Contacts of the helix formed by residues 216 - 233 (chain B) in PDB entry 5AJQ
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 TYR 216 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B HIS* 3.5 53.0 - + + +
152B ARG* 6.5 0.9 - - - -
154B ILE* 3.6 19.3 - - + -
213B PRO 3.3 26.0 - - - -
215B ASP* 1.3 83.1 + - - +
217B LYS* 1.3 104.1 + - + +
218B ALA 3.1 2.2 - - - -
219B ASP* 3.1 23.1 + - - +
220B ILE* 4.0 0.8 + - + -
284B SER* 4.2 23.1 - - - -
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Residues in contact with LYS 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B TYR* 3.3 29.9 - - - +
215B ASP 3.1 0.8 - - - -
216B TYR* 1.3 113.0 - - + +
218B ALA* 1.3 63.8 + - - +
219B ASP 3.2 0.2 - - - -
220B ILE* 3.1 14.8 + - + -
221B TRP 3.4 0.3 + - - -
279B PRO* 3.1 32.6 + - + +
280B GLU* 3.1 14.8 + - - +
282B ARG* 2.6 62.3 + - - +
283B PRO* 4.0 10.5 - - - +
284B SER* 4.4 7.6 - - - +
287B GLN* 5.7 0.4 + - - -
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Residues in contact with ALA 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ILE* 5.5 4.0 - - + -
156B ARG* 5.6 4.7 - - - +
200B ALA* 4.0 12.3 - - + +
202B GLU* 3.9 10.5 + - - +
203B VAL* 4.3 16.6 - - + -
214B TYR 4.2 0.2 + - - -
215B ASP 3.2 15.4 + - - +
216B TYR 3.1 0.6 - - - -
217B LYS* 1.3 78.5 - - - +
219B ASP* 1.3 62.7 + - - +
220B ILE 3.4 0.2 + - - -
221B TRP* 3.4 4.5 + - - +
222B SER* 3.3 24.1 + - - -
282B ARG* 3.8 9.7 - - - +
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Residues in contact with ASP 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 3.7 6.4 - - + +
149B HIS* 2.8 29.3 + - + +
154B ILE* 3.7 10.7 - - - +
155B HIS* 2.9 30.7 + - - +
156B ARG* 3.0 27.4 + - - -
158B LEU* 3.4 20.4 + - + +
216B TYR 3.1 10.9 + - - +
218B ALA* 1.3 78.1 - - - +
220B ILE* 1.3 58.1 + - - +
222B SER* 3.3 4.4 + - - -
223B LEU* 2.8 25.8 + - - +
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Residues in contact with ILE 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU* 4.9 2.5 - - + -
145B LEU* 4.6 8.3 - - + -
149B HIS* 4.2 12.6 - - + -
216B TYR* 4.4 4.0 - - + +
217B LYS* 3.1 20.3 + - + +
219B ASP* 1.3 74.6 - - - +
221B TRP* 1.3 66.1 + - - +
223B LEU* 3.3 7.1 + - + +
224B GLY* 3.1 17.3 + - - -
274B ALA* 4.2 11.2 - - + +
282B ARG* 3.9 14.1 - - + -
283B PRO 3.4 24.7 - - - +
284B SER* 4.0 2.7 - - - -
285B ALA* 3.5 37.9 - - + +
288B LEU* 3.6 23.1 - - + -
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Residues in contact with TRP 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B TYR 5.4 0.6 + - - -
198B TRP 3.6 11.4 - - - -
199B MET 3.4 10.3 + - - -
200B ALA* 3.5 25.4 - - + -
201B PRO* 3.6 24.7 - - + -
217B LYS 3.4 4.4 + - - -
218B ALA 3.7 8.1 - - - +
220B ILE* 1.3 77.7 - - - +
222B SER* 1.3 59.1 + - - +
224B GLY 3.0 15.2 + - - -
225B ILE* 3.1 26.6 + - + +
249B ILE* 4.8 10.6 - - + +
252B SER 6.0 0.2 - - - -
254B PRO* 4.1 6.3 - - + -
255B PRO* 4.0 29.6 - - + -
274B ALA 4.2 1.6 - - - -
275B LEU* 3.3 46.6 - - + +
276B ASP 3.6 22.7 - - - -
277B LYS* 3.9 16.8 - - + -
