Contacts of the helix formed by residues 225 - 235 (chain B) in PDB entry 1NYR
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 LYS 225 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B GLU* 3.0 43.8 - - - +
224B ASP* 1.3 72.5 - - - +
226B LYS* 1.3 55.1 + - - +
228B LEU* 2.7 27.9 + - - +
229B LYS* 3.1 23.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ASP* 3.7 19.0 - - - +
225B LYS* 1.3 79.9 - - - +
227B GLU* 1.3 66.8 + - + +
228B LEU 3.2 2.8 + - - -
229B LYS* 3.6 4.6 + - - +
230B ALA* 3.4 21.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B PHE* 3.6 43.4 - - + -
224B ASP* 3.0 22.4 + - - +
226B LYS* 1.3 84.8 - - + +
228B LEU* 1.3 58.8 + - - +
230B ALA* 4.6 6.5 - - - +
231B HIS* 3.6 19.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
194B GLU* 4.1 15.9 - - + +
195B PHE* 4.1 30.7 - - - +
196B LYS* 4.6 8.5 - - + +
220B THR* 3.9 19.5 - - + -
222B PHE* 4.0 15.9 - - + -
224B ASP 3.5 8.3 + - - +
225B LYS* 2.7 18.4 + - - +
227B GLU* 1.3 73.2 - - - +
229B LYS* 1.3 88.8 + - - +
231B HIS* 3.0 3.2 + - + +
232B LEU* 3.0 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LYS* 5.6 1.4 - - - +
225B LYS* 3.1 20.2 + - + +
226B LYS* 4.1 6.1 - - - +
228B LEU* 1.3 95.8 - - - +
230B ALA* 1.3 65.4 + - - +
231B HIS 2.8 0.9 + - - -
232B LEU* 3.7 24.5 - - + +
233B GLN* 2.8 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B LYS* 3.4 16.1 + - + +
227B GLU* 4.6 7.2 - - - -
229B LYS* 1.3 80.2 - - - +
231B HIS* 1.3 57.2 + - - +
233B GLN* 3.6 9.3 + - - +
234B MET* 2.8 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ARG* 5.3 0.2 + - - -
102B GLY* 3.9 28.5 + - - -
198B LEU* 5.1 1.3 - - + -
220B THR* 3.9 15.2 + - - +
222B PHE* 3.6 25.9 - + + -
227B GLU 3.6 13.8 + - - +
228B LEU* 3.0 10.7 + - + +
229B LYS 2.8 3.8 + - - -
230B ALA* 1.3 72.7 - - - +
232B LEU* 1.3 57.2 + - - +
233B GLN 3.0 1.1 - - - -
234B MET* 2.8 28.6 + - + +
235B LEU* 2.7 62.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
196B LYS* 3.3 37.5 - - + -
198B LEU* 4.3 19.7 - - + -
220B THR* 4.4 5.8 - - + -
228B LEU* 3.0 36.4 + - + +
229B LYS* 3.8 24.7 - - + +
231B HIS* 1.3 79.3 - - - +
233B GLN* 1.3 63.9 + - - +
235B LEU* 3.1 19.6 + - + +
236B GLU* 3.2 18.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LYS* 2.8 27.7 + - - +
230B ALA* 3.6 7.9 - - - +
232B LEU* 1.3 78.3 - - - +
234B MET* 1.3 57.0 + - - +
236B GLU* 2.8 24.9 + - + +
237B GLU* 3.0 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ALA 2.8 21.2 + - - +
231B HIS* 2.8 42.1 + - + +
233B GLN* 1.3 76.6 - - - +
235B LEU* 1.3 74.4 + - + +
236B GLU 3.0 4.7 + - - -
237B GLU* 3.5 17.6 + - - +
238B ARG* 3.5 45.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 4.0 30.7 - - + -
231B HIS* 2.7 41.8 + - + +
232B LEU* 3.1 15.0 + - + +
234B MET* 1.3 81.7 - - + +
236B GLU* 1.3 64.6 + - - +
238B ARG* 3.0 43.6 - - - +
239B LYS* 3.8 21.3 + - - +
----------------------------------------------------------
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