Contacts of the helix formed by residues 227 - 243 (chain B) in PDB entry 1NQI
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 227 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B GLN* 2.9 8.5 + - - -
226B PHE* 1.3 72.9 - - - +
228B ARG* 1.3 63.1 + - - +
229B ALA* 3.7 4.7 + - - +
230B LYS* 3.0 26.4 + - - +
231B LEU* 3.1 24.4 + - - +
309B ASN 2.9 28.0 + - - +
311B TYR 3.0 21.5 + - - +
312B TRP* 3.4 32.8 - - + -
398B ILE* 3.8 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B PRO* 3.9 19.5 - - + +
226B PHE* 3.8 25.4 + - + -
227B ASN* 1.3 71.8 + - - +
229B ALA* 1.3 63.8 - - - +
231B LEU* 3.2 5.4 + - - +
232B LEU* 3.0 45.5 + - + +
250B PHE* 4.6 7.7 + - - +
251B SER 5.6 0.4 - - - -
252B ASP* 2.7 24.8 + - - +
290B PHE 4.8 3.0 + - - -
291B GLY* 4.2 3.5 - - - -
292B GLY 3.5 37.5 + - - +
294B SER* 5.0 5.5 + - - -
311B TYR 4.9 0.8 + - - -
313B GLY 5.8 0.6 + - - -
317B GLU* 2.8 45.6 + - + +
318B ASP* 4.1 12.3 - - - +
321B ILE* 4.8 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ASN* 3.4 4.5 + - - +
228B ARG* 1.3 75.9 - - - +
230B LYS* 1.3 65.8 + - - +
232B LEU* 3.2 13.3 + - - +
233B ASN* 2.9 25.8 + - - -
307B PHE* 4.0 15.4 - - + +
308B PRO* 3.3 22.9 - - + +
311B TYR* 5.5 1.1 + - + -
317B GLU* 3.8 29.0 - - + +
321B ILE* 4.6 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ASN* 3.0 38.5 + - + +
229B ALA* 1.3 77.1 - - - +
231B LEU* 1.3 58.8 + - - +
233B ASN* 3.0 5.4 + - - +
234B VAL* 2.9 30.1 + - - +
308B PRO 3.8 1.7 + - - -
309B ASN* 3.3 41.1 + - - +
312B TRP* 4.4 6.7 - - + -
377B SER 6.0 0.2 - - - -
378B LEU* 4.2 9.6 - - + -
379B THR* 3.4 30.8 + - - +
398B ILE* 2.6 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ILE* 5.0 0.2 - - - -
187B PRO* 4.1 11.4 - - + -
218B ILE* 3.4 34.9 - - + +
220B GLN* 3.5 34.8 - - + +
226B PHE* 3.6 30.5 - - + -
227B ASN 3.1 17.4 + - - +
228B ARG 3.6 4.7 - - - +
230B LYS* 1.3 75.2 - - - +
232B LEU* 1.3 58.2 + - - +
234B VAL* 3.3 3.0 + - - -
235B GLY 3.0 22.7 + - - -
396B VAL* 3.8 28.5 - - + -
398B ILE* 4.0 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ILE* 3.9 11.6 - - + +
187B PRO* 3.5 30.3 - - + -
228B ARG* 3.0 49.0 + - + +
229B ALA* 3.5 11.0 - - + +
230B LYS 3.2 0.2 - - - -
231B LEU* 1.3 73.0 - - - +
233B ASN* 1.3 67.3 + - - +
235B GLY* 3.2 2.4 + - - -
236B PHE* 3.0 21.7 + - - +
250B PHE* 3.6 46.5 - - + -
307B PHE* 3.8 24.7 - - + -
321B ILE* 5.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ALA 2.9 14.6 + - - -
230B LYS 3.0 8.3 + - - +
232B LEU* 1.3 77.1 - - - +
234B VAL* 1.3 63.3 + - - +
236B PHE* 3.1 18.1 + - - +
237B LYS* 3.1 10.4 + - - +
301B PHE* 3.2 15.7 - - - -
306B GLY* 4.0 0.3 - - - -
307B PHE* 2.7 50.4 + - - +
308B PRO 3.9 0.4 + - - -
309B ASN* 2.9 23.8 + - - +
374B GLY 4.3 3.0 - - - -
375B LEU* 5.0 8.5 + - + +
378B LEU* 4.0 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ILE* 3.8 17.5 - - + -
230B LYS 2.9 19.1 + - - +
231B LEU* 3.5 8.5 - - - +
233B ASN* 1.3 77.0 - - - +
235B GLY* 1.3 64.6 + - - +