282B ARG* 3.7 12.5 - - - +
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Residues in contact with SER 222 (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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156B ARG 5.6 3.6 + - - -
158B LEU* 3.9 27.1 - - - -
198B TRP* 2.7 28.4 + - - +
199B MET* 4.4 3.5 - - - -
200B ALA 4.6 0.5 + - - -
218B ALA 3.3 13.1 + - - -
219B ASP* 3.5 11.3 + - - -
220B ILE 3.3 0.2 - - - -
221B TRP* 1.3 74.4 - - - +
223B LEU* 1.3 57.0 + - - +
225B ILE* 3.3 3.1 + - - +
226B THR* 2.8 38.2 + - - -
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Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B CYS* 4.6 4.0 - - - -
141B MET* 3.6 40.4 - - + -
142B LEU* 3.2 39.3 - - + +
145B LEU* 4.4 14.1 - - + -
158B LEU* 4.1 4.9 - - + +
219B ASP 2.8 16.9 + - - +
220B ILE* 3.4 11.9 - - + +
221B TRP 3.3 0.2 - - - -
222B SER* 1.3 71.8 - - - +
224B GLY* 1.3 59.5 + - - +
226B THR* 3.2 7.4 + - - -
227B LEU* 2.9 49.5 + - + +
270B PHE* 4.5 11.4 - - + -
274B ALA* 6.0 0.7 - - + -
288B LEU* 4.7 6.3 - - + -
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Residues in contact with GLY 224 (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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220B ILE 3.1 6.3 + - - -
221B TRP 3.0 9.7 + - - -
223B LEU* 1.3 78.6 - - - +
225B ILE* 1.3 60.3 + - - +
227B LEU* 3.2 6.8 + - - -
228B ILE* 3.2 18.4 + - - +
271B LEU* 3.3 23.9 - - - +
274B ALA* 4.7 7.4 - - - +
275B LEU* 3.7 18.6 - - - -
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Residues in contact with ILE 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B TYR 3.8 17.0 - - - +
198B TRP* 3.4 28.7 - - + +
221B TRP* 3.1 41.7 + - + +
222B SER 3.8 5.8 - - - +
224B GLY* 1.3 72.8 - - - +
226B THR* 1.3 60.8 + - - +
228B ILE* 3.1 6.7 + - + +
229B GLU* 2.8 26.5 + - - +
235B PRO* 4.0 3.4 - - + -
236B PRO* 3.8 21.7 - - + +
255B PRO* 3.7 30.7 - - + -
275B LEU* 3.9 7.4 - - + -
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Residues in contact with THR 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B MET* 4.1 19.5 - - + -
158B LEU* 3.7 3.6 + - - +
159B LYS* 3.3 26.3 + - - -
160B ALA* 3.8 24.9 - - - +
163B VAL* 4.8 0.9 - - + -
198B TRP* 3.7 1.7 - - - -
222B SER 2.8 20.9 + - - -
223B LEU* 3.4 9.0 - - - +
225B ILE* 1.3 77.7 - - - +
227B LEU* 1.3 56.2 + - - +
229B GLU* 3.2 10.4 + - - +
230B MET* 2.9 44.1 + - + +
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Residues in contact with LEU 227 (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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134B ILE* 3.9 8.0 - - + +
138B CYS* 3.7 28.9 - - + -
141B MET* 5.2 0.2 - - - -
223B LEU* 2.9 30.0 + - + +
224B GLY* 3.5 7.0 - - - +
225B ILE 3.2 0.4 - - - -
226B THR* 1.3 77.3 - - - +
228B ILE* 1.3 62.2 + - - +
230B MET* 3.3 28.6 + - + +
231B ALA* 3.0 22.9 + - - +
267B PHE* 4.0 24.7 - - + -
270B PHE* 3.4 38.6 - - + -
271B LEU* 4.1 9.9 - - + -
293B PHE* 4.6 1.6 - - + -
