Contacts of the helix formed by residues 264 - 278 (chain D) in PDB entry 1OJ7
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 TRP 264 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D HIS* 3.8 17.0 - + - -
201D GLU* 2.8 35.8 + - + -
202D GLN* 4.0 15.5 - - + -
252D LEU* 3.6 35.9 - - + -
262D GLN* 2.8 42.2 + - + +
263D ASP* 1.3 71.6 - - - +
265D ALA* 1.3 62.6 + - - +
266D THR 3.3 2.5 - - - -
267D HIS* 3.2 45.1 + + + +
268D MET* 3.0 36.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
263D ASP* 3.0 20.0 + - - +
264D TRP* 1.3 74.5 - - - +
266D THR* 1.3 66.1 + - - +
268D MET* 3.2 4.8 + - - +
269D LEU* 3.0 29.2 + - + +
292D LEU* 3.6 20.0 - - + -
368D LEU* 3.9 15.9 - - + +
369D GLY 3.8 10.1 - - - +
374D ILE* 3.7 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D VAL* 4.3 5.6 - - + -
201D GLU* 3.4 17.1 + - - +
263D ASP* 4.6 0.7 + - - -
264D TRP 3.3 0.4 - - - -
265D ALA* 1.3 76.7 - - - +
267D HIS* 1.3 58.2 + - - +
269D LEU* 3.6 1.7 + - - +
270D GLY* 2.9 26.0 + - - -
285D LEU* 3.9 25.8 - - + +
288D VAL* 3.9 15.3 - - + +
289D LEU* 3.6 48.3 - - + +
292D LEU* 3.7 16.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 267 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D ASP* 3.5 0.2 + - - -
197D VAL* 3.7 11.7 - - + -
198D HIS* 3.2 34.5 + + - -
201D GLU* 2.8 21.5 + - + +
264D TRP* 3.2 28.3 + + + +
266D THR* 1.3 81.4 - - - +
268D MET* 1.3 70.5 + - + +
270D GLY* 3.7 0.2 - - - -
271D HIS* 2.9 42.2 + + - +
281D HIS* 3.2 33.3 + + - -
285D LEU* 3.6 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 268 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D ALA* 5.6 7.0 - - + -
264D TRP* 3.0 28.4 + - + +
265D ALA 3.2 4.2 + - - +
267D HIS* 1.3 86.5 - - + +
269D LEU* 1.3 62.0 + - - +
270D GLY 3.4 0.3 + - - -
271D HIS* 3.5 37.2 + - + +
272D GLU* 3.6 18.0 + - - +
360D LEU* 4.0 3.6 - - - +
365D MET* 3.6 41.0 - - + +
368D LEU* 3.9 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 269 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D ALA 3.0 18.8 + - - +
266D THR 4.0 2.9 - - - +
268D MET* 1.3 75.6 - - - +
270D GLY* 1.3 61.2 + - - +
272D GLU 3.4 6.9 + - - -
273D LEU* 3.6 5.4 + - - +
288D VAL* 3.9 13.7 - - + -
292D LEU* 4.5 4.3 - - + -
360D LEU* 3.5 23.3 - - + -
368D LEU* 3.9 11.9 - - + -
374D ILE* 5.4 1.3 - - + -
379D SER* 3.4 28.3 - - - +
382D ILE* 3.8 42.0 - - + -
383D TYR* 2.6 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 270 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D THR 2.9 17.9 + - - -
267D HIS* 3.7 2.2 - - - -
268D MET 3.2 0.2 - - - -
269D LEU* 1.3 73.3 - - - +
271D HIS* 1.3 66.0 + - - +
272D GLU 3.1 2.5 - - - -
273D LEU* 3.0 15.0 + - - -
274D THR* 3.1 10.6 + - - -
281D HIS* 5.4 0.2 - - - -
284D THR* 3.3 38.7 + - - +
285D LEU* 5.1 0.7 - - - -
288D VAL* 4.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 271 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D VAL* 3.9 31.8 - - + +
160D LYS* 3.7 45.1 + - + +
161D GLN* 5.1 2.4 - - - -
162D ALA* 4.8 7.4 + - + +
