Contacts of the helix formed by residues 227 - 239 (chain D) in PDB entry 5DQZ
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 THR 227 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223D ILE 4.4 3.0 + - - -
224D LYS 4.2 1.0 + - - -
225D PHE 3.4 0.8 - - - -
226D ASP* 1.3 87.9 + - - +
228D VAL* 1.3 66.1 + - - +
230D PRO* 3.1 11.8 - - - +
231D LYS* 3.1 25.8 + - + +
254D ILE* 3.5 42.6 - - + -
258D SER* 6.4 0.2 - - - -
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Residues in contact with VAL 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D ALA* 3.7 16.4 - - + +
184D THR* 5.0 0.7 - - - +
187D LEU* 4.0 28.9 - - + -
223D ILE 5.5 0.6 + - - +
224D LYS* 3.5 13.7 - - + +
227D THR* 1.3 84.7 - - + +
229D VAL* 1.3 70.2 + - + +
231D LYS* 3.3 8.8 + - - +
232D ALA* 2.9 25.8 + - - +
247D VAL* 5.4 0.2 - - - +
251D CYS* 4.1 21.4 - - - -
254D ILE* 4.8 6.5 - - + -
255D PHE* 4.1 28.0 - - + -
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Residues in contact with VAL 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D TYR* 4.5 8.5 - - + -
152D LEU* 3.9 10.3 - - + -
180D ILE* 4.7 11.7 - - + -
183D ALA* 5.0 1.8 - - + -
184D THR* 4.7 9.9 - - + -
224D LYS* 3.4 40.1 + - + +
225D PHE* 4.1 17.9 - - + -
228D VAL* 1.3 79.4 - - + +
230D PRO* 1.4 72.5 - - + +
232D ALA* 3.0 9.7 + - - +
233D PHE* 3.0 47.2 + - + -
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Residues in contact with PRO 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D LEU* 4.0 20.9 - - + -
156D TYR* 3.6 34.8 - - + +
225D PHE 3.4 25.1 - - - +
226D ASP 4.1 6.7 - - - +
227D THR* 3.1 17.0 - - - +
229D VAL* 1.4 94.9 - - + +
231D LYS* 1.3 56.5 + - - +
233D PHE* 3.1 6.4 + - + +
234D GLU* 2.9 23.2 + - - +
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Residues in contact with LYS 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D THR* 3.1 14.0 + - + +
228D VAL* 3.6 9.2 - - - +
229D VAL 3.1 0.4 - - - -
230D PRO* 1.3 73.4 - - - +
232D ALA* 1.3 59.8 + - - +
234D GLU* 3.3 32.3 + - - +
235D ILE* 2.9 41.2 + - + +
238D ARG* 4.9 5.9 - - - +
247D VAL* 5.5 1.8 - - + -
250D ALA* 4.2 26.0 - - + +
251D CYS* 5.7 3.6 - - - -
254D ILE* 3.9 33.4 - - + -
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Residues in contact with ALA 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D ILE* 4.1 2.7 - - - -
179D CYS* 3.5 41.3 - - + +
180D ILE* 3.8 14.8 - - + +
183D ALA* 4.2 2.9 - - + -
228D VAL 2.9 13.6 + - - +
229D VAL* 3.2 13.7 - - - +
231D LYS* 1.3 76.9 - - - +
233D PHE* 1.3 57.4 + - - +
235D ILE* 3.9 0.3 - - - +
236D ALA* 2.9 28.2 + - - +
247D VAL* 4.5 8.5 - - - +
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Residues in contact with PHE 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D TYR* 3.7 22.7 - + - -
152D LEU* 3.8 21.1 - - + -
153D ALA* 3.6 32.3 - - + -
156D TYR* 3.9 17.9 - - + -
158D VAL* 3.7 21.6 - - + +
160D TRP* 4.3 15.3 - + - -
176D ILE* 3.6 31.4 - - + -
180D ILE* 4.3 7.4 - - + -
229D VAL* 3.0 43.6 + - + -
230D PRO 3.1 7.2 + - - +
232D ALA* 1.3 76.3 - - + +
234D GLU* 1.3 64.9 + - - +
236D ALA* 3.2 2.9 + - - +
237D ARG* 2.9 20.6 + - - +
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Residues in contact with GLU 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D TYR* 3.6 33.8 + - + -
230D PRO 2.9 8.9 + - - +
231D LYS* 3.3 39.5 + - - +
233D PHE* 1.3 74.9 - - - +
235D ILE* 1.3 59.1 + - - +
237D ARG* 3.2 7.1 + - - +
238D ARG* 3.0 50.3 + - - +
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Residues in contact with ILE 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D CYS* 4.3 4.0 - - - -
231D LYS* 2.9 25.8 + - + +
232D ALA 4.1 2.5 - - - +
234D GLU* 1.3 74.4 - - + +
236D ALA* 1.3 66.7 + - - +
238D ARG* 3.1 30.2 + - - +
239D ASN 3.0 18.4 + - - -
240D PRO* 3.4 25.6 - - + +
243D PRO 4.0 7.4 - - - +
246D GLU* 3.4 30.3 - - + +
247D VAL* 3.6 30.3 - - + -
250D ALA* 3.8 15.0 - - + -
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Residues in contact with ALA 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D VAL* 4.3 9.0 - - + -
175D THR* 4.7 8.8 - - + +
176D ILE* 3.6 37.2 - - + +
179D CYS* 4.1 9.4 - - - -
232D ALA 2.9 20.5 + - - +
233D PHE 3.2 6.5 - - - +
235D ILE* 1.3 77.7 - - - +
237D ARG* 1.3 61.6 + - - +
239D ASN* 3.2 18.0 + - - +
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Residues in contact with ARG 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D TYR* 3.3 18.2 + - + +
157D GLY* 2.8 31.3 + - - +
158D VAL* 3.8 18.3 - - + +
233D PHE 2.9 9.6 + - - +
234D GLU* 3.2 7.6 + - - +
236D ALA* 1.3 72.2 - - - +
238D ARG* 1.3 68.6 + - - +
239D ASN* 3.0 8.2 + - - +
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Residues in contact with ARG 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D LYS* 4.9 4.9 - - - +
234D GLU* 3.0 42.7 + - - +
235D ILE* 3.1 38.7 + - - +
237D ARG* 1.3 79.6 - - - +
239D ASN* 1.3 69.4 + - - +
240D PRO* 4.5 13.3 - - + +
246D GLU* 4.3 15.9 + - - +
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Residues in contact with ASN 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D THR* 4.8 14.9 + - - +
235D ILE 3.0 8.3 + - - -
236D ALA 3.6 11.7 + - - +
237D ARG 3.0 10.1 - - - +
238D ARG* 1.3 81.6 - - - +
240D PRO* 1.3 69.5 - - - +
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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