Contacts of the helix formed by residues 224 - 238 (chain B) in PDB entry 5NO6
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 SER 224 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B PRO 3.9 1.6 + - - -
223B TYR* 1.3 74.7 - - - +
225B LYS* 1.3 59.1 + - - +
226B GLY* 3.2 5.5 + - - -
227B GLN* 2.8 52.4 + - - +
228B LEU* 3.3 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B TYR 3.9 1.0 + - - -
224B SER* 1.3 76.7 + - - +
226B GLY* 1.3 56.7 + - - +
228B LEU* 3.0 17.5 - - + +
229B ARG* 2.8 47.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B SER* 3.2 5.4 + - - -
225B LYS* 1.3 77.2 - - - +
227B GLN* 1.3 62.8 + - - +
229B ARG* 3.1 21.9 + - - +
230B GLU* 2.8 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B TYR* 3.3 34.0 - - + +
224B SER* 2.8 38.0 + - - +
226B GLY* 1.3 72.8 - - - +
228B LEU* 1.3 57.9 + - - +
230B GLU* 3.0 4.4 + - - +
231B LEU* 2.8 31.2 + - + +
253B THR* 3.7 38.3 - - - +
255B LEU* 3.6 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B TYR* 3.1 45.3 - - + +
225B LYS* 3.0 45.3 - - + +
227B GLN* 1.3 76.4 - - - +
229B ARG* 1.3 60.4 + - + +
231B LEU* 3.9 16.4 - - + +
232B GLU* 2.8 43.3 + - + +
263B TRP* 4.8 9.0 - - + +
24D T 3.9 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LYS* 2.8 42.4 + - + +
226B GLY* 3.4 23.4 - - - +
228B LEU* 1.3 72.8 - - - +
230B GLU* 1.3 54.0 + - - +
232B GLU* 3.7 3.7 - - - +
233B ARG* 2.8 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B GLY 2.8 15.2 + - - +
227B GLN 3.4 7.6 - - - +
229B ARG* 1.3 69.6 - - - +
231B LEU* 1.3 57.2 + - - +
233B ARG* 3.2 28.4 + - + +
234B GLU* 2.8 39.6 + - - +
249B ILE* 3.7 29.0 - - - +
252B ALA* 5.5 9.6 - - + -
253B THR* 4.3 14.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
223B TYR* 4.1 15.5 - - + -
227B GLN 2.8 18.3 + - - +
228B LEU* 3.8 18.6 - - - +
230B GLU* 1.3 72.8 - - - +
232B GLU* 1.3 52.9 + - - +
234B GLU* 2.9 8.6 + - - +
235B TYR* 2.8 33.6 + - - +
249B ILE* 4.0 22.9 - - + +
253B THR* 4.9 2.0 - - + -
255B LEU* 4.1 14.1 - - + -
260B ILE* 4.4 26.0 - - + -
263B TRP* 4.0 50.2 - - + +
264B PHE* 4.6 5.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LEU* 2.8 32.9 + - + +
229B ARG* 3.7 4.7 - - - +
231B LEU* 1.3 71.6 - - - +
233B ARG* 1.3 59.1 + - - +
235B TYR* 3.3 5.6 + - - +
236B ALA* 2.8 30.9 + - - +
263B TRP* 3.6 21.1 - - + -
267B ARG* 2.9 40.6 + - - +
270B LYS* 5.9 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ARG* 2.8 25.9 + - + +
230B GLU* 3.2 39.5 + - + +
232B GLU* 1.3 72.0 - - - +
234B GLU* 1.3 71.5 + - - +
236B ALA* 3.6 7.6 - - - +
237B ALA* 3.0 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B GLU* 2.8 32.5 + - - +
231B LEU* 2.9 7.0 + - - +
233B ARG* 1.3 84.8 + - - +
235B TYR* 1.3 58.2 + - - +
237B ALA* 2.8 29.0 + - - +
238B ASN 2.8 12.6 + - - +
241B ILE* 5.1 0.2 - - + -
245B LYS* 3.2 34.7 + - - +
248B LYS* 5.9 1.2 - - - +
249B ILE* 3.7 35.8 - - + +
264B PHE* 4.3 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B LEU 2.8 18.1 + - - +
232B GLU* 3.7 7.0 - - - +
234B GLU* 1.3 72.2 - - - +
236B ALA* 1.3 63.7 + - - +
238B ASN 2.9 22.7 - - - +
239B LYS* 3.4 48.5 + - + +
263B TRP* 3.9 10.3 - + + -
264B PHE* 3.6 21.1 - + + -
267B ARG* 3.3 60.9 + - + -
268B ARG* 4.1 15.2 - - + +
271B GLU* 2.7 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B GLU 2.8 20.4 + - - +
233B ARG* 3.6 10.1 - - - +
235B TYR* 1.3 77.4 - - - +
237B ALA* 1.3 63.0 + - - +
238B ASN* 4.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ARG* 3.0 20.6 + - - +
234B GLU* 2.8 27.3 + - - +
236B ALA* 1.3 76.9 - - - +
238B ASN* 1.3 62.0 + - - +
245B LYS* 4.5 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B GLU 2.8 11.8 + - - +
235B TYR* 2.9 25.1 - - - +
236B ALA 3.3 1.9 - - - -
237B ALA* 1.3 76.5 + - - +
239B LYS* 1.3 85.4 + - - +
240B PHE* 3.5 16.3 + - - +
242B THR* 5.9 4.6 - - - +
245B LYS* 3.3 23.0 + - - +
264B PHE* 3.5 6.9 - - - -
----------------------------------------------------------
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