Contacts of the helix formed by residues 243 - 255 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169F ASN* 5.1 3.1 - - - -
184F VAL* 3.6 28.4 - - + +
200F LEU* 3.9 19.4 - - + +
204F SER* 4.2 8.7 + - - +
207F PHE* 3.4 31.5 + - + -
209F ARG* 3.7 37.9 - - + -
211F PHE* 3.8 21.5 - + - -
242F SER* 1.3 72.8 - - - +
244F GLN* 1.3 62.7 + - - +
246F VAL* 3.1 7.3 + - + +
247F ALA* 3.0 22.0 + - - +
272F TYR* 3.7 5.6 - - - -
401F ADP 3.4 51.4 - + - +
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Residues in contact with GLN 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200F LEU* 4.2 13.0 - - + +
204F SER 4.5 6.0 + - - +
205F GLU* 5.5 6.5 - - - -
242F SER* 3.3 12.9 - - - +
243F PHE* 1.3 78.5 - - - +
245F ALA* 1.3 56.8 + - - +
247F ALA* 3.3 7.2 + - - +
248F ASP* 2.8 67.3 + - - +
259F ILE* 4.2 13.4 - - - +
261F TYR* 3.9 17.4 + - - +
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Residues in contact with ALA 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241F GLU* 4.1 26.7 - - + +
242F SER* 2.9 23.6 + - - +
244F GLN* 1.3 73.9 - - - +
246F VAL* 1.3 64.7 - - - +
248F ASP* 3.2 12.9 + - - +
249F ALA* 3.0 23.6 + - - +
295F VAL* 4.0 6.9 - - + +
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Residues in contact with VAL 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F TYR* 6.5 0.2 - - + -
184F VAL* 4.9 6.1 - - + -
185F ALA* 4.2 35.7 - - + +
188F LEU* 4.6 5.6 - - + -
211F PHE* 3.7 47.6 - - + -
242F SER 3.5 2.4 + - - +
243F PHE* 3.1 9.1 + - + +
245F ALA* 1.3 77.0 - - - +
247F ALA* 1.3 63.0 + - - +
249F ALA* 3.2 4.7 + - - +
250F THR* 3.0 27.5 + - - +
295F VAL* 3.8 19.0 - - + +
299F VAL* 4.2 9.6 - - + +
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Residues in contact with ALA 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188F LEU* 3.8 18.3 - - + +
200F LEU* 4.3 6.7 - - + -
243F PHE 3.0 12.2 + - - +
244F GLN* 3.4 12.6 - - - +
246F VAL* 1.3 76.0 - - - +
248F ASP* 1.3 54.2 + - - +
250F THR* 3.2 2.1 + - - -
251F LEU* 2.8 40.4 + - + +
259F ILE* 3.4 36.6 - - + -
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Residues in contact with ASP 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244F GLN* 2.8 51.6 + - - +
245F ALA* 3.3 11.9 - - - +
247F ALA* 1.3 73.7 - - - +
249F ALA* 1.3 64.3 + - - +
251F LEU* 4.0 4.2 - - - +
252F ALA* 3.0 27.3 + - - +
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Residues in contact with ALA 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245F ALA 3.0 9.3 + - - +
246F VAL 3.2 7.8 + - - +
248F ASP* 1.3 79.5 - - - +
250F THR* 1.3 61.4 + - - +
252F ALA* 3.5 6.3 - - - +
253F TYR* 3.2 17.3 + - - +
295F VAL* 4.3 10.1 - - + +
296F ALA* 4.3 16.4 - - + +
299F VAL* 3.7 24.9 - - + -
300F THR* 3.8 15.8 - - + +
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Residues in contact with THR 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185F ALA* 4.6 0.9 - - - -
188F LEU* 4.1 21.3 - - + +
189F ASN 4.5 1.6 - - - +
192F LEU* 3.9 21.8 - - + -
246F VAL* 3.0 17.5 + - - +
247F ALA* 3.5 10.1 - - - -
249F ALA* 1.3 73.7 - - - +
251F LEU* 1.3 67.4 + - + +
252F ALA 3.1 1.1 - - - -
253F TYR* 3.1 4.0 + - - +
254F HIS* 3.1 24.6 + - + +
299F VAL* 3.4 17.1 - - - +
303F MET* 3.6 30.4 - - + +
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Residues in contact with LEU 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188F LEU* 5.4 0.9 - - + -
192F LEU* 3.8 22.4 - - + -
198F PRO* 3.9 18.8 - - + -
247F ALA* 2.8 28.1 + - + +
248F ASP* 4.2 4.5 - - - +
250F THR* 1.3 75.5 - - + +
252F ALA* 1.3 56.6 + - - +
254F HIS* 3.3 2.8 + - - +
255F LYS* 2.8 26.7 + - - -
256F LYS 3.5 18.1 + - - +
257F GLY 3.0 32.1 - - - +
258F GLN* 4.0 7.6 - - - +
259F ILE* 4.4 15.9 - - + +
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Residues in contact with ALA 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248F ASP 3.0 19.8 + - - +
249F ALA* 3.5 7.9 - - - +
251F LEU* 1.3 78.0 - - - +
253F TYR* 1.3 61.9 + - - +
255F LYS* 3.2 26.1 - - - +
300F THR* 5.6 2.9 - - + -
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Residues in contact with TYR 253 (chain F).
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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249F ALA 3.2 9.1 + - - +
250F THR 3.1 8.6 + - - +
252F ALA* 1.3 81.1 - - - +
254F HIS* 1.3 74.9 + + - +
255F LYS* 3.2 11.9 + - - +
300F THR* 4.3 18.8 - - + +
303F MET* 3.5 40.7 + - + -
304F ALA* 3.4 31.7 + - + +
307F ASN* 4.0 22.6 - - + +
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Residues in contact with HIS 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F ASN* 2.8 33.0 + - - -
192F LEU* 3.8 37.1 - - + +
193F ASN* 3.4 23.7 + - - -
250F THR* 3.1 30.6 + - + +
251F LEU 4.0 3.1 - - - +
253F TYR* 1.3 88.4 - + - +
255F LYS* 1.3 68.2 + - - +
256F LYS* 3.0 28.1 + - + +
303F MET* 3.9 6.7 - - - -
307F ASN* 4.4 7.6 + - - -
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Residues in contact with LYS 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251F LEU 2.8 11.1 + - - -
252F ALA* 3.2 24.0 + - - +
253F TYR* 3.2 9.5 - - - +
254F HIS* 1.3 79.3 - - - +
256F 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