Contacts of the helix formed by residues 256 - 270 (chain A) in PDB entry 4OG2
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 256 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASN 6.2 0.2 - - - +
67A VAL* 4.8 10.3 - - + -
70A LEU* 4.0 22.7 - - + -
131A LEU* 4.0 37.7 - - + -
202A ASP* 4.2 9.6 - - - +
204A PHE* 4.2 17.3 - - + -
231A THR* 4.1 23.1 - - + -
255A GLY* 1.3 81.0 - - - +
257A ALA* 1.3 60.3 + - - +
259A ASP* 2.9 22.6 + - - +
260A GLY* 2.9 25.3 + - - -
281A GLY* 3.2 15.5 - - - +
282A LEU* 3.7 2.8 - - - +
501A LEU* 4.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASN 5.5 1.1 + - - +
69A LEU* 4.1 22.9 - - + -
70A LEU* 4.3 6.8 - - + +
256A LEU* 1.3 77.0 - - - +
258A ALA* 1.3 62.4 + - - +
261A GLY* 2.9 26.7 + - - -
281A GLY 3.1 15.3 + - - +
284A THR* 3.9 24.0 - - + -
286A ASN* 5.3 0.7 - - + -
287A VAL* 3.7 17.8 - - + +
290A VAL* 4.9 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASN* 4.4 21.1 + - + +
69A LEU* 3.9 22.4 - - + +
231A THR 5.7 1.3 - - - +
257A ALA* 1.3 79.1 - - - +
259A ASP* 1.3 58.9 + - - +
261A GLY 3.9 0.3 - - - -
262A ASN* 3.0 42.1 + - - +
290A VAL* 4.0 12.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PHE* 3.3 28.0 - - + -
230A GLN 4.4 0.2 - - - +
231A THR* 3.3 37.6 + - - +
233A ASP 4.0 13.2 - - - +
236A PHE* 3.6 12.3 - - + -
255A GLY* 3.5 1.6 - - - -
256A LEU* 2.9 43.5 + - - +
257A ALA 3.5 0.5 + - - -
258A ALA* 1.3 73.7 + - - +
260A GLY* 1.3 69.0 + - - -
262A ASN* 3.3 2.4 + - - +
263A LEU* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PHE* 5.5 0.4 - - - -
253A ILE* 4.4 11.3 - - - +
255A GLY* 5.4 0.9 - - - -
256A LEU 2.9 21.9 + - - -
259A ASP* 1.3 78.8 + - - +
261A GLY* 1.3 55.6 + - - +
263A LEU* 3.3 3.9 + - - +
264A VAL* 3.0 32.9 + - - +
282A LEU* 3.8 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ALA 2.9 17.8 + - - -
260A GLY* 1.3 75.7 - - - +
262A ASN* 1.3 61.4 + - - +
264A VAL* 3.4 2.3 + - - -
265A ARG* 3.1 19.6 + - - +
282A LEU* 4.4 3.1 - - - +
287A VAL* 4.6 6.5 - - - -
290A VAL* 3.5 16.9 - - - +
291A CYS* 3.5 26.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ASP 5.0 0.4 + - - -
234A THR* 3.8 38.9 - - - +
236A PHE* 3.8 4.3 - - + -
258A ALA* 3.0 30.3 + - - +
259A ASP* 3.8 4.6 - - - +
261A GLY* 1.3 75.7 - - - +
263A LEU* 1.3 56.5 + - - +
265A ARG* 2.8 35.0 + - - +
266A GLN* 3.0 37.4 + - - +
290A VAL* 3.2 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PHE* 3.8 39.3 - - + -
229A PHE* 3.9 14.6 - - + -
236A PHE* 3.6 36.9 - - + -
240A ALA* 4.5 4.5 - - + -
253A ILE* 3.9 32.3 - - + -
259A ASP 3.0 16.8 + - - +
