Contacts of the helix formed by residues 243 - 255 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169R ASN* 5.2 2.2 - - - -
184R VAL* 3.6 33.6 - - + +
200R LEU* 3.9 20.4 - - + +
204R SER* 4.2 10.5 + - - -
207R PHE* 3.4 30.6 + - + -
208R LYS* 4.8 0.2 - - - -
209R ARG* 3.7 37.0 - - + -
211R PHE* 3.8 22.4 - + - -
242R SER* 1.3 72.8 - - - +
244R GLN* 1.3 62.5 + - - +
246R VAL* 3.1 8.2 + - + +
247R ALA* 3.0 22.2 + - - +
272R TYR* 3.7 5.2 - - - -
401R ADP 3.4 45.1 - + - -
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Residues in contact with GLN 244 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200R LEU* 4.2 13.9 - - + +
204R SER 4.5 7.3 + - - +
205R GLU* 5.5 6.3 - - - -
242R SER* 3.3 12.5 - - - +
243R PHE* 1.3 78.8 - - - +
245R ALA* 1.3 57.0 + - - +
247R ALA* 3.3 8.5 + - - +
248R ASP* 2.8 66.2 + - - +
259R ILE* 4.2 12.6 - - - +
261R TYR* 3.9 17.4 + - - +
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Residues in contact with ALA 245 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241R GLU* 4.1 27.4 - - + +
242R SER* 2.9 22.1 + - - +
244R GLN* 1.3 73.2 - - - +
246R VAL* 1.3 66.9 + - - +
248R ASP* 3.2 13.3 + - - +
249R ALA* 3.0 22.7 + - - +
295R VAL* 4.0 8.2 - - + +
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Residues in contact with VAL 246 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184R VAL* 4.9 7.2 - - + -
185R ALA* 4.2 34.8 - - + +
188R LEU* 4.7 5.2 - - + -
211R PHE* 3.7 47.3 - - + -
242R SER 3.5 2.4 + - - +
243R PHE* 3.1 8.9 + - - +
245R ALA* 1.3 77.7 - - - +
247R ALA* 1.3 63.7 + - - +
249R ALA* 3.2 4.7 + - - +
250R THR* 3.0 26.6 + - - +
295R VAL* 3.8 19.3 - - + -
299R VAL* 4.2 9.1 - - + +
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Residues in contact with ALA 247 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188R LEU* 3.8 18.8 - - + +
200R LEU* 4.2 6.7 - - + -
243R PHE 3.0 11.8 + - - +
244R GLN* 3.3 12.8 + - - +
246R VAL* 1.3 77.0 - - - +
248R ASP* 1.3 53.2 + - - +
250R THR* 3.2 2.4 + - - -
251R LEU* 2.8 40.5 + - + +
259R ILE* 3.4 36.6 - - + -
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Residues in contact with ASP 248 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244R GLN* 2.8 51.4 + - - +
245R ALA* 3.2 12.4 + - - +
247R ALA* 1.3 73.7 - - - +
249R ALA* 1.3 64.5 + - - +
251R LEU* 3.5 5.0 + - - +
252R ALA* 3.0 26.6 + - - +
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Residues in contact with ALA 249 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245R ALA 3.0 9.7 + - - +
246R VAL 3.2 8.5 + - - +
248R ASP* 1.3 78.3 - - - +
250R THR* 1.3 61.4 + - - +
252R ALA* 3.5 6.8 - - - +
253R TYR* 3.2 17.0 + - - +
295R VAL* 4.3 9.9 - - + +
296R ALA* 4.3 15.5 - - + +
299R VAL* 3.7 25.7 - - + +
300R THR* 3.8 16.3 - - + +
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Residues in contact with THR 250 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185R ALA* 4.6 1.0 - - - -
188R LEU* 4.1 21.0 - - + +
189R ASN 4.5 1.6 - - - +
192R LEU* 3.9 21.3 - - + -
246R VAL* 3.0 17.4 + - - +
247R ALA* 3.5 10.3 - - - -
249R ALA* 1.3 72.8 - - - +
251R LEU* 1.3 67.1 + - + +
252R ALA 3.1 1.3 - - - -
253R TYR* 3.1 4.0 + - - +
254R HIS* 3.1 25.2 + - + +
299R VAL* 3.4 17.1 - - - +
303R MET* 3.6 30.6 - - + +
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Residues in contact with LEU 251 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188R LEU* 5.4 1.3 - - + -
192R LEU* 3.8 22.2 - - + -
198R PRO* 3.9 19.1 - - + -
247R ALA* 2.8 30.1 + - + +
248R ASP* 4.2 4.3 - - - +
250R THR* 1.3 76.0 - - - +
252R ALA* 1.3 57.2 + - - +
254R HIS* 3.3 3.0 + - - +
255R LYS* 2.8 26.7 + - - -
256R LYS 3.5 19.1 + - - +
257R GLY 3.0 30.5 - - - +
258R GLN* 4.0 8.7 - - - +
259R ILE* 4.3 15.0 - - + +
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Residues in contact with ALA 252 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248R ASP 3.0 18.9 + - - +
249R ALA* 3.5 8.7 - - - +
251R LEU* 1.3 77.2 - - - +
253R TYR* 1.3 62.8 + - - +
255R LYS* 3.2 26.1 - - - +
300R THR* 5.6 2.9 - - + -
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Residues in contact with TYR 253 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249R ALA 3.2 10.2 + - - +
250R THR 3.1 9.2 + - - +
252R ALA* 1.3 80.9 - - - +
254R HIS* 1.3 75.3 + + - +
255R LYS* 3.2 12.3 + - - +
300R THR* 4.3 18.8 - - + +
303R MET* 3.5 39.1 + - + -
304R ALA* 3.4 31.3 + - + +
307R ASN* 4.0 22.6 - - + +
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Residues in contact with HIS 254 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189R ASN* 2.8 33.5 + - - -
192R LEU* 3.8 37.0 - - + +
193R ASN* 3.4 23.0 + - - -
250R THR* 3.1 31.1 + - + +
251R LEU 4.0 2.7 - - - +
253R TYR* 1.3 88.8 - + - +
255R LYS* 1.3 68.1 + - - +
256R LYS* 3.0 28.0 + - + +
303R MET* 3.9 5.7 - - - -
307R ASN* 4.4 7.4 - - - -
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Residues in contact with LYS 255 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251R LEU 2.8 9.8 + - - -
252R ALA* 3.2 24.6 + - - +
253R TYR 3.2 9.0 - - - +
254R HIS* 1.3 79.1 - - - +
256R 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