Contacts of the helix formed by residues 243 - 255 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169J ASN* 5.1 2.7 - - - -
184J VAL* 3.6 35.6 - - + +
188J LEU* 5.7 0.2 - - - +
200J LEU* 3.9 19.4 - - + +
204J SER* 4.2 10.5 + - - -
207J PHE* 3.4 37.7 + - + -
209J ARG* 3.7 37.7 - - + -
211J PHE* 3.8 21.3 - + - -
242J SER* 1.3 71.8 - - - +
244J GLN* 1.3 63.3 + - - +
246J VAL* 3.1 8.1 + - + +
247J ALA* 3.0 21.7 + - - +
272J TYR* 3.7 8.1 - - - -
401J ADP 3.6 34.1 - + - -
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Residues in contact with GLN 244 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200J LEU* 4.2 6.5 - - + +
204J SER 4.5 7.5 + - - +
205J GLU* 5.6 5.4 - - - -
242J SER* 3.2 12.2 + - - +
243J PHE* 1.3 78.9 - - - +
245J ALA* 1.3 56.2 + - - +
247J ALA* 3.3 6.6 + - - +
248J ASP* 2.8 65.5 + - - +
259J ILE* 4.2 19.1 - - - +
261J TYR* 3.9 17.8 + - - +
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Residues in contact with ALA 245 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241J GLU* 4.1 27.4 - - + +
242J SER* 2.9 21.9 + - - +
244J GLN* 1.3 73.0 - - - +
246J VAL* 1.3 64.9 + - - +
248J ASP* 3.2 14.0 + - - +
249J ALA* 3.0 23.2 + - - +
295J VAL* 4.0 7.7 - - + +
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Residues in contact with VAL 246 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184J VAL* 4.9 7.6 - - + -
185J ALA* 4.2 34.3 - - + +
188J LEU* 4.6 5.4 - - + -
211J PHE* 3.7 47.3 - - + -
242J SER 3.5 2.0 + - - +
243J PHE* 3.1 9.3 + - + +
245J ALA* 1.3 76.8 - - - +
247J ALA* 1.3 63.8 + - - +
249J ALA* 3.2 4.9 + - - +
250J THR* 3.0 26.8 + - - +
295J VAL* 3.7 18.8 - - + -
299J VAL* 4.2 8.9 - - + +
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Residues in contact with ALA 247 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188J LEU* 3.8 17.2 - - + +
200J LEU* 4.3 5.6 - - + -
243J PHE 3.0 12.7 + - - +
244J GLN* 3.4 12.1 - - - +
246J VAL* 1.3 77.2 - - - +
248J ASP* 1.3 53.7 + - - +
250J THR* 3.2 1.9 + - - -
251J LEU* 2.8 41.1 + - - +
259J ILE* 3.4 37.5 - - + -
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Residues in contact with ASP 248 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244J GLN* 2.8 51.0 + - - +
245J ALA* 3.2 12.4 + - - +
247J ALA* 1.3 72.8 - - - +
249J ALA* 1.3 63.3 + - - +
251J LEU* 3.5 6.0 + - - +
252J ALA* 3.0 27.8 + - - +
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Residues in contact with ALA 249 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245J ALA 3.0 9.1 + - - +
246J VAL 3.6 8.1 - - - +
248J ASP* 1.3 79.7 - - - +
250J THR* 1.3 59.5 + - - +
252J ALA* 3.5 6.4 - - - +
253J TYR* 3.2 17.3 + - - +
295J VAL* 4.3 9.9 - - + +
296J ALA* 4.3 15.7 - - + +
299J VAL* 3.7 26.0 - - + +
300J THR* 3.7 16.5 - - + +
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Residues in contact with THR 250 (chain J).
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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185J ALA* 4.6 0.9 - - - -
188J LEU* 4.1 22.1 - - + +
189J ASN 4.5 1.6 - - - +
192J LEU* 3.9 22.0 - - + -
246J VAL* 3.0 17.2 + - - +
247J ALA* 3.5 10.1 - - - -
249J ALA* 1.3 74.4 - - - +
251J LEU* 1.3 66.3 + - + +
252J ALA 3.1 1.1 - - - -
253J TYR* 3.1 4.0 + - - +
254J HIS* 3.1 25.0 + - + +
299J VAL* 3.4 16.5 - - - +
303J MET* 3.6 29.0 - - + +
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Residues in contact with LEU 251 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188J LEU* 5.5 0.9 - - + -
192J LEU* 3.8 22.7 - - + -
198J PRO* 3.9 18.6 - - + -
247J ALA* 2.8 30.1 + - + +
248J ASP* 4.2 4.7 - - - +
250J THR* 1.3 75.3 - - + +
252J ALA* 1.3 57.9 + - - +
254J HIS* 4.5 2.2 - - - +
255J LYS* 2.8 27.2 + - - -
256J LYS 3.5 17.1 + - - +
257J GLY 3.1 30.1 - - - +
258J GLN* 4.0 8.5 - - - +
259J ILE* 4.4 15.7 - - + +
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Residues in contact with ALA 252 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248J ASP 3.0 20.2 + - - +
249J ALA* 3.5 8.5 - - - +
251J LEU* 1.3 78.0 - - - +
253J TYR* 1.3 61.0 + - - +
255J LYS* 3.2 25.3 + - - +
300J THR* 5.6 2.9 - - + -
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Residues in contact with TYR 253 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249J ALA 3.2 9.2 + - - +
250J THR 3.1 8.8 + - - +
252J ALA* 1.3 82.7 - - - +
254J HIS* 1.3 75.6 + + - +
255J LYS* 3.2 12.2 + - - +
300J THR* 4.3 18.1 - - + +
303J MET* 3.5 40.4 + - + -
304J ALA* 3.4 31.8 + - + +
307J ASN* 4.0 22.5 - - + +
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Residues in contact with HIS 254 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189J ASN* 2.8 32.9 + - - -
192J LEU* 3.8 36.0 - - + +
193J ASN* 3.4 23.4 + - - -
250J THR* 3.1 30.9 + - + +
251J LEU 4.0 3.4 - - - +
253J TYR* 1.3 88.2 - + - +
255J LYS* 1.3 68.5 + - - +
256J LYS* 3.0 28.4 + - + +
303J MET* 3.9 6.5 - - - -
307J ASN* 4.5 7.8 + - - -
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Residues in contact with LYS 255 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251J LEU 2.8 9.4 + - - -
252J ALA* 3.2 24.7 + - - +
253J TYR 3.2 11.3 - - - +
254J HIS* 1.3 77.2 - - - +
256J LYS* 1.3 60.4 + - - +
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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