Contacts of the helix formed by residues 269 - 286 (chain B) in PDB entry 2JG1
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 ASN 269 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B HIS 3.8 1.4 + - - -
268B GLU* 1.3 75.0 - - - +
270B ASP* 1.3 59.7 + - - +
271B HIS* 3.3 10.3 + - - +
272B ASP* 2.9 39.5 + - - +
273B LEU* 2.9 29.0 + - - +
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Residues in contact with ASP 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B TRP* 3.6 15.7 - - + -
232B HIS* 2.8 38.6 + - - +
235B THR* 5.3 1.6 - - - +
237B TYR* 2.7 43.3 + - + +
268B GLU 5.2 0.5 - - - +
269B ASN* 1.3 74.4 - - - +
271B HIS* 1.3 59.6 + - - +
273B LEU* 3.6 2.5 + - - +
274B LEU* 3.1 35.8 + - - +
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Residues in contact with HIS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B TYR* 3.9 20.4 + + - -
269B ASN* 3.3 8.9 + - - +
270B ASP* 1.3 76.6 - - - +
272B ASP* 1.3 67.5 + - - +
274B LEU* 3.4 2.1 + - - +
275B LYS* 3.0 50.6 + - - +
307B VAL* 3.4 52.3 + - + +
308B LEU* 5.3 0.9 - - - -
309B GLU* 5.4 6.7 - - + -
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Residues in contact with ASP 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B GLU* 3.8 22.5 - - + +
269B ASN* 2.9 36.1 + - - +
271B HIS* 1.3 75.9 - - - +
273B LEU* 1.3 58.6 + - - +
275B LYS* 3.4 11.5 + - - +
276B LYS* 2.9 32.2 + - - +
302B PHE* 4.2 19.3 - - + -
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Residues in contact with LEU 273 (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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218B TRP* 4.2 23.1 - - + +
220B ILE* 3.9 27.6 - - + -
259B GLY 4.9 0.7 - - - +
260B ILE* 4.3 13.7 - - + +
263B ALA* 3.6 35.1 - - + +
264B ILE* 3.8 30.3 - - + +
268B GLU* 4.0 7.4 + - - +
269B ASN 2.9 17.1 + - - +
270B ASP* 3.8 3.8 - - - +
272B ASP* 1.3 77.2 - - - +
274B LEU* 1.3 66.9 + - + +
276B LYS* 3.8 1.6 - - - +
277B ALA* 2.9 30.9 + - + +
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Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B TRP* 4.1 15.3 - - + -
220B ILE* 4.2 22.2 - - + -
228B ALA* 5.4 0.7 - - + -
230B ALA* 3.9 19.3 - - + -
237B TYR* 3.8 37.0 - - + -
239B VAL* 3.8 31.8 - - + +
270B ASP 3.1 20.0 + - - +
271B HIS 4.0 2.9 - - - +
273B LEU* 1.3 79.8 - - + +
275B LYS* 1.3 56.9 + - - +
277B ALA* 3.6 3.4 - - + +
278B ASN* 3.0 40.7 + - - +
307B VAL* 4.1 10.3 - - + -
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Residues in contact with LYS 275 (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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271B HIS* 3.0 43.0 + - - +
272B ASP* 3.8 5.9 + - - +
274B LEU* 1.3 74.6 - - - +
276B LYS* 1.3 58.4 + - - +
278B ASN 3.5 0.2 + - - -
279B THR* 2.6 39.7 + - - -
302B PHE* 3.5 40.1 - - + +
305B ILE* 3.4 42.3 - - + +
307B VAL* 3.9 17.9 - - + +
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Residues in contact with LYS 276 (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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49B VAL* 5.0 10.3 - - + +
51B GLU* 4.2 3.4 + - - -
259B GLY* 3.5 27.8 - - - +
262B SER* 2.9 25.8 + - - +
263B ALA* 4.4 0.9 - - + +
266B ASN* 5.0 0.2 - - - +
268B GLU* 2.6 33.6 + - - +
272B ASP 2.9 18.3 + - - +
273B LEU 3.8 3.1 - - - +
275B LYS* 1.3 73.3 - - - +
277B ALA* 1.3 68.0 + - - +
279B THR* 3.3 2.0 + - - -
280B LEU* 3.1 32.6 + - + +
298B TYR* 3.4 28.0 - - + +
302B PHE* 3.7 2.4 - - + -
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Residues in contact with ALA 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ILE* 5.7 1.8 - - + -
256B THR* 3.3 34.0 + - + -
259B GLY* 4.2 5.3 - - - -
260B ILE* 3.8 27.4 - - + +
273B LEU* 2.9 18.9 + - + +
274B LEU* 3.6 11.0 - - + +
276B LYS* 1.3 78.8 - - - +
278B ASN* 1.3 66.5 + - - +
280B LEU* 3.5 1.2 + - - +
281B GLY 3.2 15.1 + - - -
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Residues in contact with ASN 278 (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* 5.8 1.4 - - - +
227B GLY* 3.6 15.4 - - - -
228B ALA* 3.7 14.1 - - - +
239B VAL* 3.6 23.3 - - + +
241B ILE* 4.1 7.6 - - + +
256B THR* 4.8 3.8 - - - +
274B LEU* 3.0 27.9 + - - +
275B LYS 4.2 1.8 - - - +
277B ALA* 1.3 81.3 - - - +
279B THR* 1.3 59.7 + - - +
281B GLY 3.3 0.9 + - - -
282B MSE 2.9 34.2 + - - +
