Contacts of the helix formed by residues 269 - 287 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C TRP* 5.7 0.2 - - - -
267C HIS 3.8 1.2 + - - -
268C GLU* 1.3 76.5 - - - +
270C ASP* 1.3 60.0 + - - +
271C HIS* 2.9 13.4 + - - +
272C ASP* 2.8 42.5 + - - +
273C LEU* 3.0 27.8 + - - +
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Residues in contact with ASP 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C TRP* 3.4 18.0 - - + -
232C HIS* 2.8 39.8 + - - +
235C THR* 5.5 0.7 - - - -
237C TYR* 2.5 38.1 + - + +
268C GLU 5.1 0.7 - - - +
269C ASN* 1.3 75.8 - - - +
271C HIS* 1.3 65.0 + - - +
273C LEU* 3.6 2.0 - - - +
274C LEU* 3.2 31.7 + - - +
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Residues in contact with HIS 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C TYR* 3.8 27.9 - + - -
269C ASN* 2.9 10.2 + - - +
270C ASP* 1.3 78.4 - - - +
272C ASP* 1.3 61.6 + - - +
274C LEU* 3.5 2.6 + - - +
275C LYS* 3.1 49.7 + - - +
307C VAL* 3.3 45.1 + - + +
309C GLU* 5.5 3.8 + - + -
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Residues in contact with ASP 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C GLU* 3.9 22.3 - - + +
269C ASN* 2.8 39.5 + - - +
271C HIS* 1.3 71.4 - - - +
273C LEU* 1.3 59.2 + - - +
275C LYS* 3.9 8.2 + - - +
276C LYS* 2.9 32.6 + - - +
302C PHE* 4.1 20.3 - - + -
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Residues in contact with LEU 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C TRP* 4.0 26.7 - - + +
220C ILE* 3.9 27.8 - - + -
259C GLY 4.9 0.7 - - - +
260C ILE* 4.3 14.1 - - + +
263C ALA* 3.5 34.0 - - + +
264C ILE* 4.1 24.7 - - + +
268C GLU* 4.2 9.7 + - - +
269C ASN 3.0 19.0 + - - +
270C ASP* 3.6 4.7 - - - +
272C ASP* 1.3 76.7 - - - +
274C LEU* 1.3 67.2 + - + +
276C LYS* 3.7 2.3 - - - +
277C ALA* 3.0 30.3 + - - +
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Residues in contact with LEU 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C TRP* 4.0 15.3 - - + -
220C ILE* 4.2 16.6 - - + -
228C ALA* 5.6 0.2 - - + -
230C ALA* 3.9 20.2 - - + -
237C TYR* 3.8 42.6 - - + -
239C VAL* 3.9 21.8 - - + +
270C ASP 3.2 18.1 + - - +
271C HIS 4.1 2.9 - - - +
273C LEU* 1.3 86.8 - - + +
275C LYS* 1.3 57.2 + - - +
277C ALA* 3.9 3.5 - - + +
278C ASN* 3.0 37.9 + - - +
307C VAL* 3.9 15.0 - - + -
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Residues in contact with LYS 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271C HIS* 3.1 36.3 + - - +
272C ASP* 3.9 4.6 + - - +
274C LEU* 1.3 74.4 - - - +
276C LYS* 1.3 56.7 + - - +
278C ASN 3.5 0.2 + - - -
279C THR* 2.6 38.9 + - - -
302C PHE* 3.5 42.6 + - + +
305C ILE* 3.5 40.3 + - + +
307C VAL* 3.8 25.6 - - + +
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Residues in contact with LYS 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C VAL* 5.3 7.8 - - + +
51C GLU* 4.6 1.6 + - - -
259C GLY* 3.5 28.3 - - - +
262C SER* 3.0 25.0 + - - +
263C ALA* 4.3 0.9 - - + +
266C ASN* 5.1 0.6 - - - +
268C GLU* 2.7 35.3 + - - +
272C ASP 2.9 19.0 + - - +
273C LEU* 3.7 4.0 - - - +
275C LYS* 1.3 75.9 - - - +
277C ALA* 1.3 61.3 + - - +
279C THR* 3.4 2.1 + - - -
280C LEU* 3.1 33.6 + - + +
298C TYR* 3.5 29.6 - - + +
302C PHE* 3.8 2.3 - - + -
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Residues in contact with ALA 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C ILE* 6.0 2.0 - - + -
256C THR* 3.2 50.3 + - + +
259C GLY* 4.1 5.8 - - - -
260C ILE* 3.7 15.3 - - + +
273C LEU* 3.0 18.1 + - + +
274C LEU* 3.9 9.4 - - + +
276C LYS* 1.3 76.3 - - - +
278C ASN* 1.3 60.3 + - - +
280C LEU* 4.1 0.3 - - - -
281C GLY 3.1 20.8 + - - -
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Residues in contact with ASN 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C ILE* 5.7 1.4 - - - +
227C GLY* 3.6 22.2 - - - -
228C ALA* 3.7 14.6 - - - +
239C VAL* 3.7 17.5 - - + +
241C ILE* 4.2 5.2 - - + +
256C THR* 4.8 3.5 - - - +
274C LEU* 3.0 29.8 + - - +
277C ALA* 1.3 78.7 - - - +
279C THR* 1.3 60.6 + - - +
281C GLY 3.3 0.5 + - - -
282C MSE 2.9 36.4 + - - +
305C ILE* 4.0 15.0 - - + -
1313C ANP 2.8 37.1 + - - +
