Contacts of the helix formed by residues 198 - 217 (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 THR 198 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B LEU* 3.4 14.4 - - - +
195B ARG 5.3 2.0 - - - +
196B GLU 3.7 11.2 - - - +
197B VAL* 1.3 78.6 - - - +
199B GLY* 1.3 63.1 + - - +
200B ASN* 3.0 19.3 + - - +
201B MET* 3.2 33.3 + - + +
202B ARG 3.2 16.3 + - - -
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Residues in contact with GLY 199 (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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192B LEU* 3.8 4.1 - - - +
198B THR* 1.3 74.4 - - - +
200B ASN* 1.3 57.0 + - - +
202B ARG* 3.1 6.5 + - - +
203B ALA* 2.9 27.1 + - - +
332B LEU 5.2 0.5 - - - +
334B TYR* 3.8 45.0 - - - +
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Residues in contact with ASN 200 (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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198B THR* 3.0 9.6 + - - +
199B GLY* 1.3 77.1 - - - +
201B MET* 1.3 57.9 + - + +
203B ALA* 3.1 5.3 + - - +
204B ILE* 2.8 44.4 + - - +
395B THR* 5.7 2.0 - - - +
397B HIS* 3.4 24.2 + - - -
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Residues in contact with MET 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B VAL* 4.0 11.7 - - + -
198B THR* 3.2 47.1 + - + +
200B ASN* 1.3 75.1 - - + +
202B ARG* 1.3 57.7 + - - +
204B ILE* 3.3 16.4 + - + +
205B LEU* 3.0 28.1 + - - +
241B LYS* 3.9 39.5 - - + +
244B LEU* 4.1 20.5 - - + +
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Residues in contact with ARG 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B TYR* 3.5 21.3 - - - +
192B LEU* 4.7 4.7 - - + -
197B VAL* 5.0 0.6 - - + +
198B THR 3.2 10.0 + - - +
199B GLY* 3.1 12.2 + - - +
201B MET* 1.3 79.1 - - - +
203B ALA* 1.3 55.6 + - - +
205B LEU* 3.4 8.3 + - + +
206B ILE* 2.9 52.2 + - + +
227B VAL* 4.0 9.7 + - - +
230B ILE* 5.1 5.3 - - + +
231B ASP* 2.4 44.4 + - - -
234B MET* 4.6 16.6 - - + -
244B LEU* 4.8 4.8 - - - +
330B THR 4.7 0.4 + - - -
331B MET 2.4 32.9 + - - -
332B LEU 3.8 11.3 + - - -
333B ASP 4.0 4.2 + - - +
334B TYR* 4.6 17.7 - - - +
337B VAL* 3.3 15.7 - - - +
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Residues in contact with ALA 203 (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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199B GLY 2.9 12.9 + - - +
200B ASN* 3.1 12.5 + - - +
202B ARG* 1.3 73.7 - - - +
204B ILE* 1.3 65.2 + - - +
206B ILE* 4.6 3.6 - - - +
207B ASP* 3.1 26.2 + - - +
332B LEU* 3.7 28.1 + - + +
397B HIS* 3.5 25.9 + - + +
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Residues in contact with ILE 204 (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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200B ASN* 2.8 35.9 + - - +
201B MET* 3.3 17.7 + - + +
203B ALA* 1.3 77.7 - - - +
205B LEU* 1.3 63.5 + - - +
207B ASP* 3.5 2.3 - - - +
208B TRP* 3.1 25.9 + - + +
397B HIS* 3.5 21.1 - - + -
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Residues in contact with LEU 205 (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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201B MET 3.0 16.2 + - - +
202B ARG* 3.7 7.2 - - + +
204B ILE* 1.3 76.1 - - + +
206B ILE* 1.3 71.0 + - + +
208B TRP* 3.2 26.9 + - + +
209B LEU* 2.9 35.4 + - + +
230B ILE* 4.2 16.4 - - + -
234B MET* 5.8 2.0 - - + -
244B LEU* 3.8 31.9 - - + +
245B GLN* 4.0 23.6 - - + -
247B VAL* 5.8 1.1 - - + -
248B GLY* 4.1 14.8 - - - +
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Residues in contact with ILE 206 (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* 2.9 39.3 + - + +
203B ALA* 4.3 3.1 - - - +
205B LEU* 1.3 75.4 - - + +
207B ASP* 1.3 65.2 + - - +
209B LEU* 2.9 11.1 + - + +
210B VAL* 2.9 21.1 + - + +
223B MET* 4.4 6.7 - - + -
227B VAL* 4.1 29.6 - - + -
230B ILE* 3.8 33.9 - - + -
331B MET* 4.2 33.7 - - + +
332B LEU* 4.2 13.5 - - + -
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Residues in contact with ASP 207 (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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203B ALA 3.1 19.6 + - - +
204B ILE 3.5 4.4 - - - +
206B ILE* 1.3 77.0 - - - +
208B TRP* 1.3 61.6 + - - +
210B VAL* 3.2 17.9 + - - +
211B GLN* 3.1 19.1 + - - -
332B LEU* 3.8 17.4 - - + +
396B LYS 5.3 0.9 - - - +
397B HIS* 3.5 27.8 - - - +
398B MET 4.9 0.2 + - - -
399B THR* 3.1 46.7 + - - +
400B VAL* 4.8 0.9 + - - +
