3 55.4 + - - +
247E ALA* 3.3 6.9 + - - +
248E ASP* 2.8 65.8 + - - +
259E ILE* 4.2 13.2 - - - +
261E TYR* 3.9 18.7 + - - +
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Residues in contact with ALA 245 (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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241E GLU* 4.1 27.4 - - + +
242E SER* 2.9 22.1 + - - +
244E GLN* 1.3 72.7 - - - +
246E VAL* 1.3 65.3 + - - +
248E ASP* 3.2 13.8 + - - +
249E ALA* 3.0 23.2 + - - +
295E VAL* 4.0 7.1 - - + +
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Residues in contact with VAL 246 (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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184E VAL* 4.9 6.7 - - + -
185E ALA* 4.2 34.8 - - + +
188E LEU* 4.6 4.9 - - + -
211E PHE* 3.7 47.3 - - + -
242E SER 3.5 2.4 + - - +
243E PHE* 3.1 9.5 + - + +
245E ALA* 1.3 77.0 - - - +
247E ALA* 1.3 63.9 + - - +
249E ALA* 3.2 4.5 + - - +
250E THR* 3.0 26.7 + - - +
295E VAL* 3.7 18.4 - - + -
299E VAL* 4.2 8.9 - - + +
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Residues in contact with ALA 247 (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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188E LEU* 3.8 17.2 - - + +
200E LEU* 4.2 6.1 - - + -
243E PHE 3.0 12.1 + - - +
244E GLN* 3.4 12.1 - - - +
246E VAL* 1.3 77.9 - - - +
248E ASP* 1.3 52.9 + - - +
250E THR* 3.2 2.3 + - - -
251E LEU* 2.8 40.8 + - + +
259E ILE* 3.4 37.2 - - + -
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Residues in contact with ASP 248 (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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244E GLN* 2.8 50.8 + - - +
245E ALA* 3.2 12.6 + - - +
247E ALA* 1.3 73.0 - - - +
249E ALA* 1.3 62.6 + - - +
251E LEU* 3.9 5.4 - - - +
252E ALA* 3.0 27.3 + - - +
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Residues in contact with ALA 249 (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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245E ALA 3.0 9.3 + - - +
246E VAL 3.6 8.1 - - - +
248E ASP* 1.3 79.9 - - - +
250E THR* 1.3 60.0 + - - +
252E ALA* 3.5 6.7 - - - +
253E TYR* 3.2 17.3 + - - +
295E VAL* 4.3 10.3 - - + +
296E ALA* 4.3 15.5 - - + +
299E VAL* 3.7 26.0 - - + +
300E THR* 3.8 16.1 - - + +
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Residues in contact with THR 250 (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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185E ALA* 4.6 0.9 - - - -
188E LEU* 4.1 21.5 - - + +
189E ASN 4.5 1.6 - - - +
192E LEU* 3.9 21.5 - - + -
246E VAL* 3.0 17.7 + - - +
247E ALA* 3.5 10.5 - - - -
249E ALA* 1.3 73.7 - - - +
251E LEU* 1.3 66.3 + - + +
252E ALA 3.1 1.1 - - - -
253E TYR* 3.1 4.0 + - - +
254E HIS* 3.1 25.0 + - + +
299E VAL* 3.4 16.8 - - - +
303E MET* 3.6 29.9 - - + +
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Residues in contact with LEU 251 (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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188E LEU* 5.5 0.9 - - + -
192E LEU* 3.8 22.4 - - + -
198E PRO* 3.9 19.1 - - + -
247E ALA* 2.8 29.7 + - + +
248E ASP* 4.2 4.5 - - - +
250E THR* 1.3 75.9 - - + +
252E ALA* 1.3 58.3 + - - +
254E HIS* 4.5 2.0 - - - +
255E LYS* 2.8 27.0 + - - -
256E LYS 3.5 17.3 + - - +
257E GLY 3.0 30.7 - - - +
258E GLN* 4.0 8.7 - - - +
259E ILE* 4.4 15.3 - - + +
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Residues in contact with ALA 252 (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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248E ASP 3.0 20.2 + - - +
249E ALA* 3.5 8.5 - - - +
250E THR 3.1 0.2 - - - -
251E LEU* 1.3 77.8 - - - +
253E TYR* 1.3 61.8 + - - +
255E LYS* 3.2 25.8 + - - +
300E THR* 5.6 2.9 - - + -
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Residues in contact with TYR 253 (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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249E ALA 3.2 9.6 + - - +
250E THR 3.1 8.8 + - - +
252E ALA* 1.3 81.9 - - - +
254E HIS* 1.3 75.0 + + - +
255E LYS* 3.2 12.6 + - - +
300E THR* 4.3 18.5 - - + +
303E MET* 3.5 40.8 + - + -
304E ALA* 3.4 31.9 + - + +
307E ASN* 4.0 22.0 - - + +
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Residues in contact with HIS 254 (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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189E ASN* 2.8 32.7 + - - -
192E LEU* 3.8 36.7 - - + +
193E ASN* 3.4 22.8 + - - -
250E THR* 3.1 30.9 + - + +
251E LEU 4.0 2.7 - - - +
253E TYR* 1.3 88.4 - + - +
255E LYS* 1.3 68.8 + - - +
256E LYS* 3.0 28.8 + - + +
303E MET* 3.9 6.3 - - - -
307E ASN* 4.4 7.8 + - - -
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Residues in contact with LYS 255 (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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251E LEU 2.8 10.1 + - - -
252E ALA* 3.2 24.2 + - - +
253E TYR 3.2 11.3 - - - +
254E HIS* 1.3 77.3 - - - +
256E LYS* 1.3 60.5 + - - +
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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