Contacts of the helix formed by residues 231 - 249 (chain D) in PDB entry 2I5B
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 231 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226D LEU* 4.4 0.2 - - - -
229D GLY 3.7 0.6 + - - -
230D ALA* 1.3 75.9 - - - +
232D VAL* 1.3 56.8 + - - +
233D LYS* 4.4 2.9 - - + +
234D GLU* 3.2 28.0 + - + +
235D ALA* 2.7 32.6 + - - +
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Residues in contact with VAL 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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103D ASN* 5.2 2.5 - - - +
136D THR* 4.1 17.7 - - + -
137D VAL* 3.7 22.4 - - + -
174D TYR* 3.6 53.4 - - + +
222D VAL* 5.5 0.2 - - - +
226D LEU* 3.9 16.4 - - + -
230D ALA 3.8 0.6 + - - -
231D GLU* 1.3 71.1 - - - +
233D LYS* 1.3 64.5 + - - +
235D ALA* 3.0 5.4 + - - +
236D ILE* 2.9 29.4 + - + +
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Residues in contact with LYS 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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174D TYR* 4.2 20.6 - - + -
192D LEU* 4.1 24.9 - - + -
194D ASP* 2.6 33.3 + - - -
197D THR* 5.1 4.8 + - - -
199D GLU* 4.5 8.4 + - - -
231D GLU* 3.4 3.2 - - + +
232D VAL* 1.3 77.8 - - - +
234D GLU* 1.3 63.0 + - - +
236D ILE* 3.2 10.9 + - - +
237D TYR* 3.0 48.2 + - + +
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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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225D GLU* 5.4 2.2 - - + +
230D ALA* 3.7 20.6 - - + +
231D GLU* 3.2 39.5 + - + +
233D LYS* 1.3 77.4 - - - +
235D ALA* 1.3 61.5 + - - +
237D TYR* 3.2 15.1 + - - +
238D ALA* 3.0 23.3 + - + +
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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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222D VAL* 4.0 10.8 - - + +
225D GLU* 3.6 34.3 - - + +
226D LEU* 4.0 22.2 - - + +
230D ALA* 4.3 1.5 - - + +
231D GLU 2.7 15.6 + - - +
232D VAL 3.3 8.1 - - - +
234D GLU* 1.3 72.3 - - - +
236D ILE* 1.3 59.5 + - - +
238D ALA* 3.1 4.5 + - - +
239D ALA* 2.8 30.2 + - - +
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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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137D VAL* 4.2 8.7 - - + -
174D TYR* 4.8 1.6 - - + -
176D VAL* 3.8 29.4 - - + -
192D LEU* 3.7 32.5 - - + -
201D LEU* 3.8 21.8 - - + -
218D PHE* 4.1 8.5 - - + -
222D VAL* 4.2 24.0 - - + -
232D VAL* 2.9 32.9 + - + +
233D LYS* 3.2 7.2 + - - +
235D ALA* 1.3 74.0 - - - +
237D TYR* 1.3 57.6 + - + +
239D ALA* 3.1 3.1 + - - +
240D LYS* 2.8 27.4 + - - +
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Residues in contact with TYR 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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192D LEU* 4.0 6.9 - - + +
199D GLU* 2.8 39.7 + - - -
201D LEU* 3.6 23.1 - - + -
233D LYS* 3.0 48.2 + - + +
234D GLU* 3.6 9.9 - - - +
236D ILE* 1.3 73.7 - - - +
238D ALA* 1.3 64.5 + - - +
240D LYS* 3.0 10.5 + - + +
241D GLU* 2.9 22.8 + - - +
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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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30D LYS* 4.7 7.2 + - - +
225D GLU* 3.7 31.2 - - + +
234D GLU* 3.0 13.5 + - + +
235D ALA 3.4 8.1 - - - +
237D TYR* 1.3 75.7 - - - +
239D ALA* 1.3 56.5 + - - +
241D GLU* 3.3 14.6 + - - +
242D PHE* 3.0 24.8 + - - +
265D LEU* 5.2 2.1 - - - +
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Residues in contact with ALA 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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218D PHE* 3.8 9.9 - - + +
221D ALA* 3.6 28.3 + - + +
222D VAL* 3.6 28.0 - - + +
235D ALA 2.8 12.8 + - - +
236D ILE 3.4 7.9 - - - +
238D ALA* 1.3 73.4 - - - +
240D LYS* 1.3 67.7 + - - +
242D PHE* 3.0 12.4 + - - +
243D ILE* 3.2 18.4 + - - +
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Residues in contact with LYS 240 (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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188D ALA* 3.1 26.2 + - - +
190D ASP* 2.8 29.1 + - - +
201D LEU* 4.3 26.9 - - + -
202D GLU 4.1 8.7 - - - +
203D SER* 3.4 28.1 - - - +
218D PHE* 3.8 6.8 - - + -
236D ILE 2.8 12.7 + - - +
237D TYR* 3.0 13.4 + - + +
239D ALA* 1.3 75.1 - - - +
241D GLU* 1.3 57.4 + - - +
243D ILE* 3.2 15.6 - - + +
244D THR* 2.8 29.2 + - - -
501D ADP 2.9 25.2 + - - +
