Contacts of the helix formed by residues 263 - 273 (chain D) in PDB entry 3O9Z
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 LEU 263 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D GLN* 4.1 29.2 - - + +
130D LEU* 6.1 0.7 - - + -
132D VAL* 3.8 22.0 - - + +
133D HIS* 3.9 28.9 - - + +
134D PRO* 4.1 10.3 - - + -
259D GLY* 2.6 33.4 - - - +
262D ASP* 1.3 86.4 - - + +
264D HIS* 1.3 67.6 + - - +
265D THR 3.3 2.9 + - - +
266D GLU* 3.3 10.4 + - + +
267D VAL* 3.3 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ILE* 4.3 3.7 - - + +
16D ARG* 3.8 51.3 + - + +
17D HIS* 3.7 24.0 + + - -
20D ALA* 4.1 4.3 - - + -
100D GLU* 2.7 28.6 + - - -
127D VAL* 3.8 17.1 - - + +
129D GLN* 3.6 30.5 + - - -
262D ASP 3.6 1.8 + - - -
263D LEU* 1.3 81.5 + - - +
265D THR* 1.3 63.0 + - - +
267D VAL* 3.4 7.8 + - - +
268D TYR* 3.0 29.2 + + + -
311D NAD 3.9 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ARG 5.1 0.3 + - - -
19D LYS* 4.8 2.9 - - - +
20D ALA* 3.7 18.5 + - - +
23D GLU* 2.8 45.6 + - + +
24D VAL* 4.1 12.8 - - + -
262D ASP 4.9 3.5 + - - -
263D LEU* 3.3 1.2 + - - +
264D HIS* 1.3 78.4 - - - +
266D GLU* 1.3 57.1 + - - +
268D TYR* 3.1 3.3 + - - +
269D ARG* 2.9 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D VAL* 3.9 30.1 - - + +
263D LEU* 3.3 13.8 + - + +
265D THR* 1.3 77.2 - - - +
267D VAL* 1.3 57.8 + - - +
269D ARG* 2.6 53.0 + - - +
270D LYS* 2.8 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 267 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D LEU* 4.7 2.9 - - + -
126D THR 4.1 7.0 - - - +
127D VAL* 4.0 37.9 - - + -
128D LEU 4.2 1.1 - - - +
129D GLN* 4.1 23.8 - - - -
132D VAL* 4.2 8.1 - - + -
263D LEU 3.3 12.9 + - - +
264D HIS 3.6 8.7 - - - +
265D THR 3.2 0.6 - - - -
266D GLU* 1.3 76.9 - - - +
268D TYR* 1.3 59.7 + - + +
270D LYS* 3.4 7.0 + - - +
271D THR* 2.6 40.0 + - - +
277D PHE* 4.2 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 268 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D PHE* 3.5 37.7 - + - -
17D HIS* 2.7 43.1 + + - +
20D ALA* 3.2 32.3 - - + -
21D ILE* 3.7 15.0 - - + +
24D VAL* 3.9 15.0 - - + -
75D SER* 2.8 19.0 + - - -
98D LEU* 3.7 21.3 - - + -
127D VAL* 5.0 2.7 - - + -
264D HIS* 3.0 23.8 + - + +
265D THR 3.5 7.4 - - - +
267D VAL* 1.3 77.0 - - + +
269D ARG* 1.3 64.0 + - - +
271D THR* 3.2 7.3 + - - -
272D LEU* 2.9 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 269 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D VAL* 4.2 11.8 - - + +
265D THR* 2.9 15.1 + - + +
266D GLU* 2.6 47.6 + - - +
268D TYR* 1.3 77.2 - - - +
270D LYS* 1.3 76.7 + - - +
272D LEU* 3.3 7.8 + - - +
273D ALA* 3.0 34.2 + - + +
275D GLU* 4.5 9.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 270 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D VAL* 3.5 27.4 - - + -
266D GLU* 2.8 37.2 + - - +
267D VAL* 3.8 4.7 - - - +
269D ARG* 1.3 83.1 - - - +
271D THR* 1.3 61.6 + - - +
273D ALA* 3.2 10.3 + - - -
274D GLY 3.2 0.2 + - - -
275D GLU* 2.8 71.5 + - + +
276D GLY* 4.8 1.3 - - - +
277D PHE* 3.9 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 271 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D TYR* 3.7 22.5 + - + +
98D LEU* 4.2 14.0 - - + +
125D TYR* 3.3 47.7 - - + +
126D THR 5.4 0.2 + - - -
267D VAL* 2.6 32.3 + - - +
268D TYR* 3.2 7.2 + - - -
270D LYS* 1.3 75.8 - - - +
272D LEU* 1.3 63.7 + - - +
274D GLY* 3.2 13.9 + - - -
276D GLY* 3.8 15.4 + - - -
277D PHE 4.9 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 272 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D THR* 4.2 24.7 - - + +
4D PHE* 4.5 9.2 - - + -
24D VAL* 3.7 37.7 - - + +
73D TYR* 3.5 35.7 - - + +
268D TYR* 2.9 22.3 + - + +
269D ARG* 3.7 5.6 - - - +
271D THR* 1.3 77.1 - - - +
273D ALA* 1.3 58.5 + - - +
274D GLY 3.3 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 273 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D ARG* 3.0 26.0 + - + +
270D LYS* 3.2 8.9 + - - +
272D LEU* 1.3 76.6 - - - +
274D GLY* 1.3 60.2 + - - +
275D GLU* 3.4 17.4 - - - +
----------------------------------------------------------
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