Contacts of the helix formed by residues 243 - 255 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169C ASN* 5.2 2.9 - - - -
184C VAL* 3.6 27.3 - - + +
188C LEU* 5.7 0.2 - - - +
200C LEU* 3.9 20.5 - - + +
204C SER* 4.2 9.4 + - - -
207C PHE* 3.4 30.3 + - + -
208C LYS* 4.8 0.2 - - - -
209C ARG* 3.7 36.3 - - + -
211C PHE* 3.8 21.5 - + - -
242C SER* 1.3 71.9 - - - +
244C GLN* 1.3 64.4 + - - +
246C VAL* 3.1 7.0 + - + +
247C ALA* 3.0 21.8 + - - +
272C TYR* 3.7 4.5 - - - -
401C ADP 3.3 52.7 - + - -
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Residues in contact with GLN 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C LEU* 4.2 6.7 - - + +
204C SER 4.5 7.3 + - - +
205C GLU* 5.5 5.8 - - - -
242C SER* 3.2 13.6 + - - +
243C PHE* 1.3 79.1 - - - +
245C ALA* 1.3 55.7 + - - +
247C ALA* 3.3 7.0 + - - +
248C ASP* 2.8 65.9 + - - +
259C ILE* 4.2 19.0 - - - +
261C TYR* 3.9 18.4 + - - +
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Residues in contact with ALA 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C GLU* 4.1 27.4 - - + +
242C SER* 2.9 22.5 + - - +
244C GLN* 1.3 73.6 - - - +
246C VAL* 1.3 65.1 - - - +
248C ASP* 3.2 13.5 + - - +
249C ALA* 3.0 22.7 + - - +
295C VAL* 4.0 6.9 - - + +
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Residues in contact with VAL 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C TYR* 6.5 0.2 - - + -
184C VAL* 4.8 7.0 - - + -
185C ALA* 4.2 34.8 - - + +
188C LEU* 4.6 5.8 - - + -
211C PHE* 3.7 47.6 - - + -
242C SER 3.5 2.4 + - - +
243C PHE* 3.1 8.2 + - + +
245C ALA* 1.3 76.2 - - - +
247C ALA* 1.3 64.0 + - - +
249C ALA* 3.2 5.0 + - - +
250C THR* 3.0 26.7 + - - +
295C VAL* 3.7 19.5 - - + +
299C VAL* 4.2 8.6 - - + +
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Residues in contact with ALA 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C LEU* 3.8 17.0 - - + +
200C LEU* 4.3 5.8 - - + -
243C PHE 3.0 12.0 + - - +
244C GLN* 3.4 13.0 - - - +
246C VAL* 1.3 77.2 - - - +
248C ASP* 1.3 53.0 + - - +
250C THR* 3.2 2.1 + - - -
251C LEU* 2.8 40.0 + - + +
259C ILE* 3.4 37.5 - - + -
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Residues in contact with ASP 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C GLN* 2.8 50.8 + - - +
245C ALA* 3.3 12.0 - - - +
247C ALA* 1.3 73.9 - - - +
249C ALA* 1.3 63.9 + - - +
251C LEU* 3.9 4.9 - - - +
252C ALA* 3.0 27.1 + - - +
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Residues in contact with ALA 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C ALA 3.0 9.7 + - - +
246C VAL 3.2 7.6 + - - +
248C ASP* 1.3 79.1 - - - +
250C THR* 1.3 60.7 + - - +
252C ALA* 3.5 6.9 - - - +
253C TYR* 3.2 17.3 + - - +
295C VAL* 4.3 10.1 - - + +
296C ALA* 4.3 15.9 - - + +
299C VAL* 3.7 25.1 - - + +
300C THR* 3.8 15.8 - - + +
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Residues in contact with THR 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C ALA* 4.6 0.7 - - - -
188C LEU* 4.1 21.7 - - + +
189C ASN 4.5 1.6 - - - +
192C LEU* 3.9 21.3 - - + -
246C VAL* 3.0 18.4 + - - +
247C ALA* 3.5 9.9 - - - -
249C ALA* 1.3 74.0 - - - +
251C LEU* 1.3 66.9 + - + +
252C ALA 3.1 1.1 - - - -
253C TYR* 3.1 3.8 + - - +
254C HIS* 3.1 25.0 + - + +
299C VAL* 3.4 16.4 - - - +
303C MET* 3.6 30.3 - - + +
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Residues in contact with LEU 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C LEU* 5.5 1.1 - - + -
192C LEU* 3.8 22.4 - - + -
198C PRO* 3.9 18.4 - - + -
247C ALA* 2.8 29.6 + - + +
248C ASP* 4.2 4.5 - - - +
250C THR* 1.3 75.1 - - + +
252C ALA* 1.3 57.3 + - - +
254C HIS* 3.3 3.0 + - - +
255C LYS* 2.8 27.2 + - - -
256C LYS 3.5 18.2 + - - +
257C GLY 3.0 30.7 - - - +
258C GLN* 4.0 8.1 - - - +
259C ILE* 4.4 16.4 - - + +
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Residues in contact with ALA 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C ASP 3.0 20.7 + - - +
249C ALA* 3.5 8.3 - - - +
250C THR 3.1 0.2 - - - -
251C LEU* 1.3 78.4 - - - +
253C TYR* 1.3 62.5 + - - +
255C LYS* 3.2 25.4 - - - +
300C THR* 5.6 2.9 - - + -
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Residues in contact with TYR 253 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249C ALA 3.2 10.2 + - - +
250C THR 3.1 7.9 + - - +
252C ALA* 1.3 81.2 - - - +
254C HIS* 1.3 75.8 + + - +
255C LYS* 3.2 11.8 + - - +
300C THR* 4.3 18.3 - - + +
303C MET* 3.5 40.2 + - + -
304C ALA* 3.4 32.7 + - + +
307C ASN* 4.0 23.2 - - + +
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Residues in contact with HIS 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C ASN* 2.8 32.5 + - - -
192C LEU* 3.8 37.9 - - + +
193C ASN* 3.4 23.2 + - - -
250C THR* 3.1 30.1 + - + +
251C LEU 3.3 2.9 + - - +
253C TYR* 1.3 89.7 - + - +
255C LYS* 1.3 68.3 + - - +
256C LYS* 3.0 29.2 + - + +
303C MET* 3.9 6.5 - - - -
307C ASN* 4.5 7.0 - - - -
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Residues in contact with LYS 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C LEU 2.8 9.8 + - - -
252C ALA* 3.2 24.0 + - - +
253C TYR* 3.2 10.6 - - - +
254C HIS* 1.3 79.5 - - - +
256C LYS* 1.3 59.4 + - - +
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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