Contacts of the helix formed by residues 203 - 222 (chain D) in PDB entry 5AQO
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 LEU 203 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179D LEU* 3.9 20.0 - - + +
182D GLU* 3.7 13.0 - - + +
183D LEU* 4.0 37.9 - - + +
186D ILE* 4.2 14.6 - - + -
199D ALA 3.9 7.9 - - - +
200D LEU* 3.1 20.7 + - + +
202D LYS* 1.4 75.6 - - + +
204D ASP* 1.3 64.5 + - - +
205D ARG 3.3 3.1 - - - -
206D ARG* 3.2 36.5 + - - +
207D VAL* 3.0 23.9 + - + +
254D VAL* 6.3 1.3 - - + -
258D ILE* 4.1 7.9 - - + -
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Residues in contact with ASP 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D CYS* 3.0 19.3 + - - +
202D LYS 3.4 0.2 - - - -
203D LEU* 1.3 76.3 - - - +
205D ARG* 1.3 62.7 + - - +
207D VAL* 3.4 2.4 + - - +
208D LYS* 2.8 63.3 + - - +
255D GLU* 4.5 6.6 - - - +
258D ILE* 3.7 18.4 - - + +
259D CYS* 3.8 20.1 - - - +
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Residues in contact with ARG 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ASP* 5.3 11.9 - - - +
61C MET* 4.5 6.2 - - + +
201D CYS 4.9 0.2 + - - -
202D LYS 4.7 7.0 + - - +
203D LEU 3.3 0.8 - - - -
204D ASP* 1.3 77.3 + - - +
206D ARG* 1.3 59.6 + - + +
208D LYS* 3.5 9.4 + - - +
209D ALA* 2.9 29.4 + - - +
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Residues in contact with ARG 206 (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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175D GLN 5.0 1.0 + - - -
178D GLU* 4.6 6.9 - - - +
179D LEU* 3.7 40.6 - - + +
182D GLU* 2.9 43.6 + - - -
202D LYS 5.4 3.3 + - - +
203D LEU* 3.2 22.9 + - - +
205D ARG* 1.3 77.0 - - + +
207D VAL* 1.4 54.7 + - - +
209D ALA* 3.4 8.1 + - + +
210D THR* 2.8 36.4 + - - -
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Residues in contact with VAL 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D LEU* 6.3 1.1 - - + -
179D LEU* 3.9 24.0 - - + -
203D LEU* 3.0 18.4 + - + +
204D ASP 3.8 4.5 - - - +
206D ARG* 1.4 73.1 - - - +
208D LYS* 1.4 57.7 + - - +
210D THR* 3.2 6.0 + - - -
211D ILE* 3.0 32.5 + - + +
251D CYS* 3.7 26.9 - - + +
254D VAL* 3.4 29.8 - - + -
255D GLU* 4.1 20.4 - - + +
258D ILE* 4.2 10.3 - - + -
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Residues in contact with LYS 208 (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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61C MET* 3.7 38.1 - - + +
63C PRO* 6.4 0.2 - - - -
204D ASP* 2.8 53.5 + - - +
205D ARG* 3.7 6.5 - - - +
207D VAL* 1.4 72.2 - - - +
209D ALA* 1.3 58.6 + - - +
211D ILE* 3.5 10.1 + - + +
212D GLU* 2.9 29.8 + - - +
255D GLU* 3.2 28.9 + - + +
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Residues in contact with ALA 209 (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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61C MET* 3.7 27.9 - - + +
205D ARG 2.9 17.7 + - - +
206D ARG* 3.6 9.9 - - + +
207D VAL 3.3 0.2 - - - -
208D LYS* 1.3 74.4 - - - +
210D THR* 1.4 57.7 + - - +
212D GLU* 3.5 2.1 + - - +
213D GLN* 3.0 43.4 + - - +
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Residues in contact with THR 210 (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 ILE* 3.7 20.5 - - + +
175D GLN* 4.2 12.8 + - - +
176D LEU* 4.1 19.5 - - + +
179D LEU* 3.5 12.7 - - - +
206D ARG 2.8 18.2 + - - -
207D VAL* 3.4 11.7 - - - -
209D ALA* 1.4 73.7 - - - +
211D ILE* 1.3 63.6 + - - +
213D GLN* 3.3 11.5 + - - +
214D PHE* 3.1 29.7 + - + -
251D CYS* 3.8 19.7 - - - -
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Residues in contact with ILE 211 (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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258C ARG* 3.7 23.6 - - - +
207D VAL* 3.0 24.2 + - + +
208D LYS* 3.6 10.1 - - - +
210D THR* 1.3 72.8 - - - +
212D GLU* 1.4 59.9 + - - +
214D PHE* 3.2 4.7 + - - +
215D MET* 2.9 33.1 + - + +
248D LEU* 3.8 12.9 - - + +
251D CYS* 3.4 31.9 - - + +
252D ASP* 4.0 8.5 - - - +
255D GLU* 3.7 35.2 - - - +
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Residues in contact with GLU 212 (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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57C ASN 4.0 3.2 - - - +
60C ALA* 3.6 18.6 - - + +
61C MET* 3.8 25.4 - - + -
261C ARG* 2.8 42.8 + - - -
208D LYS 2.9 18.9 + - - +
209D ALA 3.7 4.7 - - - +
211D ILE* 1.4 77.0 - - - +
213D GLN* 1.3 58.6 + - + +
215D MET* 3.2 3.8 + - - +
216D LYS* 2.8 60.5 + - - +
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Residues in contact with GLN 213 (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 ILE* 3.8 25.4 - - + +
175D GLN* 3.0 36.2 + - - -
209D ALA* 3.0 33.8 + - - +
210D THR* 3.3 7.6 + - - +