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Residues in contact with TRP 208 (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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204B ILE* 3.1 16.7 + - + +
205B LEU* 3.7 19.5 - - + +
207B ASP* 1.3 79.4 + - - +
209B LEU* 1.3 86.7 + - + +
211B GLN* 3.1 31.6 + - + +
212B VAL* 2.9 32.5 + - + +
245B GLN* 3.5 45.4 - - + +
249B VAL* 3.7 20.4 - - + -
272B VAL* 3.6 37.3 + - + +
273B THR* 4.2 2.7 - - + -
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Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 2.9 33.0 + - + +
206B ILE* 2.9 11.6 + - + +
208B TRP* 1.3 95.4 - - + +
210B VAL* 1.3 54.6 + - - +
212B VAL* 2.9 8.8 + - + +
213B GLN* 2.6 35.7 + - - +
223B MET* 4.3 7.0 - - + -
226B THR* 4.2 6.5 - - + -
230B ILE* 3.7 30.7 - - + -
248B GLY* 3.9 21.8 - - - +
249B VAL* 4.2 6.1 - - + +
252B MET* 3.6 28.5 - - + +
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Residues in contact with VAL 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ILE* 2.9 20.2 + - + +
207B ASP* 3.2 11.2 + - - +
209B LEU* 1.3 74.6 - - - +
211B GLN* 1.3 63.7 + - - +
213B GLN* 3.1 14.9 + - - +
214B MET* 2.9 43.2 + - + +
223B MET* 4.1 9.4 - - + -
328B GLU* 4.9 1.3 - - - +
331B MET* 3.9 28.0 - - + -
332B LEU* 5.2 0.9 - - + -
399B THR* 3.5 16.4 - - - +
400B VAL* 4.0 20.4 - - + -
403B LYS* 4.7 8.1 - - + -
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Residues in contact with GLN 211 (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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207B ASP* 3.1 25.9 + - - -
208B TRP* 3.1 34.6 + - + +
210B VAL* 1.3 76.0 - - - +
212B VAL* 1.3 57.8 + - + +
214B MET* 3.1 18.0 + - + +
215B LYS* 2.9 28.7 + - - +
399B THR* 3.5 23.2 - - + +
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Residues in contact with VAL 212 (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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208B TRP* 2.9 41.2 + - + +
209B LEU* 2.9 15.9 + - + +
211B GLN* 1.3 72.4 - - + +
213B GLN* 1.3 66.2 + - - +
215B LYS* 3.3 7.4 + - + +
216B PHE* 3.1 50.8 + - + -
249B VAL* 5.7 0.7 - - + -
252B MET* 3.7 17.7 - - - -
269B PHE* 4.6 4.0 - - + -
272B VAL* 3.7 27.1 - - + -
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Residues in contact with GLN 213 (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 2.6 15.0 + - - +
210B VAL* 3.2 14.2 - - - +
212B VAL* 1.3 73.4 - - - +
214B MET* 1.3 53.8 + - - +
216B PHE 3.5 0.3 + - - -
217B ARG 2.8 28.4 + - - -
218B LEU* 2.6 57.8 + - + +
219B LEU 3.5 8.5 + - - +
220B GLN* 3.2 20.2 + - - +
223B MET* 3.7 37.9 - - + +
252B MET* 4.2 2.9 - - + +
328B GLU* 4.4 1.2 - - - +
403B LYS* 3.5 19.7 + - - +
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Residues in contact with MET 214 (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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210B VAL* 2.9 25.4 + - + +
211B GLN* 3.7 26.0 - - + +
213B GLN* 1.3 78.2 - - - +
215B LYS* 1.3 70.2 + - - +
217B ARG* 3.2 19.4 + - - +
399B THR* 4.8 11.2 - - - +
403B LYS* 4.0 38.6 - - + +
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Residues in contact with LYS 215 (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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211B GLN 2.9 13.1 + - - +
212B VAL* 3.5 11.4 - - - +
214B MET* 1.3 79.0 - - - +
216B PHE* 1.3 72.5 + - + +
217B ARG* 3.4 5.2 + - - +
271B PHE* 4.3 22.7 - - - -
272B VAL* 3.8 28.9 - - + -
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Residues in contact with PHE 216 (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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212B VAL* 3.1 41.1 + - + +
215B LYS* 1.3 87.7 - - + +
217B ARG* 1.3 72.3 + - - +
218B LEU* 3.5 30.7 + - + +
264B PRO* 4.0 20.0 - - + -
268B ASP* 3.9 35.0 - - + -
269B PHE* 4.4 13.7 - + - -
271B PHE* 5.8 2.2 - + - -
272B VAL* 3.3 29.6 - - + -
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Residues in contact with ARG 217 (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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213B GLN 2.8 10.1 + - - -
214B MET* 3.2 16.5 + - - +
215B LYS 4.1 4.5 - - - +
216B PHE* 1.3 82.2 - - - +
218B LEU* 1.3 62.5 + - - +
219B LEU 4.2 0.3 + - - -
260B GLU* 4.7 2.9 - - - +
408B LYS* 6.3 1.2 - - - +
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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