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Residues in contact with GLU 241 (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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203D SER* 5.7 0.7 - - - -
237D TYR 2.9 11.4 + - - +
238D ALA* 3.4 16.1 - - - +
240D LYS* 1.3 78.3 - - - +
242D PHE* 1.3 63.4 + - - +
244D THR* 3.5 6.5 - - - -
245D ALA* 3.2 22.7 + - - +
265D LEU* 3.7 29.7 - - + +
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Residues in contact with PHE 242 (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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26D THR* 3.8 15.9 - - + -
29D GLU* 3.9 25.6 - - + -
30D LYS* 3.6 26.7 - - + -
217D THR* 3.8 27.8 - - + -
221D ALA* 4.2 10.1 - - + -
238D ALA 3.0 13.1 + - - +
239D ALA* 3.0 15.1 + - - +
241D GLU* 1.3 78.0 - - - +
243D ILE* 1.3 57.8 + - - +
245D ALA* 3.4 4.8 + - - +
246D ALA* 3.0 24.8 + - + +
262D HIS* 3.2 35.4 - + + -
265D LEU* 3.8 30.4 + - + +
266D ARG 5.9 0.4 - - - -
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Residues in contact with ILE 243 (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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214D ALA* 3.7 25.8 - - + +
217D THR* 3.6 28.9 - - + -
218D PHE* 3.8 21.1 - - + +
239D ALA 3.3 11.2 - - - +
240D LYS* 3.2 33.0 - - + +
242D PHE* 1.3 73.9 - - + +
244D THR* 1.3 63.8 + - - +
246D ALA* 3.9 6.7 - - + -
247D ILE* 2.6 50.0 + - + +
260D THR* 4.8 1.3 - - + -
501D ADP 3.6 31.2 - - - +
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Residues in contact with THR 244 (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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203D SER* 3.1 34.2 + - - +
204D GLU* 4.6 8.1 - - + +
206D ILE* 4.0 16.9 - - + +
240D LYS* 2.8 24.7 + - - -
241D GLU* 3.5 7.2 - - - -
243D ILE* 1.3 79.6 - - - +
245D ALA* 1.3 58.2 + - - +
247D ILE* 3.7 7.1 - - - +
248D LYS* 2.8 34.2 + - + +
501D ADP 5.0 5.5 + - + -
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Residues in contact with ALA 245 (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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241D GLU 3.2 8.8 + - - +
242D PHE 3.6 8.1 - - - +
243D ILE 3.2 0.2 - - - -
244D THR* 1.3 81.0 - - - +
246D ALA* 1.3 62.2 + - - +
248D LYS* 3.2 12.5 + - - +
249D GLU* 3.2 21.0 + - - +
264D ALA* 3.4 10.5 - - + +
265D LEU* 3.9 35.4 - - + +
268D ASN* 5.6 3.6 - - + +
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Residues in contact with ALA 246 (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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217D THR* 5.0 0.4 - - + -
242D PHE* 3.0 21.8 + - + +
243D ILE* 2.9 12.3 + - + +
245D ALA* 1.3 75.7 - - - +
247D ILE* 1.3 62.1 + - - +
249D GLU 3.6 1.2 + - - -
250D SER 3.3 9.4 + - - -
260D THR* 3.5 20.7 - - - +
261D LYS 2.8 47.7 + - - +
262D HIS* 4.4 6.1 - - - +
264D ALA* 3.8 1.3 - - + +
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Residues in contact with ILE 247 (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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206D ILE* 3.9 18.9 - - + +
208D THR* 3.9 22.0 - - + -
211D THR* 4.1 8.5 - - + -
214D ALA* 4.3 5.2 - - + -
243D ILE* 2.6 32.0 + - + +
244D THR* 3.7 3.6 - - - +
246D ALA* 1.3 70.6 - - - +
248D LYS* 1.3 64.1 + - - +
250D SER* 2.9 28.2 + - - +
260D THR* 4.0 18.4 - - + -
501D ADP 3.3 61.9 - - + +
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Residues in contact with LYS 248 (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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204D GLU* 2.7 35.6 + - - +
206D ILE* 3.7 27.6 - - + +
244D THR* 2.8 24.2 + - + +
245D ALA* 3.2 11.9 + - - +
247D ILE* 1.3 72.9 - - - +
249D GLU* 1.3 73.0 + - + +
250D SER* 3.8 1.6 + - - +
268D ASN* 6.4 0.7 - - - -
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Residues in contact with GLU 249 (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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245D ALA 3.2 15.1 + - - +
246D ALA 3.6 2.4 + - - -
247D ILE 3.1 0.8 - - - -
248D LYS* 1.3 95.2 - - + +
250D SER* 1.3 66.6 + - - +
251D PHE* 3.8 7.4 - - - +
261D LYS* 3.7 35.4 + - + +
264D ALA* 3.8 6.1 - - + -
268D ASN* 3.3 39.4 + - - +
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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
------------------------------------------------------------
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