Contacts of the helix formed by residues 229 - 240 (chain B) in PDB entry 6DXW
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 ASN 229 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188B LYS* 4.7 5.2 - - - +
189B PHE* 3.8 10.2 - - - -
227B SER 3.4 1.4 + - - -
228B GLU* 1.3 88.7 - - - +
230B PHE* 1.3 68.5 + - - +
231B GLU* 3.2 11.7 + - - +
232B ALA* 2.8 35.1 + - - +
233B ALA* 2.9 22.7 + - - +
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Residues in contact with PHE 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B LYS 3.8 19.2 + - - +
189B PHE* 4.1 6.7 - - - -
229B ASN* 1.3 75.3 - - - +
231B GLU* 1.3 82.4 + - - +
233B ALA* 3.2 2.9 + - - +
234B VAL* 2.9 44.1 + - + +
250B VAL* 3.6 32.5 - - + -
251B GLY 3.6 6.7 - - - -
252B GLY* 3.4 27.8 - - - -
256B ARG 5.4 0.4 - - - -
257B GLU* 3.7 52.9 - - + +
258B GLY 3.8 4.3 - - - -
259B VAL* 4.1 10.8 - - + -
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Residues in contact with GLU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B ASN* 3.2 9.6 + - - +
230B PHE* 1.3 97.0 - - + +
232B ALA* 1.3 61.7 + - - +
234B VAL* 3.3 10.9 + - - +
235B GLY* 3.1 19.2 + - - -
257B GLU* 4.8 8.7 - - - +
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Residues in contact with ALA 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B SER* 3.7 6.0 + - - +
228B GLU* 4.2 11.7 - - + +
229B ASN* 2.8 34.2 + - - +
231B GLU* 1.3 72.9 - - - +
233B ALA* 1.3 63.5 + - - +
235B GLY* 3.3 2.1 + - - -
236B LYS* 3.0 25.5 + - - +
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Residues in contact with ALA 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B PHE* 3.6 41.5 - - + -
223B THR* 3.7 5.4 - - + -
227B SER* 3.6 10.7 - - - -
229B ASN 2.9 12.9 + - - +
230B PHE 3.5 7.9 - - - +
232B ALA* 1.3 77.2 - - - +
234B VAL* 1.3 56.9 + - - +
236B LYS* 3.3 1.0 + - - +
237B LEU* 2.8 41.2 + - + +
250B VAL* 4.7 2.9 - - + -
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Residues in contact with VAL 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B PHE* 2.9 52.8 + - + +
231B GLU* 3.3 11.6 + - - +
233B ALA* 1.3 75.5 - - - +
235B GLY* 1.3 63.3 + - - +
237B LEU* 3.8 1.5 - - - -
238B ALA* 2.9 29.5 + - + +
250B VAL* 4.2 7.9 - - + -
259B VAL* 3.9 17.3 - - + -
261B ILE* 3.8 21.4 - - + +
271B ILE* 5.2 13.2 - - + -
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Residues in contact with GLY 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B GLU 3.1 13.8 + - - -
232B ALA* 3.7 3.4 - - - -
233B ALA 3.3 0.2 - - - -
234B VAL* 1.3 78.2 - - - +
236B LYS* 1.3 61.6 + - - +
238B ALA* 3.2 4.0 + - - +
239B LYS* 3.1 40.5 + - - +
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Residues in contact with LYS 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B LEU* 4.0 9.0 - - + +
222B ALA* 3.7 26.5 - - - +
223B THR* 3.4 20.6 - - - +
226B GLU* 3.0 32.0 + - + +
227B SER* 3.5 16.6 - - - +
232B ALA 3.0 17.4 + - - +
233B ALA 3.8 2.9 - - - +
235B GLY* 1.3 75.6 - - - +
237B LEU* 1.3 61.1 + - - +
239B LYS* 5.4 0.7 - - - -
240B THR* 2.7 44.8 + - - +
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Residues in contact with LEU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B VAL* 4.0 16.6 - - + -
219B LEU* 4.1 9.4 - - + +
220B ILE* 4.3 10.3 - - + -
223B THR* 3.4 31.9 - - + +
233B ALA* 2.8 23.1 + - + +
234B VAL 4.0 2.7 - - - +
236B LYS* 1.3 77.4 - - - +
238B ALA* 1.3 57.1 + - - +
248B TYR* 3.3 52.6 - - + -
250B VAL* 3.6 28.9 - - + -
261B ILE* 4.1 7.2 - - + -
263B ARG* 2.9 20.0 + - - -
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Residues in contact with ALA 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B VAL* 2.9 19.0 + - + +
235B GLY* 3.8 5.4 - - - +
237B LEU* 1.3 78.6 - - - +
239B LYS* 1.3 64.1 + - + +
261B ILE* 4.1 17.7 - - + +
263B ARG* 3.4 17.3 + - - +
267B GLY 3.6 0.5 - - - -
268B PRO* 3.3 37.8 - - + +
271B ILE* 4.6 10.5 - - + -
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Residues in contact with LYS 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B GLY* 3.1 24.3 + - - +
236B LYS* 5.4 0.7 - - - -
238B ALA* 1.3 85.1 - - + +
240B THR* 1.3 65.7 + - - +
241B PRO* 3.4 6.6 - - - +
263B ARG* 4.0 1.8 - - - -
266B ASP 4.0 12.4 - - - +
267B GLY* 4.9 3.6 - - - -
268B PRO* 5.0 7.9 - - + -
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Residues in contact with THR 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B ILE* 4.3 11.4 - - + -
219B LEU* 3.6 26.5 - - + +
236B LYS* 2.7 36.5 + - - +
239B LYS* 1.3 77.1 - - - +
241B PRO* 1.3 84.4 - - + +
242B LEU* 3.6 2.8 - - - +
263B ARG* 2.8 25.6 + - - +
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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