Contacts of the helix formed by residues 228 - 246 (chain B) in PDB entry 5D3O
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 ASP 228 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B ARG* 3.6 24.7 + - - +
226B ILE* 3.5 5.1 - - - +
227B PRO* 1.3 78.8 - - + +
229B PHE* 1.3 61.2 + - - +
230B MET* 3.7 7.1 + - - +
231B SER* 3.0 32.3 + - - -
232B PHE* 3.1 19.6 + - - +
547B PRO 4.9 3.0 + - - +
549B ARG 5.5 3.0 + - - +
550B GLU 4.8 12.1 - - - +
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Residues in contact with PHE 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B SER 4.6 3.1 + - - +
171B THR 4.0 11.7 - - - +
172B GLY* 3.6 16.6 - - - -
226B ILE* 3.7 16.4 - - + +
227B PRO 3.0 9.8 + - - +
228B ASP* 1.3 71.6 - - - +
230B MET* 1.3 58.0 + - - +
232B PHE* 3.2 19.2 + + - +
233B THR* 2.8 49.4 + - - -
270B VAL* 4.7 5.2 - - + -
272B THR* 3.6 24.2 - - + -
276B GLN* 3.6 44.0 - - + +
277B ARG 3.3 29.6 - - - -
278B HIS* 4.1 5.2 - - + -
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Residues in contact with MET 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B SER* 4.0 37.1 + - - +
228B ASP* 3.3 6.1 + - - +
229B PHE* 1.3 79.0 - - - +
231B SER* 1.3 62.2 + - - +
233B THR* 3.4 11.8 + - + +
234B SER* 3.3 20.8 + - - -
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Residues in contact with SER 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ASP* 3.0 36.5 + - - -
229B PHE 3.1 0.2 - - - -
230B MET* 1.3 73.4 - - - +
232B PHE* 1.3 65.5 + - - +
233B THR 3.1 1.8 - - - -
234B SER* 2.9 22.4 + - - -
235B HIS* 3.4 22.8 + - - -
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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
----------------------------------------------------------
226B ILE* 3.7 29.8 - - + -
228B ASP 3.1 10.8 + - - +
229B PHE* 3.7 26.0 - + - +
231B SER* 1.3 78.6 - - - +
233B THR* 1.3 64.6 + - - +
234B SER 3.5 0.2 + - - -
235B HIS* 3.5 14.9 + - + +
236B ILE* 3.3 51.2 + - + +
270B VAL* 4.5 6.7 - - + -
278B HIS* 6.5 0.4 - - + -
501B MET* 3.7 27.8 - - + -
526B LEU* 5.1 1.1 - - + -
530B CYS* 4.8 5.8 - - - -
532B PHE* 4.1 11.2 - + - -
545B LEU* 5.8 0.7 - - + -
547B PRO* 3.5 36.6 - - + -
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Residues in contact with THR 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B PHE* 2.8 31.4 + - - -
230B MET* 3.6 13.5 - - + +
231B SER 3.1 0.6 - - - -
232B PHE* 1.3 79.8 - - - +
234B SER* 1.3 59.3 + - - +
236B ILE* 3.3 10.3 + - - +
237B ASP* 3.2 29.0 + - - +
278B HIS* 3.0 48.1 + - + +
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Residues in contact with SER 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B MET 3.3 9.6 + - - -
231B SER* 2.9 18.0 + - - -
233B THR* 1.3 78.1 - - - +
235B HIS* 1.3 61.0 + - - +
237B ASP* 3.3 12.9 + - - +
238B GLU* 2.9 33.2 + - - +
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Residues in contact with HIS 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B SER* 3.4 25.0 + - - -
232B PHE* 3.6 15.9 - - + +
234B SER* 1.3 77.7 + - - +
236B ILE* 1.3 59.1 + - + +
238B GLU* 3.1 30.1 + - - +
239B LEU* 2.9 34.3 + - + +
529B LEU* 4.0 34.3 - - + +
545B LEU* 4.3 26.6 - - + +
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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
----------------------------------------------------------
232B PHE* 3.3 49.1 + - + +
233B THR* 3.5 10.5 - - - +
234B SER 3.3 0.6 - - - -
235B HIS* 1.3 76.3 - - + +
237B ASP* 1.3 59.2 + - - +
239B LEU* 3.3 8.6 + - + +
240B TYR* 2.9 27.6 + - + +
268B VAL* 4.6 12.6 - - + +
270B VAL* 4.2 15.5 - - + -
278B HIS* 4.1 20.2 - - + -
280B THR* 4.6 5.4 - - - +
503B MET* 4.9 2.7 - - - -
522B PHE* 4.0 24.5 - - + -
526B LEU* 4.6 13.2 - - + -
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Residues in contact with ASP 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B THR* 3.2 17.7 + - - +
234B SER* 3.4 15.0 - - - +
236B ILE* 1.3 74.5 - - - +
238B GLU* 1.3 64.6 + - - +
240B TYR* 3.3 5.3 + - - +
241B GLU* 3.0 33.4 + - + +
278B HIS* 3.0 28.7 + - - -
