Contacts of the helix formed by residues 243 - 255 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169Q ASN* 5.1 2.9 - - - -
184Q VAL* 3.6 36.2 - - + +
200Q LEU* 3.9 20.3 - - + +
204Q SER* 4.2 10.3 + - - -
207Q PHE* 3.4 32.4 + - + -
208Q LYS* 4.8 0.2 - - - -
209Q ARG* 3.7 37.5 - - + -
211Q PHE* 3.8 21.3 - + - -
242Q SER* 1.3 73.0 - - - +
244Q GLN* 1.3 63.8 + - - +
246Q VAL* 3.1 7.4 + - + +
247Q ALA* 3.0 22.0 + - - +
272Q TYR* 3.7 5.4 - - - -
401Q ADP 3.5 38.4 - + - -
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Residues in contact with GLN 244 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200Q LEU* 4.2 12.8 - - + +
204Q SER 4.5 7.3 + - - +
205Q GLU* 5.6 5.2 - - - -
242Q SER* 3.2 12.9 + - - +
243Q PHE* 1.3 79.3 - - - +
245Q ALA* 1.3 56.3 + - - +
247Q ALA* 3.3 7.5 + - - +
248Q ASP* 2.8 66.3 + - - +
259Q ILE* 4.2 13.2 - - - +
261Q TYR* 3.9 17.0 + - - +
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Residues in contact with ALA 245 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241Q GLU* 4.1 28.5 - - + +
242Q SER* 2.9 22.2 + - - +
244Q GLN* 1.3 73.0 - - - +
246Q VAL* 1.3 66.4 + - - +
248Q ASP* 3.2 12.8 + - - +
249Q ALA* 3.0 22.7 + - - +
295Q VAL* 4.0 6.9 - - + +
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Residues in contact with VAL 246 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184Q VAL* 4.9 7.0 - - + -
185Q ALA* 4.2 34.5 - - + +
188Q LEU* 4.6 5.8 - - + -
211Q PHE* 3.7 48.2 - - + -
242Q SER 3.5 2.0 + - - +
243Q PHE* 3.1 9.1 + - + +
245Q ALA* 1.3 77.0 - - - +
247Q ALA* 1.3 63.3 + - - +
249Q ALA* 3.2 4.5 + - - +
250Q THR* 3.0 27.1 + - - +
295Q VAL* 3.8 19.3 - - + -
299Q VAL* 4.2 9.8 - - + +
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Residues in contact with ALA 247 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188Q LEU* 3.8 18.8 - - + +
200Q LEU* 4.2 5.8 - - + -
243Q PHE 3.0 12.5 + - - +
244Q GLN* 3.4 12.3 - - - +
246Q VAL* 1.3 77.0 - - - +
248Q ASP* 1.3 53.3 + - - +
250Q THR* 3.2 2.1 + - - -
251Q LEU* 2.8 40.1 + - - +
259Q ILE* 3.4 36.8 - - + -
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Residues in contact with ASP 248 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244Q GLN* 2.8 52.4 + - - +
245Q ALA* 3.3 12.4 - - - +
247Q ALA* 1.3 71.8 - - - +
249Q ALA* 1.3 63.9 + - - +
251Q LEU* 3.5 5.4 + - - +
252Q ALA* 3.0 26.9 + - - +
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Residues in contact with ALA 249 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245Q ALA 3.0 10.3 + - - +
246Q VAL 3.2 7.8 + - - +
248Q ASP* 1.3 79.5 - - - +
250Q THR* 1.3 60.7 - - - +
252Q ALA* 3.5 6.8 - - - +
253Q TYR* 3.2 17.3 + - - +
295Q VAL* 4.3 9.9 - - + +
296Q ALA* 4.3 16.2 - - + +
299Q VAL* 3.7 25.1 - - + +
300Q THR* 3.8 16.1 - - + +
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Residues in contact with THR 250 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185Q ALA* 4.6 1.2 - - - -
188Q LEU* 4.1 20.5 - - + +
189Q ASN 4.5 1.8 - - - +
192Q LEU* 3.9 21.5 - - + -
246Q VAL* 3.0 17.7 + - - +
247Q ALA* 3.5 10.3 - - - -
249Q ALA* 1.3 73.8 - - - +
251Q LEU* 1.3 67.8 + - + +
252Q ALA 3.1 1.1 - - - -
253Q TYR* 3.1 4.9 + - - +
254Q HIS* 3.1 24.1 + - + +
299Q VAL* 3.4 16.9 - - - +
303Q MET* 3.6 30.4 - - + +
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Residues in contact with LEU 251 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188Q LEU* 5.5 1.1 - - + -
192Q LEU* 3.8 22.7 - - + -
198Q PRO* 3.9 18.4 - - + -
247Q ALA* 2.8 29.4 + - + +
248Q ASP* 4.2 4.0 - - - +
250Q THR* 1.3 76.1 - - + +
252Q ALA* 1.3 56.8 + - - +
254Q HIS* 3.3 3.0 + - - +
255Q LYS* 2.8 26.7 + - - -
256Q LYS 3.5 17.4 + - - +
257Q GLY 3.0 30.5 - - - +
258Q GLN* 4.0 8.5 - - - +
259Q ILE* 4.4 15.5 - - + +
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Residues in contact with ALA 252 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248Q ASP 3.0 19.8 + - - +
249Q ALA* 3.5 8.7 - - - +
251Q LEU* 1.3 78.9 - - - +
253Q TYR* 1.3 61.6 + - - +
255Q LYS* 3.2 25.7 - - - +
300Q THR* 5.6 3.1 - - + -
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Residues in contact with TYR 253 (chain Q).
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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249Q ALA 3.2 9.6 + - - +
250Q THR 3.1 9.0 + - - +
252Q ALA* 1.3 81.0 - - - +
254Q HIS* 1.3 74.7 + + - +
255Q LYS* 3.2 11.8 + - - +
300Q THR* 4.3 18.3 - - + +
303Q MET* 3.5 40.0 + - + -
304Q ALA* 3.4 31.9 + - + +
307Q ASN* 4.0 23.0 - - + +
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Residues in contact with HIS 254 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189Q ASN* 2.8 33.5 + - - -
192Q LEU* 3.8 36.3 - - + +
193Q ASN* 3.4 23.4 + - - -
250Q THR* 3.1 30.2 + - + +
251Q LEU 4.0 3.6 - - - +
253Q TYR* 1.3 89.2 - + - +
255Q LYS* 1.3 68.4 - - - +
256Q LYS* 3.0 29.0 + - + +
303Q MET* 3.9 6.5 - - - -
307Q ASN* 4.5 7.2 + - - -
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Residues in contact with LYS 255 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251Q LEU 2.8 9.2 + - - -
252Q ALA* 3.2 25.1 + - - +
253Q TYR 3.2 9.7 - - - +
254Q HIS* 1.3 79.3 - - - +
256Q LYS* 1.3 58.5 + - - +
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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