Contacts of the helix formed by residues 263 - 277 (chain A) in PDB entry 2O8C
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 ASN 263 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 3.9 21.9 - - + +
176A CYS* 4.9 0.8 - - - +
177A GLU* 3.3 45.3 - - + +
260A GLU* 4.0 14.1 + - - +
261A MET 3.0 4.5 - - - -
262A GLU* 1.3 88.6 - - - +
264A GLN* 1.3 62.6 + - - +
265A VAL 3.3 4.2 + - - -
266A ALA* 3.3 8.0 + - + +
267A VAL* 3.3 24.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A VAL* 6.4 0.9 - - + -
177A GLU* 3.3 3.4 + - - +
233A SER* 5.5 1.4 - - - -
261A MET 4.9 4.3 - - - +
262A GLU 3.5 7.1 + - - +
263A ASN* 1.3 73.4 - - - +
265A VAL* 1.3 63.9 + - + +
267A VAL* 4.3 4.9 - - - +
268A SER* 2.8 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LYS* 3.6 24.4 - - + +
152A MET* 4.7 0.9 - - - -
153A SER* 3.8 23.1 - - - +
155A VAL* 4.2 15.3 - - + -
160A GLN* 3.8 19.7 - - + +
161A VAL 4.7 0.2 - - - -
162A GLY* 3.4 27.0 - - - +
177A GLU* 3.0 14.7 + - - +
264A GLN* 1.3 81.7 - - + +
266A ALA* 1.3 63.9 + - - +
267A VAL 3.4 0.7 - - - -
268A SER* 3.5 5.6 + - - -
269A SER* 3.5 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A GLY* 3.8 11.1 - - - -
163A VAL 4.3 0.4 - - - +
164A GLY* 3.9 5.0 - - - -
175A LEU* 3.9 10.3 - - + +
176A CYS 3.7 35.7 - - - +
177A GLU* 3.7 4.0 + - + -
263A ASN* 3.3 23.2 + - + +
265A VAL* 1.3 77.4 - - - +
267A VAL* 1.3 62.0 + - - +
269A SER* 3.0 16.6 + - - -
270A LEU* 3.3 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 4.2 17.0 - - + -
233A SER* 4.8 13.5 - - - -
235A LYS* 4.0 7.8 + - - +
239A GLN* 4.5 15.7 - - - +
260A GLU 4.7 2.5 - - - +
261A MET* 4.0 39.9 - - + +
263A ASN 3.3 18.0 + - - +
264A GLN* 4.5 5.4 - - - +
266A ALA* 1.3 73.6 - - - +
268A SER* 1.3 66.3 + - - +
270A LEU* 3.2 13.6 + - + +
271A SER* 3.1 20.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LYS* 3.9 20.6 - - - -
231A ASP* 3.3 33.9 + - - +
233A SER* 4.2 16.2 + - - -
264A GLN 2.8 20.1 + - - -
265A VAL* 3.5 12.0 + - - -
266A ALA 3.3 0.2 - - - -
267A VAL* 1.3 79.2 - - - +
269A SER* 1.3 59.8 + - - +
271A SER* 3.3 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A GLY* 3.4 24.0 - - - -
150A VAL 4.4 0.2 - - - -
151A LYS* 4.0 15.2 - - - +
162A GLY 3.2 17.0 + - - -
164A GLY 2.9 26.5 + - - -
231A ASP* 4.2 6.5 - - - -
265A VAL 3.5 2.6 + - - -
266A ALA 3.0 8.1 + - - -
268A SER* 1.3 74.7 - - - +
270A LEU* 1.3 62.6 + - - +
271A SER 3.1 2.0 - - - -
272A ALA* 3.2 16.9 + - - +
273A VAL* 3.5 15.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
164A GLY* 4.1 8.3 - - - -
165A TYR 3.7 26.2 - - - +
166A VAL* 4.0 17.7 - - + -
173A LEU* 4.7 17.5 - - + +
174A GLY 3.9 12.6 - - - +
175A LEU* 4.4 18.6 - - + -
235A LYS* 4.1 6.1 - - - +
266A ALA 3.3 9.4 + - - +
