Contacts of the helix formed by residues 224 - 244 (chain D) in PDB entry 3O2Q
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 GLN 224 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D HIS 5.5 2.9 - - - +
221D PRO 6.1 0.4 - - - +
222D TYR 3.8 8.9 + - - +
223D ILE* 1.3 78.1 - - - +
225D TYR* 1.3 66.1 + - - +
226D ASN* 3.2 21.9 + - - +
227D VAL* 3.1 32.1 + - + +
228D LEU* 3.2 15.3 + - - +
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Residues in contact with TYR 225 (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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196D PRO* 4.8 8.8 - - - +
213D LEU* 3.5 63.0 - - + +
214D ASP* 4.8 4.5 - - - -
216D ILE* 3.7 29.3 - - + +
217D PRO 4.6 3.5 + - - +
218D ARG* 3.5 52.1 + - - +
223D ILE 3.7 4.9 + - - -
224D GLN* 1.3 71.7 - - - +
226D ASN* 1.3 63.0 + - - +
228D LEU* 3.5 1.9 + - - -
229D TRP* 3.1 33.5 + + + +
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Residues in contact with ASN 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D ARG* 4.7 12.2 + - - +
224D GLN* 3.5 26.1 + - - +
225D TYR* 1.3 81.8 + - + +
227D VAL* 1.3 70.1 + - - +
229D TRP* 3.8 7.0 - - - +
230D GLU* 3.3 28.5 + - + +
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Residues in contact with VAL 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D GLN* 3.1 35.4 + - + +
226D ASN* 1.3 84.8 + - - +
228D LEU* 1.3 63.2 + - + +
230D GLU* 3.1 9.2 + - - +
231D GLU* 3.0 48.7 + - + +
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Residues in contact with LEU 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D TYR* 4.3 7.9 - - - +
141D LEU* 4.1 9.6 - - + -
158D TRP* 4.5 14.4 - - + +
162D SER* 5.9 0.7 - - - +
194D LEU* 3.6 33.8 - - + +
213D LEU* 4.1 6.1 - - + -
216D ILE* 3.6 22.0 - - + -
223D ILE* 3.6 29.8 - - + -
224D GLN 3.2 11.2 + - - +
225D TYR 3.9 4.9 - - - +
227D VAL* 1.3 77.6 - - + +
229D TRP* 1.3 61.3 + - - +
231D GLU* 3.2 23.7 + - - +
232D GLY 2.8 25.1 + - - -
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Residues in contact with TRP 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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194D LEU 3.6 13.7 - - - -
195D SER* 3.7 24.9 - - - -
196D PRO* 4.0 7.2 - - + -
213D LEU* 3.8 19.2 - - + +
225D TYR* 3.1 25.5 + + + +
226D ASN* 3.8 8.7 - - - +
227D VAL 3.3 0.2 - - - -
228D LEU* 1.3 77.8 - - - +
230D GLU* 1.3 77.7 + - - +
232D GLY 3.2 1.7 + - - -
233D LYS* 3.0 57.5 + - + +
269D MET* 3.7 25.1 - - + -
270D PHE* 4.0 16.8 - + - -
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Residues in contact with GLU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D ASN* 3.3 13.3 + - + +
227D VAL* 3.1 11.9 + - + +
229D TRP* 1.3 85.2 - - - +
231D GLU* 1.3 59.7 + - + +
233D LYS* 3.3 32.7 + - - +
234D ALA* 2.8 30.8 + - - +
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Residues in contact with GLU 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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137D TYR* 4.7 2.9 + - - -
162D SER* 4.3 15.0 + - - -
190D LEU* 5.1 3.0 - - + +
194D LEU* 4.1 12.0 - - + +
227D VAL* 3.0 36.1 + - + +
228D LEU* 3.5 24.1 - - - +
230D GLU* 1.3 77.3 - - + +
232D GLY* 1.3 63.5 + - - +
234D ALA* 3.9 6.1 - - - +
235D ALA* 3.0 24.4 + - - +
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Residues in contact with GLY 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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190D LEU 5.0 0.7 - - - -
191D ILE* 4.0 14.6 - - - +
194D LEU* 3.8 26.0 - - - +
195D SER* 6.3 0.4 - - - -
228D LEU 2.8 18.9 + - - -
229D TRP* 3.2 3.1 + - - -
231D GLU* 1.3 71.7 - - - +
233D LYS* 1.3 57.0 + - - +
235D ALA* 3.4 7.2 + - - +
236D LEU* 3.1 26.3 + - - +
270D PHE* 5.8 2.9 - - - -
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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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229D TRP* 3.0 58.6 + - + +
230D GLU* 3.3 36.4 + - - +
232D GLY* 1.3 72.1 - - - +
234D ALA* 1.3 66.5 + - - +
235D ALA 3.1 1.3 - - - -
236D LEU* 3.2 8.7 + - + +
237D GLU* 3.0 23.7 + - - +
270D PHE* 5.1 9.9 - - + -
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Residues in contact with ALA 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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230D GLU 2.8 20.7 + - - +
231D GLU* 3.9 7.9 - - - +
233D LYS* 1.3 72.6 - - - +
235D ALA* 1.3 56.5 + - - +
237D GLU* 3.3 7.4 + - - +
238D GLN* 2.9 35.9 + - + +
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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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169D ILE* 4.5 13.0 - - + +
187D VAL* 3.8 14.7 - - + +
190D LEU* 4.4 17.9 - - + -
