Contacts of the helix formed by residues 243 - 255 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169M ASN* 5.1 3.8 - - - -
184M VAL* 3.6 33.9 - - + +
200M LEU* 3.9 19.4 - - + +
204M SER* 4.2 10.1 + - - +
207M PHE* 3.4 30.8 + - + -
208M LYS* 4.8 0.2 - - - -
209M ARG* 3.7 37.0 - - + -
211M PHE* 3.8 22.7 - + - -
242M SER* 1.3 72.3 - - - +
244M GLN* 1.3 63.4 + - - +
246M VAL* 3.1 8.2 + - + +
247M ALA* 3.0 22.0 + - - +
272M TYR* 3.7 5.6 - - - -
401M ADP 3.4 45.1 - + - -
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Residues in contact with GLN 244 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200M LEU* 4.2 7.5 - - + +
204M SER 4.5 7.3 + - - +
205M GLU* 5.6 5.6 - - - -
242M SER* 3.1 13.4 - - - +
243M PHE* 1.3 78.6 - - - +
245M ALA* 1.3 55.8 + - - +
247M ALA* 3.3 7.1 + - - +
248M ASP* 2.8 67.4 + - - +
259M ILE* 4.2 19.3 - - - +
261M TYR* 3.9 16.7 + - - +
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Residues in contact with ALA 245 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241M GLU* 4.1 27.8 - - + +
242M SER* 2.9 21.6 + - - +
244M GLN* 1.3 73.2 - - - +
246M VAL* 1.3 66.8 + - - +
248M ASP* 3.2 13.6 + - - +
249M ALA* 3.0 22.7 + - - +
295M VAL* 4.0 7.5 - - + +
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Residues in contact with VAL 246 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171M TYR* 6.4 0.2 - - + -
184M VAL* 4.9 6.7 - - + -
185M ALA* 4.2 35.0 - - + +
188M LEU* 4.6 4.5 - - + -
211M PHE* 3.7 48.2 - - + -
242M SER 3.5 2.4 + - - +
243M PHE* 3.1 8.9 + - - +
245M ALA* 1.3 77.0 - - - +
247M ALA* 1.3 63.3 + - - +
249M ALA* 3.2 4.9 + - - +
250M THR* 3.0 27.5 + - - +
295M VAL* 3.7 18.8 - - + +
299M VAL* 4.2 9.5 - - + +
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Residues in contact with ALA 247 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188M LEU* 3.8 18.1 - - + +
200M LEU* 4.3 6.1 - - + -
243M PHE 3.0 11.8 + - - +
244M GLN* 3.4 13.0 - - - +
246M VAL* 1.3 77.8 - - - +
248M ASP* 1.3 52.3 + - - +
250M THR* 3.2 2.3 + - - -
251M LEU* 2.8 40.8 + - - +
259M ILE* 3.4 37.2 - - + -
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Residues in contact with ASP 248 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244M GLN* 2.8 51.5 + - - +
245M ALA* 3.2 12.0 + - - +
247M ALA* 1.3 73.9 - - - +
249M ALA* 1.3 63.2 - - - +
251M LEU* 4.0 4.6 - - - +
252M ALA* 3.0 26.9 + - - +
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Residues in contact with ALA 249 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245M ALA 3.0 9.1 + - - +
246M VAL 3.2 7.8 + - - +
248M ASP* 1.3 78.9 - - - +
250M THR* 1.3 61.3 + - - +
252M ALA* 3.5 6.6 - - - +
253M TYR* 3.2 17.5 + - - +
295M VAL* 4.3 9.9 - - + +
296M ALA* 4.3 15.9 - - + +
299M VAL* 3.7 25.7 - - + +
300M THR* 3.7 15.8 - - + +
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Residues in contact with THR 250 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185M ALA* 4.6 1.0 - - - -
188M LEU* 4.1 21.1 - - + +
189M ASN 4.5 1.6 - - - +
192M LEU* 3.9 22.4 - - + -
246M VAL* 3.0 17.2 + - - +
247M ALA* 3.5 9.6 - - - -
249M ALA* 1.3 73.7 - - - +
251M LEU* 1.3 67.0 + - + +
252M ALA 3.1 1.1 - - - -
253M TYR* 3.1 4.0 + - - +
254M HIS* 3.1 24.7 + - + +
299M VAL* 3.4 17.4 - - - +
303M MET* 3.6 30.5 - - + +
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Residues in contact with LEU 251 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188M LEU* 5.5 1.6 - - + -
192M LEU* 3.8 21.8 - - + -
198M PRO* 3.9 18.8 - - + -
247M ALA* 2.8 29.4 + - + +
248M ASP* 4.2 4.5 - - - +
250M THR* 1.3 76.2 - - + +
252M ALA* 1.3 57.0 + - - +
254M HIS* 3.3 2.2 + - - +
255M LYS* 2.8 27.0 + - - -
256M LYS 3.5 18.7 + - - +
257M GLY 3.1 29.6 - - - +
258M GLN* 4.0 8.3 - - - +
259M ILE* 4.4 15.3 - - + +
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Residues in contact with ALA 252 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248M ASP 3.0 20.0 + - - +
249M ALA* 3.5 9.0 - - - +
251M LEU* 1.3 78.1 - - - +
253M TYR* 1.3 61.7 + - - +
255M LYS* 3.2 25.3 + - - +
300M THR* 5.6 3.4 - - + -
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Residues in contact with TYR 253 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249M ALA 3.2 10.0 + - - +
250M THR 3.1 9.4 + - - +
252M ALA* 1.3 81.5 - - - +
254M HIS* 1.3 75.0 + + - +
255M LYS* 3.2 12.3 + - - +
300M THR* 4.3 18.5 - - + +
303M MET* 3.5 39.6 + - + -
304M ALA* 3.4 31.8 + - + +
307M ASN* 4.0 23.3 - - + +
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Residues in contact with HIS 254 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189M ASN* 2.8 34.0 + - - -
192M LEU* 3.8 37.3 - - + +
193M ASN* 3.4 23.0 + - - -
250M THR* 3.1 30.0 + - + +
251M LEU 4.0 2.7 - - - +
253M TYR* 1.3 88.3 - + - +
255M LYS* 1.3 67.4 + - - +
256M LYS* 3.0 29.5 + - + +
303M MET* 3.9 6.3 - - - -
307M ASN* 4.5 7.2 - - - -
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Residues in contact with LYS 255 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251M LEU 2.8 10.2 + - - -
252M ALA* 3.2 25.1 + - - +
253M TYR 3.2 9.5 - - - +
254M HIS* 1.3 79.1 - - - +
256M LYS* 1.3 59.9 + - - +
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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