305B ILE* 4.2 12.1 - - + -
1312B ANP 2.7 35.7 + - - +
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Residues in contact with THR 279 (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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275B LYS 2.6 25.9 + - - -
276B LYS 3.7 4.0 - - - -
278B ASN* 1.3 76.1 - - - +
280B LEU* 1.3 58.3 + - - +
282B MSE 3.2 7.6 + - - +
283B LEU* 2.8 34.9 + - + +
298B TYR* 3.4 51.6 - - + +
301B LEU* 4.3 6.3 - - + -
302B PHE* 3.4 17.8 - - - +
305B ILE* 3.2 17.0 - - - +
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Residues in contact with LEU 280 (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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45B VAL* 4.1 6.7 - - + -
49B VAL* 4.0 21.8 - - + -
255B SER* 3.3 29.4 - - - +
258B ALA 4.4 1.1 - - - -
259B GLY* 3.5 33.2 - - - +
262B SER* 5.9 0.2 - - - -
276B LYS* 3.1 20.5 + - + +
277B ALA 3.9 0.9 - - - +
279B THR* 1.3 72.8 - - - +
281B GLY* 1.3 64.6 + - - +
283B LEU* 4.3 8.5 - - + -
284B ASN 3.1 17.0 + - - -
293B VAL* 3.5 17.5 - - + +
295B LEU* 4.3 12.1 - - + -
298B TYR* 3.8 26.2 - - + -
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Residues in contact with GLY 281 (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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252B SER* 2.8 42.5 + - - -
255B SER* 4.0 0.8 - - - -
256B THR* 3.7 4.4 + - - -
277B ALA 3.2 10.7 + - - -
278B ASN 3.3 3.3 + - - -
280B LEU* 1.3 77.4 - - - +
282B MSE 1.3 60.8 + - - +
284B ASN 3.4 1.6 + - - -
285B ALA* 3.2 8.1 + - - +
1312B ANP 3.4 21.9 - - - +
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Residues in contact with MSE 282 (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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241B ILE* 3.8 33.9 - - + -
242B PRO* 3.8 24.0 - - + +
244B ILE* 3.5 46.0 - - + +
278B ASN 2.9 19.5 + - - +
279B THR 3.5 4.5 - - - +
281B GLY* 1.3 72.4 - - - +
283B LEU* 1.3 65.1 + - - +
285B ALA* 3.1 11.3 + - - +
286B GLN* 3.4 8.8 + - - +
301B LEU* 3.7 29.2 - - + -
305B ILE* 4.6 12.3 - - - -
1312B ANP 3.5 28.0 - - - +
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Residues in contact with LEU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B THR* 2.8 22.8 + - + +
280B LEU* 4.3 4.0 - - + -
282B MSE 1.3 72.2 - - - +
284B ASN* 1.3 59.9 + - - +
286B GLN* 3.1 31.0 - - - +
287B GLU* 2.9 25.0 - - - +
293B VAL* 3.7 23.8 - - + -
294B ASN* 3.2 34.5 - - + +
295B LEU* 4.4 1.6 - - + -
297B ASN* 3.7 16.6 - - + +
298B TYR* 3.8 34.3 - - + -
301B LEU* 3.8 13.2 - - + -
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Residues in contact with ASN 284 (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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248B ASN 3.5 5.2 + - - +
249B PRO 4.1 1.8 + - - -
250B VAL 2.8 27.5 + - - -
251B GLY 3.1 2.0 - - - -
252B SER* 3.1 20.4 + - - +
255B SER* 3.3 22.9 - - - +
280B LEU 3.1 8.0 + - - +
281B GLY 3.6 8.5 - - - +
283B LEU* 1.3 76.9 - - - +
285B ALA* 1.3 60.6 + - - +
286B GLN 3.1 0.4 - - - -
287B GLU* 3.1 15.2 + - - +
288B ALA 4.3 0.2 + - - -
289B GLN 3.8 6.8 + - - +
291B GLY* 2.8 26.0 + - - -
292B TYR 3.0 21.9 + - - +
293B VAL* 3.8 1.7 - - + +
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Residues in contact with ALA 285 (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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244B ILE* 4.8 1.8 - - + -
246B VAL* 3.5 8.2 - - + +
247B LEU 2.8 36.9 + - - +
248B ASN 3.3 10.4 - - - +
249B PRO* 3.9 10.8 - - + -
252B SER* 3.6 14.6 - - - +
281B GLY 3.2 4.4 + - - +
282B MSE 3.1 10.4 + - - +
284B ASN* 1.3 77.9 - - - +
286B GLN* 1.3 49.8 + - - +
287B GLU 3.4 0.9 - - - -
1312B ANP 4.0 28.9 - - + +
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Residues in contact with GLN 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ILE* 3.9 23.0 - - + +
245B SER* 3.2 24.9 + - - +
247B LEU* 3.9 19.2 - - - +
282B MSE 3.6 5.4 - - - +
283B LEU* 3.1 34.2 - - - +
285B ALA* 1.3 77.0 - - - +
287B GLU* 1.3 67.7 + - - +
288B ALA 3.8 1.1 - - - -
297B ASN* 3.3 26.6 + - - +
301B LEU* 4.0 15.2 - - - +
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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
------------------------------------------------------------
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