Contacts of the helix formed by residues 227 - 239 (chain D) in PDB entry 4DAJ
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 GLU 227 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163C PHE* 3.8 4.5 - - + -
166C TYR* 3.6 25.2 + - - -
167C PHE* 3.3 40.5 - - + -
170C THR* 4.9 0.9 + - - -
171C ARG* 4.0 15.8 + - - +
224D PHE 4.3 1.7 + - - +
225D LEU 3.0 1.9 - - - -
226D SER* 1.3 78.9 - - - +
228D PRO* 1.3 76.1 - - - +
229D THR* 2.6 28.8 + - - +
230D ILE* 3.4 19.7 - - + +
231D THR* 2.8 27.4 + - - -
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Residues in contact with PRO 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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166C TYR* 5.5 3.1 - - - +
171C ARG* 5.9 0.2 - - - +
252C ARG* 5.2 5.2 - - - +
226D SER 3.9 5.2 - - - +
227D GLU* 1.3 98.4 - - + +
229D THR* 1.3 62.8 + - + +
231D THR* 3.2 7.9 - - + +
232D PHE* 2.9 27.5 + - - +
510D VAL* 4.8 1.2 - - - +
513D ASN* 3.8 30.7 - - - +
514D THR* 3.6 21.1 + - - +
516D CYS 5.7 2.5 - - - +
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Residues in contact with THR 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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163C PHE* 3.3 17.9 - - - -
166C TYR* 5.6 0.9 - - - +
245C ILE* 3.6 14.4 - - + +
248C ILE* 5.5 5.4 - - + -
249C LEU* 3.8 25.3 - - + +
252C ARG* 4.5 17.3 - - - +
227D GLU* 2.6 25.8 + - - +
228D PRO* 1.3 74.6 - - + +
230D ILE* 1.3 69.8 + - - +
231D THR 3.0 1.3 - - - -
232D PHE* 2.9 9.6 + - - +
233D GLY 2.9 20.4 + - - -
514D THR* 4.5 13.9 - - + -
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Residues in contact with ILE 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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163C PHE* 3.8 23.7 - - + -
245C ILE* 4.7 4.7 - - - -
206D TRP* 6.2 3.4 - - + -
224D PHE* 3.5 41.1 - - + +
225D LEU* 4.6 3.4 - - + -
227D GLU* 3.4 24.0 - - + +
229D THR* 1.3 80.0 + - - +
231D THR* 1.3 68.2 + - - +
233D GLY* 3.5 1.3 + - - +
234D THR* 3.0 34.1 + - - +
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Residues in contact with THR 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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225D LEU* 3.3 33.6 + - + +
227D GLU 2.8 16.4 + - - -
228D PRO* 3.2 11.6 - - + +
230D ILE* 1.3 78.4 - - - +
232D PHE* 1.3 66.9 + - - +
234D THR* 3.0 5.4 + - - -
235D ALA* 2.9 19.4 + - - +
510D VAL* 3.6 24.7 - - + -
525D TRP* 6.2 1.8 - - + -
2000D 0HK 3.8 22.0 - - + +
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Residues in contact with PHE 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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244C THR* 5.3 3.6 - - - -
245C ILE* 4.9 8.5 - - + -
248C ILE* 5.4 13.5 - - + -
228D PRO 2.9 10.8 + - - +
229D THR* 3.3 10.3 - - - +
231D THR* 1.3 71.6 - - - +
233D GLY* 1.3 61.3 + - - +
235D ALA* 2.8 23.3 + - + +
236D ILE* 2.9 46.7 + - + +
240D TYR* 4.8 8.3 - + - -
510D VAL* 4.1 9.4 - - + -
511D LEU* 3.1 53.2 - - + -
514D THR* 3.3 32.5 - - + +
515D PHE* 5.6 2.2 - + - -
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Residues in contact with GLY 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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241C MET* 3.4 27.5 - - - +
245C ILE* 3.5 25.3 - - - +
229D THR 2.9 14.1 + - - -
230D ILE 3.8 1.6 - - - -
232D PHE* 1.3 73.7 - - - +
234D THR* 1.3 56.5 + - - +
236D ILE* 3.3 3.7 + - - +
237D ALA* 2.9 24.3 + - - +
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Residues in contact with THR 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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241C MET* 5.4 0.4 - - - -
199D TRP* 3.6 34.8 - - + -
224D PHE* 5.2 5.3 - - + -
225D LEU* 5.0 6.3 - - + +
230D ILE* 3.0 24.9 + - - +
231D THR* 3.0 5.8 + - - -
233D GLY* 1.3 72.8 - - - +
235D ALA* 1.3 60.9 + - - +
237D ALA* 4.5 4.5 - - + +
238D ALA* 2.9 38.7 + - + +
2000D 0HK 3.7 12.7 - - + -
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Residues in contact with ALA 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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231D THR 2.9 11.0 + - - +
232D PHE* 2.8 15.1 + - + +
234D THR* 1.3 76.0 - - - +
236D ILE* 1.3 56.2 + - - +
239D PHE* 2.5 31.9 + - - +
240D TYR* 2.9 21.8 + - + -
507D ASN* 3.4 22.9 - - + +
510D VAL* 4.8 10.8 - - + -
2000D 0HK 4.0 14.0 - - + +
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Residues in contact with ILE 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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236C ILE* 4.3 15.5 - - + -
241C MET* 3.7 31.6 - - + -
244C THR* 4.5 10.1 - - - +
245C ILE* 5.9 0.2 - - + -
232D PHE* 2.9 51.1 + - + +
233D GLY 3.5 6.5 - - - +
235D ALA* 1.3 76.3 - - - +
237D ALA* 1.3 63.8 + - - +
240D TYR* 3.0 28.3 + - + -
241D MET* 2.8 28.8 + - - +
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Residues in contact with ALA 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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237C ALA* 3.9 24.2 - - + +
241C MET* 3.7 18.6 - - + -
233D GLY 2.9 19.7 + - - +
234D THR* 4.4 4.3 - - + +
236D ILE* 1.3 75.0 - - - +
238D ALA* 1.3 57.2 + - - +
241D MET* 3.9 9.7 - - - +
242D PRO* 3.2 19.9 - - - +
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Residues in contact with ALA 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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152D ASN* 4.3 10.7 - - - +
155D VAL* 4.0 17.7 - - - +
199D TRP* 4.5 4.0 - - + -
234D THR* 2.9 31.9 + - + +
237D ALA* 1.3 78.0 - - + +
239D PHE* 1.3 58.2 + - - +
242D PRO* 3.1 15.6 - - - +
2000D 0HK 4.2 22.8 - - + +
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Residues in contact with PHE 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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155D VAL* 5.5 0.2 - - + -
235D ALA 2.5 17.6 + - - +
238D ALA* 1.3 74.8 - - - +
240D TYR* 1.3 85.1 + + - +
242D PRO* 2.8 7.5 - - - +
243D VAL* 2.8 53.1 + - + +
499D PHE* 3.6 14.1 - + - -
500D ILE* 4.8 1.1 - - - -
503D TRP* 3.4 41.3 - + + -
504D THR* 3.3 39.9 - - + -
507D ASN* 3.4 34.8 - - + +
2000D 0HK 3.5 8.7 - - - +
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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