267D HIS* 2.9 30.4 + + + +
268D MET* 3.7 34.5 - - + +
269D LEU 3.4 0.2 - - - -
270D GLY* 1.3 75.6 - - - +
272D GLU* 1.3 61.6 + - + +
274D THR* 3.2 5.0 + - - +
275D ALA* 3.0 28.9 + - - +
281D HIS* 3.9 26.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 272 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D LYS 4.9 4.4 + - - +
268D MET 3.6 7.0 - - - +
269D LEU 3.4 7.8 + - - +
270D GLY 3.1 0.6 - - - -
271D HIS* 1.3 80.0 - - - +
273D LEU* 1.3 56.7 + - - +
275D ALA* 4.0 10.1 - - - +
276D MET* 3.1 32.2 + - - +
356D LEU* 3.3 17.6 - - + +
359D LYS* 3.4 31.4 - - + +
360D LEU* 3.5 33.3 + - + +
363D HIS* 2.7 36.1 + - - +
365D MET* 4.8 2.4 - - - +
383D TYR* 3.8 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 273 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D LEU 3.6 8.3 + - - +
270D GLY 3.0 7.3 + - - +
272D GLU* 1.3 75.4 - - - +
274D THR* 1.3 59.5 + - - +
277D HIS* 2.9 45.1 + - + +
278D GLY 3.6 0.7 + - - -
279D LEU* 4.1 7.6 + - + +
284D THR* 3.6 25.6 - - + +
287D ILE* 4.6 5.4 - - + -
288D VAL* 3.9 28.0 - - + -
343D LEU* 4.0 30.5 - - + -
348D LEU* 5.2 0.7 - - + -
352D SER* 5.2 0.4 - - - +
356D LEU* 3.5 30.5 - - + -
383D TYR* 4.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 274 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ASN* 3.3 38.4 - - + +
153D SER* 5.7 0.2 - - - +
155D LYS* 5.9 1.7 + - - +
160D LYS* 3.6 16.5 - - + -
270D GLY 3.1 6.6 + - - -
271D HIS* 3.2 7.3 + - - -
273D LEU* 1.3 73.8 - - - +
275D ALA* 1.3 63.3 + - - +
278D GLY* 2.9 24.4 + - - -
279D LEU 2.8 30.3 + - - +
281D HIS* 3.8 10.6 + - - -
284D THR* 3.3 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 275 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D SER* 6.0 0.7 - - - -
158D GLY* 3.5 35.1 - - - +
159D ASP 4.3 1.3 - - - +
160D LYS* 3.9 22.6 - - + +
271D HIS 3.0 17.0 + - - +
272D GLU* 4.0 10.3 - - - +
274D THR* 1.3 77.4 - - - +
276D MET* 1.3 60.8 + - - +
278D GLY 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 276 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D GLU* 3.1 18.7 + - - +
275D ALA* 1.3 81.6 - - - +
277D HIS* 1.3 84.4 + - + +
278D GLY 3.8 0.2 - - - -
352D SER* 3.9 13.5 - - - +
355D ALA* 3.6 37.5 - - + +
356D LEU* 3.6 25.6 - - + +
359D LYS* 4.4 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 277 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D LEU* 2.9 27.6 + - + +
276D MET* 1.3 99.5 + - + +
278D GLY* 1.3 63.1 + - - +
279D LEU* 3.3 8.1 + - + +
343D LEU* 6.0 0.2 - - + -
348D LEU* 3.4 51.2 - - + +
352D SER* 2.7 40.8 + - - -
356D LEU* 4.8 0.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 278 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ASN* 4.8 7.3 + - - -
186D ARG* 5.7 1.4 + - - -
273D LEU 3.6 0.2 + - - -
274D THR* 2.9 19.9 + - - -
275D ALA 4.7 0.2 - - - -
276D MET 3.8 0.4 - - - -
277D HIS* 1.3 78.0 - - - +
279D LEU* 1.3 66.2 + - - +
280D ASP* 3.6 4.5 + - - +
----------------------------------------------------------
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