Contacts of the helix formed by residues 229 - 245 (chain D) in PDB entry 1JST
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 229 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227D LEU 3.6 3.9 + - - +
228D GLN* 1.3 75.0 + - - +
230D GLU* 1.3 61.4 + - - +
232D LEU* 3.1 16.9 + - - +
233D HIS* 3.0 24.5 + - - +
312D ASN* 4.3 12.1 - - - +
334D MET* 4.7 12.4 + - - +
338D GLU* 2.5 29.6 + - - -
412D LYS* 2.8 19.6 + - - +
413D TYR* 2.9 18.3 + - - -
418D TYR* 3.4 16.5 + - - -
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Residues in contact with GLU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C ARG* 4.1 11.7 - - - +
228D GLN* 3.1 0.8 - - + +
229D ASN* 1.3 80.5 - - - +
231D THR* 1.3 55.5 + - - +
233D HIS* 3.3 2.6 + - - +
234D LEU* 3.0 40.8 + - + +
268D GLU* 3.4 32.9 - - + +
310D THR* 2.7 22.8 + - - -
312D ASN* 2.9 29.2 + - - +
313D GLN* 3.3 30.3 + - - +
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Residues in contact with THR 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D LEU* 4.3 13.2 - - + -
228D GLN* 3.0 10.2 + - - +
230D GLU* 1.3 74.5 - - - +
232D LEU* 1.3 60.6 + - - +
234D LEU* 4.4 2.0 - - - -
235D ALA* 2.9 26.5 + - - +
261D MET* 4.4 4.7 - - - -
264D ALA* 3.4 25.2 - - + +
265D SER* 3.7 25.4 - - - +
268D GLU* 3.4 17.4 - - - +
269D GLU* 2.4 28.7 + - - +
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Residues in contact with LEU 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D VAL* 4.6 1.1 - - + +
218D LEU* 3.8 36.1 - - + +
219D VAL* 3.8 31.2 - - + +
222D GLY* 6.0 2.7 - - - -
228D GLN 3.6 2.5 + - - +
229D ASN* 3.1 15.3 + - - +
231D THR* 1.3 77.0 - - - +
233D HIS* 1.3 66.5 + - - +
235D ALA* 3.2 6.9 + - - +
236D VAL* 3.0 32.9 + - + +
261D MET* 4.6 10.0 - - + +
338D GLU* 4.0 20.9 - - + +
341D LEU* 3.5 23.6 - - + -
412D LYS* 5.1 2.7 - - - +
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Residues in contact with HIS 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D ASN* 3.0 23.8 + - - -
230D GLU* 3.5 9.0 - - - +
232D LEU* 1.3 80.4 - - + +
234D LEU* 1.3 59.2 + - - +
236D VAL* 3.5 2.6 + - - +
237D ASN* 3.1 21.5 + - - +
310D THR* 3.7 21.1 - - - +
311D VAL* 4.0 28.5 - - + +
312D ASN* 3.8 24.7 + - + +
334D MET* 5.5 3.6 - - - -
337D GLY 3.8 18.2 + - - -
338D GLU* 4.7 17.5 - - + -
341D LEU* 3.5 35.6 - - + +
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Residues in contact with LEU 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D GLU* 3.0 35.8 + - - +
233D HIS* 1.3 71.6 - - - +
235D ALA* 1.3 68.2 + - - +
237D ASN* 3.1 6.4 + - - +
238D TYR* 3.0 51.2 + - + +
264D ALA* 3.7 15.9 - - + +
267D PHE* 3.8 23.1 - - + -
268D GLU* 4.0 23.1 - - + +
306D LEU 4.3 6.7 - - - +
307D ALA 5.3 0.2 - - - -
308D ALA* 3.4 30.5 - - + +
310D THR* 3.5 5.4 - - + -
313D GLN* 4.6 0.2 - - - +
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Residues in contact with ALA 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D LEU* 3.9 14.6 - - + -
231D THR 2.9 14.9 + - - +
232D LEU 3.3 8.7 - - - +
234D LEU* 1.3 77.0 - - - +
236D VAL* 1.3 63.9 + - - +
238D TYR* 3.3 2.6 + - - +
239D ILE* 3.0 27.9 + - - +
260D ALA* 3.9 13.5 - - + +
261D MET* 3.6 35.0 - - - +
264D ALA* 3.7 1.0 - - + +
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Residues in contact with VAL 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D ARG* 3.2 31.9 - - - +
215D VAL* 3.6 36.1 - - + -
218D LEU* 4.5 6.3 - - + -
232D LEU* 3.0 25.5 + - + +
233D HIS 4.1 3.6 - - - +
235D ALA* 1.3 74.5 - - - +
237D ASN* 1.3 64.0 + - - +
239D ILE* 3.1 9.5 + - + +
240D ASP* 2.9 27.3 + - - +
341D LEU* 4.1 20.9 - - + +
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Residues in contact with ASN 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D CYS* 3.6 16.8 + - - +
195D PRO* 5.8 1.8 - - - +
233D HIS 3.1 14.3 + - - +
234D LEU* 3.1 13.2 + - - +
236D VAL* 1.3 78.5 - - - +
238D TYR* 1.3 68.5 + - - +
240D ASP* 3.1 6.4 + - - +
