Contacts of the helix formed by residues 225 - 240 (chain J) in PDB entry 5AYZ
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 LYS 225 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223J ASN 5.1 6.1 + - - +
224J PHE* 1.3 73.3 - - - +
226J PRO* 1.3 71.1 - - + +
227J GLU* 3.0 19.0 + - + +
228J GLU* 3.1 30.9 + - - +
229J LEU* 2.9 19.5 + - - +
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Residues in contact with PRO 226 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224J PHE 3.7 0.4 - - - -
225J LYS* 1.3 85.7 - - + +
227J GLU* 1.3 75.3 + - - +
229J LEU* 3.3 14.4 + - + -
230J HIS* 3.1 26.6 + - + +
258J GLN* 3.3 50.0 - - + +
259J PHE* 3.8 30.5 - - + -
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Residues in contact with GLU 227 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225J LYS* 3.2 24.3 - - + +
226J PRO* 1.3 86.2 - - - +
228J GLU* 1.3 59.3 + - + +
231J PRO* 3.0 24.1 - - - +
258J GLN* 5.0 4.5 - - - +
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Residues in contact with GLU 228 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223J ASN 4.8 0.9 - - - +
224J PHE* 3.5 23.6 - - + -
225J LYS* 3.3 43.5 + - - +
227J GLU* 1.3 78.8 - - - +
229J LEU* 1.3 65.6 + - - +
230J HIS 3.4 1.1 - - - -
231J PRO* 3.6 6.1 - - - +
232J THR* 2.8 31.6 + - - +
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Residues in contact with LEU 229 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221J LEU* 3.6 42.3 - - + +
224J PHE* 3.7 20.4 - - + -
225J LYS 2.9 17.1 + - - +
226J PRO* 3.3 5.3 + - + +
228J GLU* 1.3 78.8 - - - +
230J HIS* 1.3 75.4 + - + +
232J THR* 3.3 4.0 + - - -
233J ALA* 2.8 25.8 + - - +
247J ALA* 4.1 12.1 - - + -
259J PHE* 3.8 31.6 - - + +
264J ILE* 3.9 23.6 - - + -
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Residues in contact with HIS 230 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226J PRO* 3.1 24.3 + - + +
229J LEU* 1.3 84.0 - - + +
231J PRO* 1.3 71.5 - - + +
233J ALA* 3.2 5.9 + - - +
234J THR* 2.8 30.2 + - - +
258J GLN 3.1 24.3 + - - -
259J PHE* 3.3 18.7 - - - -
260J CYS 3.2 26.6 + - - -
261J GLY* 3.6 11.0 - - - -
262J PRO* 4.9 5.9 - - + +
263J HIS* 5.5 0.4 + - - +
264J ILE* 4.2 9.3 - - + +
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Residues in contact with PRO 231 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227J GLU 3.0 28.5 - - - +
228J GLU* 3.6 9.2 - - - +
230J HIS* 1.3 89.5 - - + +
232J THR* 1.3 62.0 + - - +
234J THR* 3.2 9.3 + - - +
235J VAL* 3.1 28.8 + - + +
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Residues in contact with THR 232 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205J LEU* 3.5 45.8 - - + +
221J LEU* 4.0 22.4 - - + -
224J PHE* 3.8 16.9 - - + -
228J GLU* 2.8 21.9 + - - +
229J LEU 3.3 4.2 + - - -
230J HIS 3.2 0.6 - - - -
231J PRO* 1.3 76.2 - - - +
233J ALA* 1.3 65.7 + - - +
235J VAL* 3.4 4.4 + - - +
236J LEU* 3.2 23.9 + - + +
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Residues in contact with ALA 233 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221J LEU* 4.2 6.5 - - + +
229J LEU 2.8 16.4 + - - +
230J HIS* 3.2 7.4 + - - +
232J THR* 1.3 76.7 - - - +
234J THR* 1.3 58.6 + - - +
236J LEU* 3.5 5.3 + - - +
237J LYS* 3.0 33.3 + - - +
245J VAL* 4.3 5.8 - - + +
263J HIS* 3.7 27.8 - - + +
264J ILE* 3.7 19.5 - - + -
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Residues in contact with THR 234 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230J HIS* 2.8 19.1 + - - +
231J PRO* 3.4 11.1 - - - +
232J THR 3.1 0.2 - - - -
233J ALA* 1.3 75.6 - - - +
235J VAL* 1.3 66.1 + - + +
237J LYS* 3.9 1.7 - - - +
238J ALA* 3.0 25.2 + - + +
262J PRO* 5.9 0.2 - - - +
263J HIS* 3.4 33.0 + - + +
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Residues in contact with VAL 235 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205J LEU* 4.2 31.6 - - + -
209J VAL* 5.2 2.5 - - + -
231J PRO 3.1 14.7 + - - +
232J THR 3.9 6.3 - - - +
234J THR* 1.3 76.1 - - + +
236J LEU* 1.3 58.9 + - - +
238J ALA* 3.2 7.3 + - - +
239J GLN* 2.9 51.2 + - + +
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Residues in contact with LEU 236 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205J LEU* 4.0 6.5 - - + -
208J ALA* 3.5 47.1 - - + +
209J VAL* 4.1 13.0 - - + +
212J ALA* 4.6 2.7 - - + -
219J VAL* 3.9 17.3 - - + -
221J LEU* 4.1 15.3 - - + -
232J THR* 3.2 20.4 + - + +
233J ALA* 3.8 3.6 - - - +
235J VAL* 1.3 79.3 - - - +
237J LYS* 1.3 54.5 + - - +
239J GLN* 3.2 0.4 + - - -
240J PHE* 2.7 60.2 + - + +
243J VAL* 6.1 4.9 - - + -
245J VAL* 4.4 13.9 - - + -
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Residues in contact with LYS 237 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233J ALA 3.0 20.1 + - - +
234J THR 3.9 1.8 - - - +
236J LEU* 1.3 76.4 - - - +
238J ALA* 1.3 63.6 + - - +
240J PHE 4.2 1.8 - - - -
241J PRO* 3.3 40.4 + - + +
242J SER 5.6 0.2 - - - -
243J VAL 3.1 26.8 + - - +
244J ALA* 4.1 1.4 - - - +
245J VAL* 4.0 7.6 - - + -
263J HIS* 3.5 47.3 - - + +
265J ASP* 2.8 36.3 + - - -
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Residues in contact with ALA 238 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234J THR* 3.0 19.8 + - + +
235J VAL* 3.2 7.2 + - - +
237J LYS* 1.3 79.4 - - - +
239J GLN* 1.3 62.1 + - + +
241J PRO* 4.0 6.1 - - - +
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Residues in contact with GLN 239 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209J VAL* 4.7 14.0 - - - +
213J GLU* 5.6 2.6 + - - -
235J VAL* 2.9 34.7 + - + +
238J ALA* 1.3 79.3 - - + +
240J PHE* 1.3 94.8 + - + +
241J PRO* 3.5 6.9 - - - +
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Residues in contact with PHE 240 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209J VAL* 4.0 22.7 - - + -
212J ALA* 3.5 32.8 - - + -
213J GLU* 3.7 35.7 - - + -
236J LEU* 2.7 33.6 + - + +
237J LYS* 4.0 2.4 - - - +
239J GLN* 1.3 104.7 - - + +
241J PRO* 1.3 65.9 - - - +
242J SER* 3.0 6.3 + - - -
243J VAL* 3.0 36.2 + - + +
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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