Contacts of the helix formed by residues 261 - 266 (chain D) in PDB entry 3NJ4
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 THR 261 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C LYS* 4.1 11.9 - - + +
406C LEU 4.0 16.8 - - - +
407C THR* 3.7 22.4 - - + +
242D THR* 4.1 1.1 - - - -
260D THR* 1.3 81.2 + - - +
262D MET* 1.3 60.6 + - - +
263D ASP* 3.5 15.3 + - - +
264D GLU* 3.3 25.7 + - + +
265D ALA* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C THR* 4.5 4.2 + - + +
217D VAL* 4.1 9.9 - - + -
219D ALA* 5.6 3.8 - - - -
242D THR* 4.0 15.4 - - + +
261D THR* 1.3 72.8 - - - +
263D ASP* 1.3 59.2 + - - +
265D ALA* 3.6 8.1 - - + -
266D CYS* 2.8 59.3 + - + +
272D PHE* 3.3 22.0 - - + -
281D ILE* 3.5 21.8 - - + +
282D ILE* 4.1 20.2 - - - -
286D HIS* 3.4 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D THR* 3.1 12.9 + - - +
262D MET* 1.3 77.8 - - - +
264D GLU* 1.3 59.9 + - + +
266D CYS* 3.2 15.8 - - - -
267D GLN* 3.2 15.3 - - - +
285D ARG* 2.6 33.3 + - - -
286D HIS* 2.8 19.8 + - - -
289D GLN* 3.7 6.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C LYS* 2.6 42.3 + - - +
260D THR* 4.0 10.0 - - - +
261D THR* 3.3 19.8 + - - +
262D MET 3.2 0.2 - - - -
263D ASP* 1.3 79.1 - - + +
265D ALA* 1.3 64.8 - - - +
267D GLN* 3.1 30.4 + - - +
268D GLU* 4.2 7.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D VAL* 3.8 24.9 - - + +
240D ILE* 4.3 10.1 - - + -
242D THR* 4.8 2.0 - - + -
260D THR* 3.9 11.4 + - - +
261D THR 3.0 17.8 + - - +
262D MET* 3.6 13.7 - - + -
264D GLU* 1.3 73.8 - - - +
266D CYS* 1.3 61.2 + - - +
267D GLN 3.0 5.6 - - - -
268D GLU* 2.9 22.5 + - - +
269D GLY 3.1 12.3 + - - -
272D PHE* 4.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D MET* 2.8 33.3 + - + +
263D ASP 3.2 25.8 - - - -
264D GLU 3.2 0.6 - - - -
265D ALA* 1.3 73.1 - - - +
267D GLN* 1.3 60.2 + - - +
268D GLU 3.3 1.1 + - - -
269D GLY 4.3 0.7 + - - +
272D PHE* 3.6 11.1 - - + -
286D HIS* 3.7 33.2 - - + +
289D GLN* 3.2 32.8 - - - -
290D MET* 3.4 27.5 - - + +
291D LYS 4.7 0.5 + - - -
----------------------------------------------------------
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