191D ILE* 3.9 14.8 - - + -
231D GLU 3.0 18.8 + - - +
232D GLY* 3.6 6.5 - - - +
233D LYS 3.1 0.2 - - - -
234D ALA* 1.3 75.0 - - - +
236D LEU* 1.3 65.0 + - - +
238D GLN* 3.3 10.1 + - - +
239D LEU* 3.0 22.7 + - - +
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Residues in contact with LEU 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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191D ILE* 3.6 30.2 - - + +
232D GLY 3.1 14.0 + - - +
233D LYS* 3.2 10.7 + - + +
235D ALA* 1.3 72.2 - - - +
237D GLU* 1.3 62.4 + - - +
239D LEU* 3.0 4.0 + - + +
240D LEU* 2.9 41.2 + - + +
260D LEU* 4.4 21.5 - - + -
263D ILE* 4.6 7.4 - - + -
270D PHE* 3.4 47.8 - - + -
273D GLU* 4.8 13.9 - - + -
274D VAL* 5.7 2.7 - - + -
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Residues in contact with GLU 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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233D LYS 3.0 16.2 + - - +
234D ALA* 3.8 6.1 - - - +
236D LEU* 1.3 76.6 - - - +
238D GLN* 1.3 64.6 + - - +
240D LEU* 3.3 20.7 + - - +
241D LYS* 3.0 54.4 + - + +
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Residues in contact with GLN 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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169D ILE* 4.2 26.7 - - + +
170D LEU* 6.2 0.3 - - - +
172D LEU* 4.5 10.2 - - + +
173D ASP* 5.5 3.3 - - - +
187D VAL* 6.0 0.2 - - + -
234D ALA* 2.9 21.4 + - + +
235D ALA* 3.6 10.1 - - - +
236D LEU 3.3 0.2 - - - -
237D GLU* 1.3 78.3 - - - +
239D LEU* 1.3 61.1 + - - +
241D LYS* 3.6 24.6 + - - +
242D PHE* 3.1 24.4 + - - +
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Residues in contact with LEU 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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172D LEU* 4.8 7.4 - - + +
184D ILE* 4.0 30.5 - - + -
187D VAL* 4.3 12.1 - - + -
188D GLU 5.0 2.9 - - - +
191D ILE* 3.7 23.3 - - + -
235D ALA 3.0 11.9 + - - +
236D LEU 3.0 9.1 + - - +
238D GLN* 1.3 75.0 - - - +
240D LEU* 1.3 64.3 + - - +
242D PHE* 3.3 10.3 + - + +
243D MET* 3.2 23.6 + - - +
256D ALA* 4.3 13.0 - - + -
259D SER* 4.6 11.2 - - - -
260D LEU* 3.8 28.0 - - + -
263D ILE* 4.0 8.3 - - + -
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Residues in contact with LEU 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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236D LEU* 2.9 33.2 + - + +
237D GLU* 3.8 21.3 - - - +
239D LEU* 1.3 74.5 - - - +
241D LYS* 1.3 62.7 + - - +
243D MET* 3.3 18.7 + - - +
244D VAL* 3.6 13.7 + - - +
260D LEU* 4.1 22.7 - - + -
273D GLU* 4.2 33.4 - - + +
274D VAL* 5.1 0.4 - - + -
277D ALA* 3.7 30.3 - - + +
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Residues in contact with LYS 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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237D GLU* 3.0 45.4 + - + +
238D GLN* 3.8 21.9 - - - +
240D LEU* 1.3 76.0 - - - +
242D PHE* 1.3 62.4 + - - +
244D VAL* 3.3 22.9 + - + +
245D HIS* 3.3 11.6 + - - +
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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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172D LEU* 3.2 47.8 - - + -
173D ASP* 5.3 3.8 - - - -
180D ARG* 4.2 9.0 - - + -
184D ILE* 3.8 27.6 - - + -
238D GLN 3.1 16.1 + - - +
239D LEU* 3.5 13.0 - - + +
240D LEU 3.3 0.4 - - - -
241D LYS* 1.3 79.5 - - - +
243D MET* 1.3 66.4 + - + +
245D HIS* 3.3 20.3 + - + +
248D ILE* 3.5 33.3 - - + +
252D ASN* 3.9 23.8 - - + -
256D ALA* 4.9 2.9 - - + -
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Residues in contact with MET 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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239D LEU* 3.2 13.7 + - - +
240D LEU* 3.5 10.5 - - - +
241D LYS 3.2 0.2 - - - -
242D PHE* 1.3 78.1 - - + +
244D VAL* 1.3 62.8 + - + +
245D HIS 3.3 0.4 + - - -
248D ILE* 4.1 21.0 - - + +
253D LEU* 4.4 17.0 - - + +
256D ALA* 3.6 24.9 - - + -
257D LEU* 3.5 36.6 - - + +
260D LEU* 3.2 38.6 - - + -
277D ALA* 4.7 14.6 - - + +
278D TYR* 4.6 4.3 - - + -
281D LEU* 4.6 16.5 - - + +
286D PRO* 5.4 0.9 - - - +
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Residues in contact with VAL 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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240D LEU 3.6 11.0 + - - +
241D LYS* 3.3 20.2 + - + +
243D MET* 1.3 78.0 - - + +
245D HIS* 1.3 64.9 + - - +
246D PRO* 3.3 9.0 - - - +
277D ALA* 5.4 7.9 - - + +
280D THR* 3.8 30.3 - - + -
281D LEU* 5.5 4.0 - - + +
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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
------------------------------------------------------------
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