260A GLY 3.7 4.0 - - - +
262A ASN* 1.3 73.6 - - - +
264A VAL* 1.3 65.4 + - - +
266A GLN* 3.3 1.7 + - + -
267A LEU* 2.9 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ILE* 3.6 19.1 - - + -
260A GLY 3.0 21.4 + - - +
261A GLY* 3.7 5.8 - - - +
263A LEU* 1.3 76.1 - - - +
265A ARG* 1.3 64.7 + - - +
267A LEU* 3.3 9.2 + - - +
268A ARG* 3.2 22.3 + - - +
276A ILE* 4.2 12.0 - - + +
282A LEU* 4.0 14.8 - - + -
291A CYS* 4.0 13.9 - - + -
294A LEU 3.4 23.3 - - - +
298A VAL* 4.0 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A THR 5.0 0.2 + - - -
261A GLY 3.1 12.4 + - - +
262A ASN* 2.8 33.3 + - - +
264A VAL* 1.3 76.9 - - - +
266A GLN* 1.3 81.8 + - - +
268A ARG* 3.2 5.5 + - - +
269A GLU* 2.9 55.0 + - - +
290A VAL* 3.1 26.8 + - - +
291A CYS* 3.9 20.1 - - + +
292A LYS* 6.2 0.9 - - - -
294A LEU* 4.0 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A THR 2.7 27.7 + - - -
235A ASP* 3.8 4.9 - - - +
236A PHE* 2.8 40.6 + - + -
237A GLN* 3.8 2.9 + - - +
240A ALA* 5.0 2.5 - - + -
262A ASN* 3.0 20.0 + - - +
263A LEU* 3.9 4.0 - - - +
265A ARG* 1.3 93.8 - - - +
267A LEU* 1.3 65.4 + - - +
269A GLU* 3.2 19.1 + - - +
270A LEU* 2.9 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PHE* 4.2 12.3 - - + -
240A ALA* 3.9 26.0 - - + +
243A ALA* 5.3 0.9 - - + -
244A ILE* 3.9 19.5 - - + +
251A VAL* 3.8 33.7 - - + -
253A ILE* 4.0 13.2 - - + -
263A LEU* 2.9 37.7 + - + +
264A VAL* 3.6 6.1 - - - +
266A GLN* 1.3 76.6 - - - +
268A ARG* 1.3 60.9 + - - +
270A LEU* 3.3 7.0 + - - +
271A GLY 3.3 0.3 + - - -
272A TYR* 3.0 40.4 + - + +
276A ILE* 4.6 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A VAL 3.2 13.2 + - - +
265A ARG 3.6 6.3 - - - +
267A LEU* 1.3 75.6 - - - +
269A GLU* 1.3 65.5 + - - +
271A GLY* 3.0 14.9 + - - -
272A TYR* 2.9 32.6 + - - +
273A GLN* 3.4 11.3 + - - +
274A GLY 2.8 29.9 + - - -
275A ALA* 4.8 0.6 - - - +
276A ILE* 3.5 29.9 - - + +
294A LEU* 3.7 47.1 + - + +
296A ASP 4.3 16.0 + - - -
297A GLY* 5.6 3.2 - - - -
298A VAL* 5.6 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ARG* 2.9 50.9 + - - +
266A GLN* 3.6 23.3 - - - +
268A ARG* 1.3 76.2 - - - +
270A LEU* 1.3 59.8 + - + +
271A GLY* 3.1 4.3 + - - -
294A LEU* 4.1 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A GLN* 4.1 32.1 - - + +
240A ALA* 3.6 27.8 - - + -
241A THR* 4.0 20.6 - - - +
244A ILE* 3.6 25.3 - - + +
266A GLN* 2.9 24.6 + - + +
268A ARG 3.1 0.4 - - - -
269A GLU* 1.3 77.8 - - + +
271A GLY* 1.3 57.7 + - - +
272A TYR 3.5 2.4 + - - -
----------------------------------------------------------
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