267A VAL* 3.2 15.2 + - + +
269A SER* 1.3 79.1 + - - +
271A SER* 1.3 59.0 + - - +
273A VAL* 3.3 4.9 + - + -
274A ILE* 3.0 39.5 + - + +
291A LEU* 5.4 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ALA 3.1 14.5 + - - -
231A ASP 4.2 1.6 - - - -
232A PHE 2.7 28.4 + - - -
233A SER* 5.0 0.2 - - - -
235A LYS* 3.4 20.8 - - - +
267A VAL 3.1 7.5 + - - -
268A SER* 3.3 14.6 - - - -
270A LEU* 1.3 78.0 - - - +
272A ALA* 1.3 60.9 + - - +
274A ILE* 3.5 1.6 - - - +
275A LYS* 3.3 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A VAL* 3.9 21.6 - - + +
227A ARG* 4.9 8.7 + - + +
230A ALA* 3.6 18.4 + - + +
231A ASP* 3.2 22.2 + - - +
269A SER* 3.2 9.6 + - - +
271A SER* 1.3 79.5 - - - +
273A VAL* 1.3 57.9 + - - +
275A LYS* 3.5 1.4 + - - +
276A PHE* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A VAL* 3.7 25.8 - - + +
148A VAL 3.7 5.4 - - - +
149A GLY* 3.5 16.4 - - - +
164A GLY 3.4 23.3 - - - +
166A VAL* 3.7 26.7 - - + +
200A VAL* 4.2 4.5 - - + -
269A SER 3.5 13.0 - - - +
270A LEU* 3.3 11.1 + - + +
272A ALA* 1.3 75.7 - - - +
274A ILE* 1.3 64.7 + - - +
276A PHE* 3.1 15.3 + - - +
277A LEU* 3.2 22.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A VAL* 4.5 7.0 - - + -
173A LEU* 5.0 7.2 - - + -
235A LYS* 3.4 35.2 - - + +
238A TYR* 5.3 12.6 - - + +
239A GLN* 5.5 3.1 - - + -
270A LEU* 3.0 40.2 + - + +
271A SER* 3.5 8.3 - - - +
273A VAL* 1.3 75.5 - - - +
275A LYS* 1.3 68.5 + - + +
277A LEU* 2.9 19.5 - - - +
279A LEU* 3.8 37.0 + - + +
280A LEU* 5.2 7.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ARG* 3.3 13.6 + - - +
230A ALA* 4.3 17.4 + - + +
232A PHE* 3.7 20.8 + - - +
234A THR 5.4 2.0 + - - -
235A LYS* 4.5 17.8 - - - +
238A TYR* 5.7 11.8 - - - -
271A SER* 3.3 36.9 + - - +
272A ALA* 3.7 3.4 - - - +
273A VAL 3.2 0.4 - - - -
274A ILE* 1.3 84.6 - - + +
276A PHE* 1.3 63.8 + - - +
277A LEU 3.5 4.6 - - - +
278A GLU* 5.5 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LYS* 5.4 4.9 - - - -
124A SER* 4.0 10.5 - - - -
127A ASN* 3.8 26.6 + - + -
147A VAL* 3.7 26.5 - - + -
198A GLU* 3.6 23.3 - - - -
200A VAL* 3.8 17.9 - - + -
225A THR* 3.7 24.0 - - + -
227A ARG* 3.5 42.9 + - - +
272A ALA 2.9 17.6 + - - +
273A VAL* 3.1 10.5 + - - +
275A LYS* 1.3 81.0 - - - +
277A LEU* 1.3 74.0 + - + +
278A GLU* 3.9 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLY 5.0 1.3 - - - +
127A ASN* 3.8 30.1 - - + +
129A SER* 6.1 0.2 - - - +
147A VAL* 4.4 11.7 - - + +
166A VAL* 4.2 31.6 - - + -
168A SER* 6.4 1.3 - - - -
273A VAL* 3.2 19.9 + - + +
274A ILE* 2.9 18.5 - - - +
275A LYS* 3.7 4.5 - - - +
276A PHE* 1.3 96.0 - - + +
278A GLU* 1.3 59.6 + - - +
279A LEU* 2.8 25.7 + - + +
----------------------------------------------------------
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