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Residues in contact with ILE 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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224B GLY 3.2 8.8 + - - +
225B ILE* 3.1 9.0 + - + +
227B LEU* 1.3 76.1 - - - +
229B GLU* 1.3 58.0 + - - +
231B ALA* 3.2 7.2 + - - +
232B GLN* 2.9 55.7 + - - +
234B GLU 4.7 2.2 - - - +
236B PRO* 4.0 21.1 - - + -
255B PRO* 3.9 30.7 - - + +
256B THR 4.5 7.6 - - - +
257B LEU* 4.5 5.2 - - + -
271B LEU* 3.7 20.0 - - + -
275B LEU* 3.8 27.1 - - + -
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Residues in contact with GLU 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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119B ASP* 4.2 11.4 - - - +
122B MET* 3.7 2.7 - - + +
159B LYS* 3.8 0.3 - - - -
160B ALA* 2.9 43.1 + - + +
161B GLY 4.6 0.9 + - - -
198B TRP* 2.9 36.2 + - - +
225B ILE 2.8 13.0 + - - +
226B THR* 3.2 8.3 + - - +
228B ILE* 1.3 78.4 - - - +
230B MET* 1.3 55.4 + - - +
233B ILE* 2.7 51.7 + - - +
234B GLU 3.8 10.5 - - - -
235B PRO* 4.0 16.8 - - + +
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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
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118B VAL* 4.0 30.5 - - + -
122B MET* 3.5 7.7 - - - +
128B GLY* 3.4 4.9 - - - -
129B LEU* 2.9 34.5 - - + -
134B ILE* 3.9 19.3 - - + -
137B VAL* 3.7 39.0 - - + -
141B MET* 4.8 0.2 - - - -
160B ALA* 4.4 10.8 - - + -
163B VAL* 5.6 1.1 - - - -
226B THR* 2.9 29.1 + - + +
227B LEU* 3.4 36.8 - - + +
228B ILE 3.2 0.2 - - - -
229B GLU* 1.3 76.5 - - - +
231B ALA* 1.3 60.3 - - - +
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Residues in contact with ALA 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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128B GLY* 4.2 9.1 - - - -
129B LEU 4.5 1.1 - - - +
134B ILE* 3.6 12.7 - - + +
227B LEU 3.0 16.8 + - - +
228B ILE 3.2 4.9 + - - +
230B MET* 1.3 78.7 + - - +
232B GLN* 1.3 59.4 + - + +
233B ILE 3.7 0.4 - - - -
257B LEU* 3.8 21.1 - - + -
262B LYS* 4.9 5.9 + - - -
263B TRP* 3.6 37.3 - - + -
267B PHE* 4.2 2.2 - - + -
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Residues in contact with GLN 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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228B ILE* 2.9 31.3 + - - +
231B ALA* 1.3 83.4 - - + +
233B ILE* 1.3 69.7 + - - +
234B GLU* 3.0 20.0 + - - +
235B PRO 6.0 0.2 - - - -
236B PRO* 5.8 2.4 - - - +
256B THR 5.2 1.6 + - - -
257B LEU* 3.5 13.7 - - + +
258B LEU* 2.7 50.6 + - + +
259B THR 4.6 0.7 + - - -
263B TRP* 5.0 4.4 + - + +
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Residues in contact with ILE 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ASP* 5.8 1.1 - - - +
122B MET* 3.7 28.3 - - + +
123B LEU* 5.6 5.6 - - + +
126B ASP* 4.3 14.1 - - - +
127B ARG* 3.8 30.7 - - - +
128B GLY* 3.7 17.7 - - - +
229B GLU* 2.7 34.2 + - - +
231B ALA 3.7 1.2 - - - -
232B GLN* 1.3 73.5 - - - +
234B GLU* 1.3 71.7 + - + +
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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