237B LYS* 3.0 4.2 + - - +
238B GLU* 2.9 31.1 + - + +
378B LEU* 4.2 11.2 - - + -
380B TYR* 3.8 45.1 - - + -
394B ILE* 5.3 0.4 - - + -
396B VAL* 3.8 14.1 - - + -
398B ILE* 4.2 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ILE* 3.5 16.2 - - - -
216B TYR* 5.3 0.8 - - - -
218B ILE* 3.7 28.0 - - - +
231B LEU 3.0 11.3 + - - -
232B LEU 3.2 3.8 + - - -
234B VAL* 1.3 76.3 - - - +
236B PHE* 1.3 64.2 + - - +
238B GLU* 4.8 1.3 - - - -
239B ALA* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ILE* 3.5 11.5 - - + +
232B LEU 3.0 12.5 + - - +
233B ASN 3.3 8.7 - - - +
235B GLY* 1.3 78.3 - - - +
237B LYS* 1.3 70.7 + - + +
240B LEU* 3.3 40.8 + - + +
248B PHE* 3.4 49.3 - + + -
250B PHE* 4.9 0.7 - - + -
298B LYS* 4.5 9.9 - - + -
301B PHE* 3.4 52.7 - + + -
302B LEU* 3.9 15.7 - - + -
375B LEU* 3.9 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ASN 3.1 5.5 + - - +
234B VAL 3.0 4.8 + - - +
236B PHE* 1.3 89.8 - - + +
238B GLU* 1.3 64.1 + - - +
240B LEU* 3.4 17.5 + - + +
241B LYS* 3.6 15.7 + - - +
375B LEU* 4.0 31.6 - - + +
378B LEU* 4.1 17.7 - - + -
380B TYR* 3.7 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B TYR* 4.8 1.7 - - - -
234B VAL* 2.9 33.6 + - + +
235B GLY* 4.1 2.5 - - - +
237B LYS* 1.3 69.7 - - - +
239B ALA* 1.3 68.2 + - - +
241B LYS* 2.7 53.0 + - - +
242B ASP* 3.7 6.2 + - - +
380B TYR* 2.6 28.6 + - - +
382B VAL* 3.8 17.5 - - - +
385B VAL* 4.9 5.9 - - - +
394B ILE* 3.4 34.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ALA* 3.6 31.6 - - + -
185B ILE* 4.9 0.2 - - + -
216B TYR* 3.8 27.5 - - + -
235B GLY 2.9 18.6 + - - +
236B PHE 4.0 2.9 - - - +
238B GLU* 1.3 77.3 - - - +
240B LEU* 1.3 57.1 + - - +
242B ASP* 2.8 26.3 + - - +
243B TYR 3.4 0.7 + - - -
245B TYR* 3.4 11.3 - - + -
248B PHE* 4.2 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B PHE* 3.3 50.1 + - + +
237B LYS* 3.6 12.6 - - + +
238B GLU 3.2 0.8 - - - -
239B ALA* 1.3 77.9 - - - +
241B LYS* 1.3 59.9 + - - +
242B ASP 3.2 0.2 - - - -
243B TYR 3.4 24.4 + - - +
244B ASP* 4.7 3.9 - - - +
245B TYR* 3.9 25.4 - - + +
248B PHE* 3.8 13.5 - - + -
298B LYS* 4.3 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LYS* 3.7 15.0 - - - +
238B GLU* 2.7 52.2 + - - +
240B LEU* 1.3 78.6 - - - +
242B ASP* 1.3 64.3 + - - +
380B TYR* 4.3 4.9 + - - -
382B VAL* 5.2 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ARG* 6.0 3.0 - - + +
216B TYR* 2.7 35.0 + - - +
238B GLU 4.6 4.2 - - - +
239B ALA 2.8 5.7 + - - +
241B LYS* 1.3 84.6 - - - +
243B TYR* 1.3 64.4 + - + +
245B TYR* 4.7 0.4 - - - +
387B ARG* 2.6 48.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ARG* 3.3 30.5 + - - +
172B THR* 4.8 3.3 + - - +
181B LYS* 3.8 33.2 + - + -
212B ASP* 2.6 33.1 + - - -
239B ALA 3.4 1.6 + - - -
240B LEU* 3.4 18.5 - - - +
241B LYS 3.7 1.0 - - - -
242B ASP* 1.3 82.7 - - + +
244B ASP* 1.3 67.3 + - + +
245B TYR* 3.0 51.2 + + + +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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