Contacts of the helix formed by residues 219 - 235 (chain B) in PDB entry 2JGZ
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 219 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ARG* 3.5 50.3 - - - +
213B GLN* 3.5 2.9 + - - -
217B ARG 4.2 0.6 + - - -
218B LEU* 1.3 75.9 - - - +
220B GLN* 1.3 64.5 + - - +
221B GLU* 3.2 16.2 + - + +
222B THR* 3.2 18.1 + - - +
223B MET 3.4 7.3 + - - -
259B GLU* 3.7 13.5 - - + +
260B GLU* 3.1 27.3 + - - +
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Residues in contact with GLN 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B GLN* 3.2 13.8 + - - +
218B LEU 3.5 1.6 + - - -
219B LEU* 1.3 71.3 - - - +
221B GLU* 1.3 65.3 + - - +
223B MET* 3.1 13.9 + - - +
224B TYR* 3.1 39.7 + - + -
303B LEU* 3.6 19.1 - - + -
307B ARG* 5.6 1.3 - - - +
324B LYS* 3.7 32.3 + - - +
328B GLU* 3.1 32.6 + - - +
403B LYS* 2.6 28.6 + - - -
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Residues in contact with GLU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ARG* 3.5 35.5 + - - +
219B LEU* 3.2 22.2 - - + +
220B GLN* 1.3 75.2 + - - +
222B THR* 1.3 57.8 + - - +
224B TYR* 2.9 4.1 + - - -
225B MET* 2.8 27.2 + - - +
259B GLU* 4.1 18.2 - - + +
301B LEU* 3.5 14.8 - - + +
303B LEU* 3.5 16.1 - - + +
304B HIS* 4.5 16.2 - - + -
307B ARG* 3.4 31.3 + - - -
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Residues in contact with THR 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B GLN* 5.8 0.2 - - - -
218B LEU* 4.3 15.3 - - + -
219B LEU* 3.2 11.7 + - - +
221B GLU* 1.3 77.2 - - - +
223B MET* 1.3 62.8 + - - +
225B MET* 4.4 6.1 - - - -
226B THR* 2.9 31.3 + - - +
252B MET* 4.4 4.7 - - + +
255B ALA* 3.7 6.8 - - + +
256B SER* 3.6 37.5 - - - +
259B GLU* 3.7 15.4 - - - +
260B GLU* 2.6 26.4 + - - +
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Residues in contact with MET 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ILE* 4.4 5.2 - - + -
209B LEU* 4.3 18.8 - - + -
210B VAL* 4.1 17.9 - - + -
213B GLN* 3.7 48.9 - - - +
219B LEU 3.4 2.0 + - - -
220B GLN* 3.1 17.0 + - - +
221B GLU 3.1 0.6 - - - -
222B THR* 1.3 80.6 - - - +
224B TYR* 1.3 63.5 - - - +
226B THR* 3.2 12.5 + - + -
227B VAL* 3.3 30.6 + - + +
252B MET* 4.0 13.0 - - + -
328B GLU* 5.1 0.4 - - - +
331B MET* 3.8 24.5 - - + -
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Residues in contact with TYR 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 GLN* 3.1 35.9 + - + -
221B GLU 2.9 6.3 + - - +
223B MET* 1.3 81.9 - - - +
225B MET* 1.3 62.0 + - - +
227B VAL* 3.3 5.8 + - + +
228B SER* 3.0 21.8 + - - -
301B LEU* 3.7 19.1 - - + +
302B PRO* 3.9 26.6 - - + +
303B LEU* 4.0 30.5 - - + -
324B LYS* 4.1 2.9 + - + +
327B MET* 3.3 26.8 - - + +
328B GLU* 3.1 32.2 + - - +
330B THR* 5.3 0.9 - - - -
331B MET* 3.6 33.9 - - + -
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Residues in contact with MET 225 (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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221B GLU 2.8 13.4 + - - +
222B THR* 3.8 1.8 - - - +
224B TYR* 1.3 77.2 - - - +
226B THR* 1.3 64.1 + - - +
228B SER* 3.3 4.2 - - - -
229B ILE* 2.9 34.5 + - + +
254B ILE* 5.8 0.4 - - - -
255B ALA* 3.7 30.7 - - + +
258B TYR* 3.4 32.1 - - + -
259B GLU* 3.4 33.2 - - + +
297B LEU* 4.2 18.2 - - - +
298B GLY 6.3 0.4 - - - -
299B ARG 5.7 1.1 - - - +
301B LEU* 3.9 23.9 - - + +
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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
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209B LEU* 4.2 10.5 - - + -
222B THR 2.9 17.4 + - - -
223B MET* 3.3 15.9 - - + -
225B MET* 1.3 75.7 - - - +
227B VAL* 1.3 64.2 + - - +
229B ILE* 3.2 3.9 + - - +
230B ILE* 2.9 45.4 + - + +
248B GLY 4.1 2.7 - - - +
251B ALA* 3.9 5.8 - - + +
252B MET* 3.1 52.1 - - + +
255B ALA* 3.6 5.8 - - - +
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Residues in contact with VAL 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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202B ARG* 4.0 13.7 - - - +
206B ILE* 4.1 20.2 - - + -
223B MET* 3.3 31.0 + - + +
224B TYR* 3.3 8.5 + - + +
226B THR* 1.3 74.6 - - + +
228B SER* 1.3 57.1 + - - +
230B ILE* 3.3 8.5 + - + +