241D ARG* 2.8 53.1 + - - +
308D ALA* 3.1 25.4 - - + +
309D PRO 4.2 9.1 + - - -
310D THR* 5.2 3.1 - - + -
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Residues in contact with TYR 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D LEU* 3.0 37.0 + - + +
235D ALA 3.8 2.5 - - - +
237D ASN* 1.3 94.7 + - - +
239D ILE* 1.3 57.1 + - - +
241D ARG* 3.9 8.9 - - - -
242D PHE* 2.9 30.0 + - - +
260D ALA* 3.7 25.1 - - + -
263D LEU* 4.2 8.3 - - + -
264D ALA* 3.6 26.9 - - + -
267D PHE* 4.1 6.4 - - - +
298D VAL* 4.8 3.3 - - + +
302D LEU* 3.5 26.5 - - + +
306D LEU* 2.8 62.1 + - + +
308D ALA* 4.4 3.8 - - + -
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Residues in contact with ILE 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D TYR* 5.2 0.2 - - - +
211D ARG* 5.6 5.6 - - + +
214D LEU* 3.6 32.3 - - + -
215D VAL* 5.7 2.7 - - + -
218D LEU* 3.7 23.8 - - + -
235D ALA 3.0 22.4 + - - +
236D VAL* 3.5 10.5 - - + +
237D ASN 3.1 0.2 - - - -
238D TYR* 1.3 75.4 - - - +
240D ASP* 1.3 65.1 + - - +
242D PHE* 3.7 3.9 - - - +
243D LEU* 2.9 51.3 + - + +
256D VAL* 4.0 11.9 - - + +
257D GLY* 3.7 10.3 - - - -
260D ALA* 3.4 16.6 - - + -
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Residues in contact with ASP 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D PRO* 3.8 21.2 - - + +
199D TYR* 2.6 32.1 + - + +
211D ARG* 3.0 32.9 + - - -
236D VAL* 2.9 23.3 + - - +
237D ASN* 3.7 5.4 - - - +
239D ILE* 1.3 79.2 - - - +
241D ARG* 1.3 53.8 + - - +
243D LEU 3.9 0.2 - - - -
244D SER* 2.5 38.2 + - - -
348D LEU* 3.5 18.2 - - - +
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Residues in contact with ARG 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D CYS* 3.3 44.9 - - - +
194D LYS 4.9 1.6 - - - +
195D PRO* 4.4 13.2 - - + -
196D LYS* 4.3 1.8 + - - +
237D ASN* 2.8 49.7 + - - +
238D TYR* 3.9 7.2 - - - +
240D ASP* 1.3 73.5 - - - +
242D PHE* 1.3 67.1 + - - +
244D SER* 3.3 11.5 + - - -
245D SER* 2.9 20.8 + - - -
301D VAL* 4.8 0.6 - - - +
302D LEU* 3.3 37.6 + - + +
305D ASP* 2.6 43.8 + - - +
308D ALA* 3.7 6.9 - - - +
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Residues in contact with PHE 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A THR* 4.1 4.0 - - + -
238D TYR 2.9 20.5 + - - +
239D ILE* 3.7 5.4 - - - +
241D ARG* 1.3 76.9 - - - +
243D LEU* 1.3 57.6 + - + +
245D SER* 2.9 6.9 + - - -
246D MET* 2.7 53.6 + - + +
248D VAL* 3.9 15.0 - - + -
256D VAL* 3.8 28.5 - - + -
294D MET* 4.3 5.8 - - - -
297D LEU* 3.6 26.7 - - + -
298D VAL* 3.7 33.0 - - + -
301D VAL* 3.5 39.7 - - + -
302D LEU* 4.3 2.4 - - + +
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Residues in contact with LEU 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D TYR* 3.5 31.4 - - + +
200D MET* 4.9 2.5 - - + -
203D GLN* 3.0 24.7 + - - +
206D ILE* 3.5 25.8 - - + -
211D ARG* 5.5 4.0 - - + -
239D ILE* 2.9 39.1 + - + +
242D PHE* 1.3 80.8 - - + +
244D SER* 1.3 61.7 + - - +
245D SER 3.1 0.4 + - - -
246D MET 3.6 5.3 + - - +
248D VAL* 3.4 38.4 - - + -
253D LEU* 3.9 17.0 - - + -
256D VAL* 4.6 4.5 - - + -
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Residues in contact with SER 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D PRO* 3.4 2.6 - - - +
196D LYS* 3.3 51.0 + - - -
199D TYR* 3.2 27.6 - - - -
202D LYS* 3.8 16.3 + - - -
240D ASP 2.5 23.3 + - - -
241D ARG* 3.5 6.7 - - - -
242D PHE 3.1 0.6 - - - -
243D LEU* 1.3 77.7 - - - +
245D SER* 1.3 57.5 + - - +
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Residues in contact with SER 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LYS* 5.7 2.6 + - - -
67A LEU* 5.9 3.1 - - - +
196D LYS* 3.3 14.5 + - - +
241D ARG 2.9 15.8 + - - -
242D PHE 2.9 4.2 + - - -
243D LEU 4.5 0.2 - - - -
244D SER* 1.3 79.3 - - - +
246D MET* 1.3 64.1 + - - +
247D SER 4.1 0.7 + - - -
301D VAL* 4.0 20.1 + - - +
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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