212D GLU* 1.3 76.9 - - + +
214D PHE* 1.3 61.2 + - - +
216D LYS* 3.3 9.8 + - + +
217D ILE* 3.1 25.6 + - - +
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Residues in contact with PHE 214 (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 VAL* 4.0 14.6 - - + -
172D ILE* 3.6 36.6 - - + -
173D ALA* 3.9 12.6 - - - -
176D LEU* 4.4 4.0 - - + -
210D THR* 3.1 29.4 + - + -
211D ILE 3.2 6.7 + - - +
213D GLN* 1.3 75.0 - - - +
215D MET* 1.4 61.8 + - - +
217D ILE* 3.3 6.4 + - - +
218D LEU* 3.1 25.9 + - - +
244D VAL* 3.7 27.4 - - + +
247D PHE* 3.5 46.2 - + + -
248D LEU* 3.8 14.4 - - + -
251D CYS* 4.0 16.6 - - - -
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Residues in contact with MET 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C ARG* 3.7 54.7 - - + +
261C ARG* 3.8 44.4 - - + +
262C ARG* 4.1 16.4 - - + -
211D ILE* 2.9 28.1 + - + +
212D GLU* 3.2 9.1 + - - +
214D PHE* 1.4 75.6 - - - +
216D LYS* 1.3 57.1 + - - +
218D LEU* 3.2 12.5 + - + +
219D GLU* 3.0 31.5 + - + +
248D LEU* 4.0 15.0 - - + -
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Residues in contact with LYS 216 (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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57C ASN* 2.8 49.4 + - - +
261C ARG* 3.9 6.5 - - - +
212D GLU* 2.8 47.6 + - - +
213D GLN* 3.3 7.8 + - + +
215D MET* 1.3 72.1 - - - +
217D ILE* 1.4 59.2 + - + +
219D GLU* 3.3 13.1 + - - +
220D GLU* 3.0 30.4 + - - +
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Residues in contact with ILE 217 (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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165D LEU* 4.2 19.1 - - + +
168D SER* 3.5 31.4 - - - +
169D VAL* 3.6 25.1 - - + -
172D ILE* 3.7 18.4 - - + -
213D GLN 3.1 18.7 + - - +
214D PHE* 3.5 9.6 - - + +
215D MET 3.3 0.2 - - - -
216D LYS* 1.4 75.8 - - - +
218D LEU* 1.4 56.8 + - - +
220D GLU* 3.1 12.7 + - - +
221D ILE* 2.9 49.7 + - + +
244D VAL* 4.1 7.0 - - + -
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Residues in contact with LEU 218 (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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258C ARG* 6.3 0.2 - - + -
262C ARG* 3.9 34.8 - - + +
214D PHE 3.1 14.9 + - - +
215D MET* 3.2 17.4 + - - +
217D ILE* 1.4 73.9 - - - +
219D GLU* 1.3 57.8 + - - +
221D ILE* 3.3 7.7 + - + +
222D ASP* 2.9 37.0 + - - +
241D VAL* 4.1 35.2 - - + +
244D VAL* 3.8 23.3 - - + -
245D GLN* 4.6 7.6 - - + +
248D LEU* 3.9 26.9 - - + -
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Residues in contact with GLU 219 (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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261C ARG* 2.8 48.7 + - - +
262C ARG* 5.1 12.8 - - + -
265C THR* 2.7 48.4 + - + +
215D MET* 3.0 13.3 + - + +
216D LYS* 3.7 17.2 - - - +
217D ILE 3.3 0.2 - - - -
218D LEU* 1.3 75.2 - - - +
220D GLU* 1.3 61.4 + - - +
222D ASP* 3.5 15.3 + - - +
223D THR* 3.4 17.4 - - - +
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Residues in contact with GLU 220 (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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164D HIS* 5.0 9.1 + - - -
165D LEU* 3.5 31.4 - - + +
216D LYS 3.0 14.8 + - - +
217D ILE* 3.1 14.8 + - - +
219D GLU* 1.3 74.9 - - - +
221D ILE* 1.3 61.8 + - - +
223D THR* 2.7 33.5 + - + +
224D LEU* 4.3 3.8 + - - +
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Residues in contact with ILE 221 (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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283C GLU 4.9 0.5 - - - +
285C ASP* 6.0 0.2 - - + -
162D LEU* 5.0 2.2 - - + -
165D LEU* 4.0 19.7 - - + -
217D ILE* 2.9 36.8 + - + +
218D LEU* 3.6 13.5 - - + +
220D GLU* 1.3 76.1 - - - +
222D ASP* 1.3 59.8 + - - +
224D LEU* 3.1 36.7 + - + +
237D ARG* 3.7 33.2 - - + +
240D LEU* 3.9 24.7 - - + -
241D VAL* 3.8 27.1 - - + +
244D VAL* 5.1 0.4 - - + -
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Residues in contact with ASP 222 (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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262C ARG* 2.8 62.0 + - - +
265C THR* 6.5 0.2 - - + -
266C ALA* 5.3 9.2 - - + +
269C ARG* 5.3 0.3 + - - -
282C ILE* 5.4 1.6 - - - +
283C GLU 3.5 22.3 + - - +
284C ILE* 3.8 25.0 - - + +
285C ASP 4.5 0.9 + - - -
218D LEU 2.9 21.8 + - - +
219D GLU* 3.6 11.6 - - - +
220D GLU 3.2 0.4 - - - -
221D ILE* 1.3 80.1 - - - +
223D THR* 1.3 57.8 + - - +
224D LEU 3.2 2.2 + - - +
225D ILE* 5.8 0.7 - - - +
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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
------------------------------------------------------------
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