Contacts of the helix formed by residues 243 - 255 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169H ASN* 5.2 3.1 - - - -
184H VAL* 3.6 34.0 - - + +
188H LEU* 5.7 0.2 - - - +
200H LEU* 3.9 19.6 - - + +
204H SER* 4.2 10.1 + - - -
207H PHE* 3.4 27.9 + - + -
208H LYS* 4.8 0.2 - - - -
209H ARG* 3.7 36.8 - - + -
211H PHE* 3.8 22.2 - + - -
242H SER* 1.3 72.1 - - - +
244H GLN* 1.3 63.8 + - - +
246H VAL* 3.1 7.3 + - + +
247H ALA* 2.9 22.0 + - - +
272H TYR* 3.7 8.7 - - - -
401H ADP 3.5 45.3 - + - -
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Residues in contact with GLN 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200H LEU* 4.2 13.8 - - + +
204H SER 4.5 7.5 + - - +
205H GLU* 5.4 6.1 - - - -
242H SER* 3.1 14.0 + - - +
243H PHE* 1.3 78.5 - - - +
245H ALA* 1.3 56.3 + - - +
247H ALA* 3.3 7.2 + - - +
248H ASP* 2.8 65.5 + - - +
259H ILE* 4.2 13.4 - - - +
261H TYR* 3.9 17.7 + - - +
208O LYS* 4.6 16.5 - - - +
275O PHE* 5.5 7.4 - - - -
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Residues in contact with ALA 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241H GLU* 4.1 26.7 - - + +
242H SER* 2.9 22.9 + - - +
244H GLN* 1.3 72.9 - - - +
246H VAL* 1.3 65.0 - - - +
248H ASP* 3.2 14.2 + - - +
249H ALA* 3.0 22.7 + - - +
295H VAL* 4.0 7.3 - - + +
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Residues in contact with VAL 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171H TYR* 6.5 0.2 - - + -
184H VAL* 4.9 6.3 - - + -
185H ALA* 4.2 35.0 - - + +
188H LEU* 4.6 6.1 - - + -
211H PHE* 3.7 47.8 - - + -
242H SER 3.5 2.0 + - - +
243H PHE* 3.1 9.3 + - + +
245H ALA* 1.3 76.4 - - - +
247H ALA* 1.3 63.8 + - - +
249H ALA* 3.2 5.0 + - - +
250H THR* 3.0 26.4 + - - +
295H VAL* 3.8 18.8 - - + -
299H VAL* 4.2 8.9 - - + +
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Residues in contact with ALA 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188H LEU* 3.8 17.4 - - + +
200H LEU* 4.2 6.1 - - + -
243H PHE 2.9 11.7 + - - +
244H GLN* 3.4 13.2 - - - +
246H VAL* 1.3 77.0 - - - +
248H ASP* 1.3 52.7 + - - +
250H THR* 3.2 2.3 + - - -
251H LEU* 2.8 39.8 + - - +
259H ILE* 3.4 37.7 - - + -
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Residues in contact with ASP 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244H GLN* 2.8 49.2 + - - +
245H ALA* 3.3 12.1 - - - +
247H ALA* 1.3 73.8 - - - +
249H ALA* 1.3 63.3 + - - +
251H LEU* 3.9 4.4 - - - +
252H ALA* 2.9 27.2 + - - +
208O LYS* 3.7 23.4 + - - -
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Residues in contact with ALA 249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245H ALA 3.0 9.3 + - - +
246H VAL 3.2 7.6 + - - +
248H ASP* 1.3 79.5 - - - +
250H THR* 1.3 61.8 + - - +
252H ALA* 3.5 6.8 - - - +
253H TYR* 3.2 17.2 + - - +
295H VAL* 4.3 9.6 - - + +
296H ALA* 4.3 16.4 - - + +
299H VAL* 3.7 25.1 - - + -
300H THR* 3.8 15.4 - - + +
303H MET* 5.1 0.2 - - - +
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Residues in contact with THR 250 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185H ALA* 4.6 0.7 - - - -
188H LEU* 4.1 22.3 - - + +
189H ASN 4.5 1.6 - - - +
192H LEU* 3.9 21.3 - - + -
246H VAL* 3.0 17.4 + - - +
247H ALA* 3.5 9.9 - - - -
249H ALA* 1.3 73.9 - - - +
251H LEU* 1.3 67.0 + - + +
252H ALA 3.1 0.9 - - - -
253H TYR* 3.1 3.8 + - - +
254H HIS* 3.1 24.4 + - + +
299H VAL* 3.4 17.1 - - - +
303H MET* 3.6 30.5 - - + +
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Residues in contact with LEU 251 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188H LEU* 5.5 1.3 - - + -
192H LEU* 3.8 22.4 - - + -
198H PRO* 3.9 18.8 - - + -
247H ALA* 2.8 29.8 + - + +
248H ASP* 4.2 4.3 - - - +
250H THR* 1.3 75.9 - - + +
252H ALA* 1.3 58.2 + - - +
254H HIS* 3.3 3.2 + - - +
255H LYS* 2.8 27.0 + - - -
256H LYS 3.5 17.6 + - - +
257H GLY 3.0 31.0 - - - +
258H GLN* 4.0 7.9 - - - +
259H ILE* 4.3 15.9 - - + +
277O GLN* 5.9 4.0 - - - +
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Residues in contact with ALA 252 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248H ASP 2.9 20.6 + - - +
249H ALA* 3.5 8.5 - - - +
250H THR 3.1 0.2 - - - -
251H LEU* 1.3 78.2 - - - +
253H TYR* 1.3 61.7 + - - +
255H LYS* 3.2 26.1 - - - +
300H THR* 5.6 2.9 - - + -
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Residues in contact with TYR 253 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249H ALA 3.2 10.0 + - - +
250H THR 3.1 8.6 + - - +
252H ALA* 1.3 81.4 - - - +
254H HIS* 1.3 75.5 + + - +
255H LYS* 3.2 12.2 + - - +
300H THR* 4.3 19.4 - - + +
303H MET* 3.5 39.7 + - + -
304H ALA* 3.4 31.6 + - + +
307H ASN* 4.0 23.2 - - + +
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Residues in contact with HIS 254 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H ASN* 2.8 33.6 + - - -
192H LEU* 3.8 36.4 - - + +
193H ASN* 3.4 23.4 + - - -
250H THR* 3.1 31.1 + - + +
251H LEU 4.0 2.7 - - - +
253H TYR* 1.3 88.4 - + - +
255H LYS* 1.3 68.3 + - - +
256H LYS* 3.0 29.6 + - + +
303H MET* 3.9 5.9 - - - -
307H ASN* 4.5 7.0 - - - -
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Residues in contact with LYS 255 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251H LEU 2.8 9.8 + - - -
252H ALA* 3.2 25.7 + - - +
253H TYR 3.2 11.5 - - - +
254H HIS* 1.3 77.9 - - - +
256H LYS* 1.3 60.1 + - - +
239O ARG* 5.7 16.2 - - - +
294O THR* 6.2 1.6 - - - +
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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