Contacts of the helix formed by residues 243 - 255 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169L ASN* 5.1 2.9 - - - -
184L VAL* 3.6 37.1 - - + +
200L LEU* 3.9 19.6 - - + +
204L SER* 4.2 10.3 + - - -
207L PHE* 3.4 36.4 + - + -
208L LYS* 4.8 0.4 - - - -
209L ARG* 3.7 37.0 - - + -
211L PHE* 3.8 23.3 - + - -
242L SER* 1.3 72.7 - - - +
244L GLN* 1.3 63.6 + - - +
246L VAL* 3.1 7.4 + - + +
247L ALA* 3.0 22.3 + - - +
272L TYR* 3.7 7.9 - - - -
401L ADP 3.6 32.5 - + - -
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Residues in contact with GLN 244 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200L LEU* 4.2 7.8 - - + +
204L SER 4.5 7.1 + - - +
205L GLU* 5.6 5.4 - - - -
242L SER* 3.2 12.9 + - - +
243L PHE* 1.3 79.3 - - - +
245L ALA* 1.3 56.0 + - - +
247L ALA* 3.3 7.3 + - - +
248L ASP* 2.8 66.9 + - - +
259L ILE* 4.2 18.4 - - - +
261L TYR* 3.9 17.3 + - - +
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Residues in contact with ALA 245 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241L GLU* 4.1 27.6 - - + +
242L SER* 2.9 22.7 + - - +
244L GLN* 1.3 73.4 - - - +
246L VAL* 1.3 66.0 + - - +
248L ASP* 3.2 13.9 + - - +
249L ALA* 3.0 22.7 + - - +
295L VAL* 4.0 7.0 - - + +
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Residues in contact with VAL 246 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184L VAL* 4.9 7.0 - - + -
185L ALA* 4.2 34.5 - - + +
188L LEU* 4.6 5.8 - - + -
211L PHE* 3.7 47.8 - - + -
242L SER 3.5 2.2 + - - +
243L PHE* 3.1 9.1 + - + +
245L ALA* 1.3 77.4 - - - +
247L ALA* 1.3 64.0 + - - +
249L ALA* 3.2 4.7 + - - +
250L THR* 3.0 27.1 + - - +
295L VAL* 3.8 19.3 - - + -
299L VAL* 4.2 9.6 - - + +
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Residues in contact with ALA 247 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188L LEU* 3.8 18.4 - - + +
200L LEU* 4.3 5.4 - - + -
243L PHE 3.0 12.5 + - - +
244L GLN* 3.4 12.6 - - - +
246L VAL* 1.3 76.6 - - - +
248L ASP* 1.3 53.3 + - - +
250L THR* 3.2 1.9 + - - -
251L LEU* 2.8 40.4 + - + +
259L ILE* 3.4 37.5 - - + -
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Residues in contact with ASP 248 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244L GLN* 2.8 51.2 + - - +
245L ALA* 3.2 12.6 + - - +
247L ALA* 1.3 72.3 - - - +
249L ALA* 1.3 63.5 + - - +
251L LEU* 3.5 5.4 + - - +
252L ALA* 3.0 27.1 + - - +
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Residues in contact with ALA 249 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245L ALA 3.0 9.6 + - - +
246L VAL 3.2 7.4 + - - +
248L ASP* 1.3 79.3 - - - +
250L THR* 1.3 61.1 - - - +
252L ALA* 3.5 7.3 - - - +
253L TYR* 3.2 16.6 + - - +
295L VAL* 4.3 10.1 - - + +
296L ALA* 4.3 16.4 - - + +
299L VAL* 3.7 24.2 - - + +
300L THR* 3.8 15.6 - - + +
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Residues in contact with THR 250 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185L ALA* 4.6 0.7 - - - -
188L LEU* 4.1 21.6 - - + +
189L ASN 4.5 1.8 - - - +
192L LEU* 3.9 21.3 - - + -
246L VAL* 3.0 17.4 + - - +
247L ALA* 3.5 10.1 - - - -
249L ALA* 1.3 73.7 - - - +
251L LEU* 1.3 67.9 + - + +
252L ALA 3.1 0.9 - - - -
253L TYR* 3.1 4.2 + - - +
254L HIS* 3.1 24.5 + - + +
299L VAL* 3.4 16.7 - - - +
303L MET* 3.6 30.6 - - + +
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Residues in contact with LEU 251 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188L LEU* 5.5 1.3 - - + -
192L LEU* 3.8 23.1 - - + -
198L PRO* 3.9 18.2 - - + -
247L ALA* 2.8 27.9 + - + +
248L ASP* 4.2 4.3 - - - +
250L THR* 1.3 75.9 - - + +
252L ALA* 1.3 56.8 + - - +
254L HIS* 3.3 3.0 + - - +
255L LYS* 2.8 27.2 + - - -
256L LYS 3.5 17.4 + - - +
257L GLY 3.1 30.1 - - - +
258L GLN* 4.0 8.7 - - - +
259L ILE* 4.3 15.5 - - + +
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Residues in contact with ALA 252 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248L ASP 3.0 19.2 + - - +
249L ALA* 3.5 8.7 - - - +
251L LEU* 1.3 79.0 - - - +
253L TYR* 1.3 62.4 + - - +
255L LYS* 3.2 25.6 - - - +
300L THR* 5.6 2.7 - - + -
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Residues in contact with TYR 253 (chain L).
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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249L ALA 3.2 9.8 + - - +
250L THR 3.1 9.4 + - - +
252L ALA* 1.3 81.9 - - - +
254L HIS* 1.3 74.9 + + - +
255L LYS* 3.2 12.2 + - - +
300L THR* 4.3 18.5 - - + +
303L MET* 3.5 40.9 + - + -
304L ALA* 3.4 31.8 + - + +
307L ASN* 4.0 22.6 - - + +
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Residues in contact with HIS 254 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189L ASN* 2.8 33.2 + - - -
192L LEU* 3.8 36.7 - - + +
193L ASN* 3.4 23.4 + - - -
250L THR* 3.1 29.8 + - + +
251L LEU 4.0 3.4 - - - +
253L TYR* 1.3 89.6 - + - +
255L LYS* 1.3 68.4 - - - +
256L LYS* 3.0 27.8 + - + +
303L MET* 3.9 6.3 - - - -
307L ASN* 4.5 7.2 + - - -
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Residues in contact with LYS 255 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251L LEU 2.8 10.2 + - - -
252L ALA* 3.2 25.7 + - - +
253L TYR 3.2 10.9 - - - +
254L HIS* 1.3 76.9 - - - +
256L LYS* 1.3 59.7 + - - +
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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