Contacts of the helix formed by residues 227 - 239 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A PHE* 4.4 8.1 - - + -
166A TYR* 3.3 32.8 + - + -
167A PHE* 3.9 21.3 - - + -
170A THR* 5.0 2.4 + - - -
171A ARG* 3.7 19.7 + - - +
252A ARG* 4.4 0.7 + - - -
224B PHE 4.6 0.6 + - - -
225B LEU 3.0 9.9 - - - +
226B SER* 1.3 78.5 - - - +
228B PRO* 1.3 89.1 - - + +
229B THR* 3.0 26.1 + - - +
230B ILE* 2.9 33.0 - - + +
231B THR* 3.0 3.3 + - - -
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Residues in contact with PRO 228 (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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252A ARG* 4.5 8.7 - - - +
226B SER 3.4 5.8 - - - +
227B GLU* 1.3 107.2 - - - +
229B THR* 1.3 55.8 + - - +
231B THR* 3.4 7.4 - - - +
232B PHE 2.9 22.3 + - - -
510B VAL* 4.9 0.2 - - - +
513B ASN* 4.1 19.1 - - - +
514B THR* 3.0 41.6 + - - +
516B CYS 5.2 4.0 - - - +
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Residues in contact with THR 229 (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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163A PHE* 3.3 18.2 - - - -
245A ILE* 3.6 13.6 - - - +
248A ILE* 3.9 27.6 - - + -
249A LEU* 4.0 15.0 - - + +
252A ARG* 4.0 16.2 - - - +
227B GLU* 3.0 20.4 - - - +
228B PRO* 1.3 75.6 - - - +
230B ILE* 1.3 60.9 + - - +
232B PHE* 2.8 20.8 + - - +
233B GLY 2.9 13.2 + - - -
514B THR* 4.0 16.8 - - + -
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Residues in contact with ILE 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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163A PHE* 4.0 22.4 - - + -
167A PHE* 5.9 2.9 - - + -
245A ILE* 4.8 3.8 - - - -
206B TRP* 6.1 3.8 - - + -
224B PHE* 3.1 39.7 - - + +
225B LEU* 4.4 6.3 - - + -
227B GLU* 2.9 39.9 - - + +
229B THR* 1.3 75.4 + - - +
231B THR* 1.3 56.6 + - - +
233B GLY* 3.5 1.1 + - - +
234B THR* 2.8 35.7 + - - +
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Residues in contact with THR 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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225B LEU* 2.6 47.6 + - + +
227B GLU 3.0 2.0 + - - -
228B PRO* 3.4 12.0 - - - +
229B THR 3.2 0.2 - - - -
230B ILE* 1.3 80.9 - - - +
232B PHE* 1.3 61.6 + - - +
234B THR* 3.2 3.6 + - - -
235B ALA* 2.9 21.1 + - - +
510B VAL* 3.7 18.6 - - + -
513B ASN* 5.5 4.0 - - - +
2000B 0HK 3.7 25.6 - - + +
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Residues in contact with PHE 232 (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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244A THR* 4.6 8.5 - - - -
245A ILE* 4.4 5.4 - - + -
248A ILE* 4.2 28.3 - - + -
228B PRO 2.9 6.4 + - - +
229B THR* 2.8 12.8 + - - +
231B THR* 1.3 75.2 - - - +
233B GLY* 1.3 66.2 + - - +
235B ALA* 2.7 18.5 + - + +
236B ILE* 3.0 43.5 + - + +
240B TYR* 4.8 7.6 - + - -
510B VAL* 4.0 8.0 - - + +
511B LEU* 3.6 50.0 - - + -
514B THR* 3.3 21.5 - - + +
515B PHE* 5.2 2.9 - + - -
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Residues in contact with GLY 233 (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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241A MET* 3.7 22.1 - - - +
245A ILE* 3.3 25.0 - - - +
229B THR 2.9 14.1 + - - -
230B ILE 3.5 1.3 + - - -
232B PHE* 1.3 72.8 - - - +
234B THR* 1.3 63.1 + - - +
236B ILE* 3.1 8.6 + - - +
237B ALA* 2.9 21.7 + - - +
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Residues in contact with THR 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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199B TRP* 3.7 26.5 - - + -
224B PHE* 5.4 2.8 - - + -
225B LEU* 3.9 12.0 - - + +
230B ILE* 2.8 23.2 + - - +
231B THR* 3.3 11.4 - - - -
233B GLY* 1.3 76.3 - - - +
235B ALA* 1.3 61.8 + - - +
237B ALA* 3.3 6.2 + - + +
238B ALA* 2.9 26.5 + - + +
2000B 0HK 3.6 20.2 - - + -
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Residues in contact with ALA 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 THR 2.9 11.4 + - - +
232B PHE* 2.7 20.0 + - + +
234B THR* 1.3 72.6 - - - +
236B ILE* 1.3 55.1 + - - +
239B PHE* 2.7 36.7 + - - +
240B TYR* 3.2 14.8 + - + -
507B ASN* 3.3 22.2 - - - +
510B VAL* 4.4 13.5 - - + -
2000B 0HK 3.9 14.3 - - + -
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Residues in contact with ILE 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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236A ILE* 4.7 14.1 - - + -
237A ALA* 6.0 0.2 - - - -
241A MET* 3.6 34.8 - - + +
244A THR* 4.1 11.2 - - + +
245A ILE* 5.3 0.2 - - + -
232B PHE* 3.0 53.5 + - + +
233B GLY* 3.4 6.7 - - - +
235B ALA* 1.3 76.2 - - - +
237B ALA* 1.3 66.1 + - - +
240B TYR* 3.4 20.4 - - + -
241B MET* 3.1 25.1 + - - +
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Residues in contact with ALA 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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237A ALA* 5.0 17.0 - - + +
241A MET* 4.4 17.2 - - + +
233B GLY 2.9 12.9 + - - +
234B THR* 3.7 9.4 - - + +
236B ILE* 1.3 81.5 - - - +
238B ALA* 1.3 59.3 + - + +
241B MET* 4.1 9.9 - - - +
242B PRO* 3.1 20.4 - - - +
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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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152B ASN* 3.7 15.9 - - - +
155B VAL* 3.8 14.7 - - - +
199B TRP* 4.4 11.7 - - + -
234B THR* 2.9 20.1 + - + +
237B ALA* 1.3 74.5 - - + +
239B PHE* 1.3 57.1 + - - +
242B PRO* 3.4 14.2 - - - +
2000B 0HK 3.5 32.8 - - + -
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Residues in contact with PHE 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 ALA 2.7 18.7 + - - +
237B ALA 3.2 1.0 - - - -
238B ALA* 1.3 73.8 - - - +
240B TYR* 1.3 92.0 + + - +
241B MET 3.2 2.0 - - - -
242B PRO* 2.9 13.4 - - - +
243B VAL* 3.0 34.0 + - + +
499B PHE* 3.6 20.2 - + - -
500B ILE* 4.6 2.2 - - - -
503B TRP* 3.3 50.5 - + + -
504B THR* 4.1 24.7 - - + -
507B ASN* 3.3 37.7 - - + +
2000B 0HK 3.3 15.9 - - - +
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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