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Residues in contact with THR 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C LYS 2.6 26.4 + - - -
276C LYS 3.4 3.6 + - - -
278C ASN* 1.3 76.3 - - - +
280C LEU* 1.3 56.8 + - - +
282C MSE 3.3 6.5 + - - +
283C LEU* 2.9 40.2 + - + +
298C TYR* 3.4 51.8 - - + +
301C LEU* 4.2 6.3 - - + -
302C PHE* 3.4 18.2 - - - +
305C ILE* 3.2 16.2 - - - +
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Residues in contact with LEU 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C VAL* 4.1 7.6 - - + -
49C VAL* 3.9 25.4 - - + -
255C SER* 3.5 27.6 - - - +
258C ALA 4.4 0.7 - - - -
259C GLY* 3.5 32.5 - - - +
262C SER* 6.0 0.2 - - - -
276C LYS* 3.1 20.2 + - + +
277C ALA 4.1 0.7 - - - +
279C THR* 1.3 72.3 - - - +
281C GLY* 1.3 65.2 + - - +
283C LEU* 3.4 7.2 + - + -
284C ASN* 3.0 19.4 + - - +
293C VAL* 3.7 11.0 - - + +
295C LEU* 4.1 17.3 - - + -
298C TYR* 3.8 26.7 - - + -
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Residues in contact with GLY 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C SER* 2.8 42.1 + - - -
255C SER* 4.0 1.5 - - - -
256C THR* 3.6 5.8 + - - -
277C ALA 3.1 10.9 + - - -
278C ASN 3.3 2.4 + - - -
280C LEU* 1.3 76.6 - - - +
282C MSE 1.3 60.0 + - - +
284C ASN* 3.6 0.5 + - - +
285C ALA* 3.3 6.2 + - - +
1313C ANP 3.3 22.2 - - - +
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Residues in contact with MSE 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C ILE* 3.9 24.7 - - + -
242C PRO* 3.7 28.0 - - + +
244C ILE* 3.5 36.6 - - + +
278C ASN 2.9 21.2 + - - +
279C THR* 3.7 4.3 - - - +
281C GLY* 1.3 73.2 - - - +
283C LEU* 1.3 66.3 + - - +
285C ALA* 3.0 14.9 + - - +
286C GLN* 3.2 16.6 + - - +
301C LEU* 4.0 22.9 - - + -
305C ILE* 4.3 16.6 - - - -
1313C ANP 3.5 30.5 - - - +
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Residues in contact with LEU 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C THR* 2.9 23.8 + - + +
280C LEU* 3.4 10.3 + - + +
282C MSE 1.3 72.1 - - - +
284C ASN* 1.3 66.8 + - - +
286C GLN* 3.3 20.3 + - - +
287C GLU* 3.4 17.9 + - - +
292C TYR 4.2 1.6 - - - -
293C VAL* 3.9 22.4 - - + -
294C ASN* 3.4 30.4 + - + +
295C LEU* 4.5 1.6 - - + -
297C ASN* 3.8 21.1 - - + +
298C TYR* 4.0 30.3 - - + -
301C LEU* 3.7 21.1 - - + -
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Residues in contact with ASN 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C ASN 3.3 7.7 + - - +
250C VAL 2.8 24.6 + - - -
251C GLY 3.9 0.7 - - - -
252C SER* 2.9 26.1 + - - +
255C SER* 3.3 24.2 - - - +
280C LEU 3.0 8.2 + - - +
281C GLY 3.6 8.5 - - - +
283C LEU* 1.3 77.2 - - - +
285C ALA* 1.3 56.8 + - - +
287C GLU* 2.9 28.8 + - - +
289C GLN 3.7 3.1 - - - +
291C GLY* 2.8 28.4 + - - -
292C TYR 3.2 19.0 + - - +
293C VAL* 3.9 1.9 - - + +
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Residues in contact with ALA 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C ILE* 4.6 0.4 - - + -
246C VAL* 3.6 23.3 - - + +
247C LEU 2.8 30.0 + - - -
248C ASN 3.0 19.2 + - - -
249C PRO* 3.9 6.7 - - + -
252C SER* 3.5 13.4 + - - +
281C GLY 3.3 4.7 + - - +
282C MSE 3.0 12.6 + - - +
284C ASN* 1.3 78.6 - - - +
286C GLN* 1.3 51.0 + - - +
1313C ANP 4.1 17.7 - - + +
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Residues in contact with GLN 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C ILE* 3.5 29.3 - - + +
245C SER* 3.5 30.4 + - - +
246C VAL 4.9 0.2 - - - -
247C LEU* 3.5 22.2 - - - +
282C MSE 3.2 13.9 + - - +
283C LEU* 3.6 15.7 - - - +
284C ASN 3.1 0.6 - - - -
285C ALA* 1.3 76.6 - - - +
287C GLU* 1.3 65.1 + - + +
297C ASN* 4.6 11.4 + - - +
301C LEU* 3.8 21.1 - - - +
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Residues in contact with GLU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C LEU* 4.0 2.5 - - - -
248C ASN* 3.2 19.2 + - - +
283C LEU 3.4 10.6 - - - +
284C ASN 2.9 14.8 + - - +
286C GLN* 1.3 85.7 - - - +
288C ALA* 1.3 64.5 + - - +
289C GLN* 3.3 11.7 + - - +
292C TYR* 3.4 51.3 - - + +
293C VAL* 4.3 2.7 - - - -
294C ASN* 3.3 29.4 + - - +
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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
------------------------------------------------------------
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