231B ASP* 2.9 44.1 + - - +
331B MET* 4.0 31.4 - - + +
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Residues in contact with SER 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 TYR 3.0 13.5 + - - -
225B MET* 3.3 14.6 - - - -
227B VAL* 1.3 74.2 - - - +
229B ILE* 1.3 67.1 + - - +
231B ASP* 3.3 4.8 + - - +
232B ARG* 2.9 35.8 + - - +
299B ARG* 3.1 42.1 + - - +
300B PRO 5.2 0.2 + - - -
301B LEU* 4.5 9.1 - - - +
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Residues in contact with ILE 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B MET* 2.9 37.9 + - + +
226B THR 3.7 3.6 - - - +
228B SER* 1.3 74.9 - - - +
230B ILE* 1.3 66.4 + - - +
232B ARG* 3.2 12.0 + - - +
233B PHE* 2.8 24.0 + - + +
251B ALA* 3.8 30.1 - - + +
254B ILE* 3.7 29.4 - - + -
255B ALA 4.3 0.9 - - - +
289B ILE* 3.9 29.4 - - + -
293B LEU* 4.1 11.6 - - + +
297B LEU* 4.6 12.8 - - + +
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Residues in contact with ILE 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B TYR* 4.9 0.4 - - - +
202B ARG* 5.1 4.3 - - + +
205B LEU* 4.2 7.4 - - + -
206B ILE* 3.8 21.3 - - + -
209B LEU* 3.7 30.5 - - + -
226B THR* 2.9 27.0 + - + +
227B VAL* 3.5 7.9 - - - +
229B ILE* 1.3 76.1 - - - +
231B ASP* 1.3 65.7 + - - +
233B PHE* 3.8 4.3 - - - +
234B MET* 2.9 53.7 + - + +
247B VAL* 4.5 12.7 - - + +
248B GLY* 4.0 12.3 - - - -
251B ALA* 3.6 14.6 - - + -
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Residues in contact with ASP 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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187B VAL* 3.8 20.9 - - + -
191B TYR* 2.5 28.3 + - - +
202B ARG* 2.4 35.7 + - - -
227B VAL* 2.9 23.6 + - - +
228B SER* 3.8 4.8 - - - +
230B ILE* 1.3 77.9 - - - +
232B ARG* 1.3 61.7 + - - +
235B GLN* 3.1 28.2 + - - +
299B ARG* 5.6 0.7 - - - +
337B VAL* 3.3 22.5 - - - +
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Residues in contact with ARG 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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185B GLN* 3.3 54.5 + - - +
186B ALA 4.6 0.2 - - - +
187B VAL* 3.6 17.3 - - + -
228B SER* 2.9 27.9 + - - +
229B ILE* 3.9 7.1 - - - +
231B ASP* 1.3 75.8 - - - +
233B PHE* 1.3 66.7 + - - +
235B GLN* 3.4 25.6 + - - +
236B ASN* 4.5 4.9 + - - +
237B ASN* 5.3 0.3 + - - -
293B LEU* 3.7 40.9 + - + +
296B GLY* 2.5 30.3 + - - -
297B LEU* 4.5 7.5 - - - +
299B ARG* 3.6 21.9 - - - +
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Residues in contact with PHE 233 (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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229B ILE* 2.8 19.8 + - + +
230B ILE* 3.8 2.9 - - - +
232B ARG* 1.3 78.6 - - - +
234B MET* 1.3 68.1 + - - +
236B ASN 3.3 5.0 + - - -
237B ASN* 3.1 54.9 + - + +
239B VAL* 4.2 11.4 - - + -
247B VAL* 4.1 33.2 - - + -
285B MET* 4.5 2.9 - - + -
288B LYS* 4.1 28.5 - - + -
289B ILE* 3.6 41.7 - - + -
292B ALA* 3.7 24.9 - - + -
293B LEU* 3.7 7.3 - - + +
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Residues in contact with MET 234 (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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191B TYR* 3.8 20.2 - - + +
192B LEU* 4.2 7.2 - - + -
195B ARG* 2.9 23.0 + - - +
197B VAL* 4.4 14.4 - - + -
202B ARG* 4.6 15.9 - - + -
205B LEU* 5.8 2.5 - - + -
230B ILE* 2.9 34.2 + - + +
233B PHE* 1.3 80.2 - - + +
235B GLN* 1.3 66.5 + - - +
236B ASN 2.8 1.7 + - - -
237B ASN 2.9 19.6 - - - +
239B VAL* 3.3 33.4 - - - -
244B LEU* 3.9 22.0 - - + -
247B VAL* 5.2 7.4 - - + -
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Residues in contact with GLN 235 (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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186B ALA 3.2 22.6 + - - -
187B VAL* 3.8 6.8 - - - +
188B ARG* 2.9 53.2 + - - +
191B TYR* 3.6 30.2 - - + -
195B ARG* 2.8 13.7 + - - -
231B ASP 3.1 18.7 + - - +
232B ARG* 3.4 25.2 + - - +
234B MET* 1.3 76.7 - - - +
236B ASN* 1.3 74.4 + - - +
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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
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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