Contacts of the helix formed by residues 243 - 255 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169N ASN* 5.1 3.4 - - - -
184N VAL* 3.6 36.2 - - + +
200N LEU* 3.9 19.8 - - + +
204N SER* 4.2 10.5 + - - +
207N PHE* 3.4 30.8 + - + -
208N LYS* 4.8 0.2 - - - -
209N ARG* 3.7 36.8 - - + -
211N PHE* 3.8 22.9 - + - -
242N SER* 1.3 72.0 - - - +
244N GLN* 1.3 62.1 + - - +
246N VAL* 3.1 7.8 + - + +
247N ALA* 3.0 22.0 + - - +
272N TYR* 3.7 10.1 - - - -
401N ADP 3.6 36.6 - + - -
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Residues in contact with GLN 244 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200N LEU* 4.2 8.0 - - + +
204N SER 4.5 7.3 + - - +
205N GLU* 5.5 5.4 - - - +
242N SER* 3.1 12.9 - - - +
243N PHE* 1.3 78.8 - - - +
245N ALA* 1.3 55.6 + - - +
247N ALA* 3.3 7.3 + - - +
248N ASP* 2.8 66.1 + - - +
259N ILE* 4.2 18.4 - - - +
261N TYR* 3.9 18.2 + - - +
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Residues in contact with ALA 245 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241N GLU* 4.1 27.6 - - + +
242N SER* 2.9 23.1 + - - +
244N GLN* 1.3 72.7 - - - +
246N VAL* 1.3 66.8 + - - +
248N ASP* 3.2 13.4 + - - +
249N ALA* 3.0 22.9 + - - +
295N VAL* 4.0 8.1 - - + +
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Residues in contact with VAL 246 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184N VAL* 4.9 7.0 - - + -
185N ALA* 4.2 35.0 - - + +
188N LEU* 4.6 5.2 - - + -
211N PHE* 3.7 48.2 - - + -
242N SER 3.5 1.8 + - - +
243N PHE* 3.1 8.5 + - + +
245N ALA* 1.3 76.8 - - - +
247N ALA* 1.3 64.0 + - - +
249N ALA* 3.2 4.9 + - - +
250N THR* 3.0 26.8 + - - +
295N VAL* 3.7 18.8 - - + -
299N VAL* 4.2 9.8 - - + +
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Residues in contact with ALA 247 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188N LEU* 3.8 18.1 - - + +
200N LEU* 4.3 3.6 - - + -
243N PHE 3.0 12.0 + - - +
244N GLN* 3.4 14.8 - - - +
246N VAL* 1.3 77.4 - - - +
248N ASP* 1.3 52.6 + - - +
250N THR* 3.2 2.1 + - - -
251N LEU* 2.8 41.1 + - - +
259N ILE* 3.4 37.5 - - + -
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Residues in contact with ASP 248 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244N GLN* 2.8 50.5 + - - +
245N ALA* 3.2 12.8 + - - +
247N ALA* 1.3 73.6 - - - +
249N ALA* 1.3 62.6 + - - +
251N LEU* 4.0 4.6 - - - +
252N ALA* 3.0 27.8 + - - +
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Residues in contact with ALA 249 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245N ALA 3.0 9.7 + - - +
246N VAL 3.6 7.4 - - - +
248N ASP* 1.3 78.4 - - - +
250N THR* 1.3 62.1 + - - +
252N ALA* 3.5 6.4 - - - +
253N TYR* 3.2 16.8 + - - +
295N VAL* 4.3 9.9 - - + +
296N ALA* 4.3 16.4 - - + +
299N VAL* 3.7 24.9 - - + +
300N THR* 3.8 15.8 - - + +
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Residues in contact with THR 250 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185N ALA* 4.6 0.9 - - - -
188N LEU* 4.1 21.1 - - + +
189N ASN 4.5 1.6 - - - +
192N LEU* 3.9 21.1 - - + -
246N VAL* 3.0 17.2 + - - +
247N ALA* 3.5 10.3 - - - -
249N ALA* 1.3 73.5 - - - +
251N LEU* 1.3 66.2 + - + +
252N ALA 3.1 1.1 - - - -
253N TYR* 3.1 3.8 + - - +
254N HIS* 3.1 24.9 + - + +
299N VAL* 3.4 17.4 - - - +
303N MET* 3.6 30.3 - - + +
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Residues in contact with LEU 251 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188N LEU* 5.5 0.9 - - + -
192N LEU* 3.8 22.7 - - + -
198N PRO* 3.9 19.1 - - + -
247N ALA* 2.8 29.0 + - + +
248N ASP* 4.2 4.3 - - - +
250N THR* 1.3 77.0 - - + +
252N ALA* 1.3 56.9 + - - +
254N HIS* 3.3 2.8 + - - +
255N LYS* 2.8 26.5 + - - -
256N LYS 3.5 19.0 + - - +
257N GLY 3.1 29.8 - - - +
258N GLN* 4.0 8.3 - - - +
259N ILE* 4.4 15.0 - - + +
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Residues in contact with ALA 252 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248N ASP 3.0 19.4 + - - +
249N ALA* 3.5 8.3 - - - +
251N LEU* 1.3 77.7 - - - +
253N TYR* 1.3 61.4 + - - +
255N LYS* 3.2 25.7 - - - +
300N THR* 5.6 3.1 - - + -
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Residues in contact with TYR 253 (chain N).
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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249N ALA 3.2 10.6 + - - +
250N THR 3.1 9.0 + - - +
252N ALA* 1.3 81.4 - - - +
254N HIS* 1.3 75.6 + + - +
255N LYS* 3.2 12.2 + - - +
300N THR* 4.3 18.3 - - + +
303N MET* 3.5 40.3 + - + -
304N ALA* 3.4 31.2 + - + +
307N ASN* 4.0 23.6 - - + +
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Residues in contact with HIS 254 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189N ASN* 2.8 32.8 + - - -
192N LEU* 3.8 36.3 - - + +
193N ASN* 3.4 24.1 + - - -
250N THR* 3.1 30.0 + - + +
251N LEU 3.3 3.3 + - - +
253N TYR* 1.3 89.7 - + - +
255N LYS* 1.3 68.8 + - - +
256N LYS* 3.0 28.3 + - + +
303N MET* 3.9 6.3 - - - -
307N ASN* 4.4 7.4 + - - -
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Residues in contact with LYS 255 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251N LEU 2.8 10.3 + - - -
252N ALA* 3.2 25.3 + - - +
253N TYR* 3.2 9.1 - - - +
254N HIS* 1.3 79.3 - - - +
256N LYS* 1.3 60.8 + - - +
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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