280B THR* 3.0 24.0 + - + +
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Residues in contact with GLU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B SER* 2.9 19.5 + - - +
235B HIS* 3.1 33.9 + - - +
237B ASP* 1.3 75.9 - - - +
239B LEU* 1.3 64.4 + - + +
241B GLU* 3.3 5.0 + - - +
242B SER* 3.0 25.6 + - - -
529B LEU* 5.7 1.0 - - - +
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Residues in contact with LEU 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 HIS* 2.9 20.9 + - + +
236B ILE* 3.6 9.6 - - + +
237B ASP 3.3 0.2 - - - -
238B GLU* 1.3 75.0 - - + +
240B TYR* 1.3 58.1 + - - +
242B SER* 3.4 5.6 + - - -
243B ALA* 3.0 30.5 + - - +
521B HIS* 5.4 0.3 + - - -
522B PHE* 3.4 26.7 - - + -
525B ASP* 3.5 38.5 - - + +
526B LEU* 3.8 38.6 - - + +
529B LEU* 4.0 20.6 - - + -
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Residues in contact with TYR 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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236B ILE* 2.9 17.5 + - + +
237B ASP* 3.5 7.2 - - - +
238B GLU 3.2 0.2 - - - -
239B LEU* 1.3 77.0 - - - +
241B GLU* 1.3 71.6 + - - +
243B ALA 3.3 1.4 + - - -
244B LYS* 3.0 47.9 + - + +
266B TRP* 2.9 79.6 + + - +
267B GLY* 3.9 1.1 - - - -
268B VAL* 3.8 14.4 - - + -
280B THR* 3.6 40.4 - - + +
281B GLY* 3.4 14.4 - - - -
282B ASP* 4.9 1.0 + - - -
522B PHE* 3.8 10.0 - - + -
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Residues in contact with GLU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ASP* 3.0 21.3 + - + +
238B GLU* 3.9 4.9 - - - +
240B TYR* 1.3 89.4 - - + +
242B SER* 1.3 63.6 + - - +
244B LYS* 3.3 37.1 + - - +
245B LYS* 3.5 21.5 + - - +
280B THR* 4.9 5.9 - - - +
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Residues in contact with SER 242 (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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238B GLU 3.0 18.2 + - - -
239B LEU* 3.5 8.5 - - - -
240B TYR 3.2 0.2 - - - -
241B GLU* 1.3 77.8 - - - +
243B ALA* 1.3 60.0 + - - +
244B LYS 3.4 0.7 + - - -
245B LYS* 3.5 30.3 + - - +
246B GLN* 3.9 3.1 - - - +
521B HIS* 3.8 15.2 - - - -
525B ASP* 3.8 16.8 + - - -
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Residues in contact with ALA 243 (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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239B LEU 3.0 16.1 + - - +
242B SER* 1.3 74.9 - - - +
244B LYS* 1.3 64.0 + - - +
245B LYS 3.2 0.6 + - - -
246B GLN* 3.4 10.9 + - - +
266B TRP* 3.6 25.6 - - + -
518B LYS* 3.2 34.5 - - - +
521B HIS* 3.5 22.2 - - + +
522B PHE* 4.3 6.3 - - + +
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Residues in contact with LYS 244 (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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240B TYR* 3.0 35.5 + - + +
241B GLU* 3.3 33.5 + - - +
242B SER 3.2 0.4 - - - -
243B ALA* 1.3 79.2 - - - +
245B LYS* 1.3 62.5 + - + +
246B GLN 3.4 5.0 + - - +
247B SER* 4.2 4.7 + - - -
266B TRP* 3.9 15.3 - - + +
518B LYS* 4.0 13.4 + - + -
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Residues in contact with LYS 245 (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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241B GLU* 3.5 21.6 + - - +
242B SER* 3.6 19.1 - - - +
243B ALA 3.2 0.4 - - - -
244B LYS* 1.3 79.3 - - + +
246B GLN* 1.3 60.0 + - - +
247B SER* 3.0 17.0 + - - -
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Residues in contact with GLN 246 (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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242B SER 3.9 4.7 - - - +
243B ALA 3.4 10.9 + - - +
244B LYS 3.3 1.4 - - - -
245B LYS* 1.3 78.0 - - - +
247B SER* 1.3 60.0 + - - +
248B GLY 3.6 5.7 + - - +
517B VAL* 4.7 19.7 - - + +
518B LYS* 3.4 26.2 + - + +
521B HIS* 3.4 43.6 + - + -
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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
------------------------------------------------------------
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