Contacts of the helix formed by residues 237 - 252 (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 ASN 237 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D GLU* 3.1 46.8 + - + +
235D PRO 3.4 0.6 - - - -
236D GLU* 1.3 75.0 - - - +
238D TYR* 1.3 64.6 + - - +
239D ASP* 3.2 13.0 + - - +
240D VAL* 3.1 34.0 + - + +
241D ARG* 3.0 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A GLY* 5.5 1.1 - - - -
1A LEU* 4.3 22.7 + - + +
2A ASN 5.8 0.2 - - - -
3A ASN* 4.1 4.0 + - - -
14D PHE* 4.1 5.0 - - - -
15D GLY* 3.3 12.1 - - - -
16D LYS* 3.1 43.5 + - + -
177D PRO* 3.6 28.3 - - + +
178D VAL* 4.0 9.4 - - + -
181D TYR* 3.2 26.7 - - - +
236D GLU 3.2 6.6 + - - +
237D ASN* 1.3 71.1 + - - +
239D ASP* 1.3 67.7 + - - +
241D ARG* 3.3 1.0 + - - +
242D ALA* 2.7 45.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 239 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2A LYS 4.2 7.8 - - - +
-1A ALA 4.0 10.4 - - - +
0A GLY* 3.5 25.2 + - - -
1A LEU 4.6 0.7 + - - -
209A ASP* 3.5 33.6 - - + +
237D ASN* 3.2 9.6 + - - +
238D TYR* 1.3 86.6 - - - +
240D VAL* 1.3 58.3 + - + +
242D ALA* 3.6 6.3 - - - +
243D ASN* 3.0 36.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 240 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ASP* 5.2 3.4 - - - +
227D ASP* 3.4 40.5 - - + +
230D LYS* 3.8 27.1 - - + +
231D ALA* 3.5 25.6 - - + +
234D GLU* 4.8 1.8 - - - +
237D ASN* 3.1 33.7 + - + +
239D ASP* 1.3 77.2 - - + +
241D ARG* 1.3 64.5 + - - +
243D ASN* 3.2 4.5 + - - +
244D VAL* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 241 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D PRO* 5.5 3.6 - - - +
177D PRO* 4.1 6.8 - - + +
180D THR* 2.9 53.2 + - - +
181D TYR* 3.6 22.8 + - + +
183D LEU* 3.8 5.5 - - - +
188D VAL* 3.6 29.9 - - - +
231D ALA* 3.8 28.8 + - - +
234D GLU 4.4 1.3 - - - -
235D PRO* 2.8 55.7 + - - +
237D ASN 3.0 22.0 + - - +
238D TYR 3.9 2.9 - - - +
240D VAL* 1.3 75.1 - - - +
242D ALA* 1.3 57.0 + - - +
244D VAL* 3.5 7.5 + - - +
245D MET* 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LEU* 4.5 12.5 - - + +
209A ASP 6.1 0.4 - - - +
14D PHE* 4.0 13.1 - - + -
177D PRO* 3.8 23.5 - - + +
238D TYR* 2.7 33.6 + - + +
239D ASP* 3.6 7.9 - - - +
241D ARG* 1.3 72.4 - - - +
243D ASN* 1.3 56.6 + - - +
245D MET* 3.8 1.7 - - - +
246D TRP* 3.0 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LEU* 5.7 2.8 - - - +
209A ASP* 3.3 32.2 + - - +
210A ALA* 3.7 2.8 - - - -
211A LYS* 2.9 33.6 + - - +
212A ILE* 4.3 7.1 + - - +
223D THR* 4.2 13.3 - - + +
227D ASP* 2.8 30.1 + - + +
239D ASP 3.0 18.7 + - - +
240D VAL 3.2 2.4 + - - +
242D ALA* 1.3 76.8 - - - +
244D VAL* 1.3 57.2 + - - +
246D TRP* 3.9 3.3 - - - +
247D ALA* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D PRO* 4.5 18.4 - - + +
188D VAL* 5.6 3.6 - - + +
191D GLY 5.6 0.7 - - - -
192D VAL* 4.2 22.0 - - + +
223D THR* 5.7 1.6 - - + +
224D LEU* 4.6 12.3 - - + +
227D ASP* 3.9 29.4 - - + +
228D GLY* 4.2 8.3 - - - +
231D ALA* 4.4 11.9 - - + -
240D VAL 3.1 15.9 + - - +
241D ARG* 3.9 9.4 - - - +
242D ALA 3.3 0.2 - - - -
243D ASN* 1.3 72.8 - - - +
245D MET* 1.3 66.8 + - - +
247D ALA* 3.4 6.1 + - - +
248D ALA* 3.1 23.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D PHE* 4.3 8.3 - - + -
137D LEU* 3.8 37.0 - - + +
140D PRO* 3.6 20.6 - - + +
145D GLU* 4.7 0.5 - - - +
175D LEU* 3.8 27.8 - - + -
176D ASP 4.0 10.5 - - - +
177D PRO* 3.6 29.2 - - + -
180D THR* 3.6 25.4 - - + -
241D ARG 3.0 18.2 + - - +
242D ALA* 3.8 5.6 - - - +
244D VAL* 1.3 77.6 - - - +
246D TRP* 1.3 62.0 + - - +
248D ALA* 3.3 4.7 + - - +
249D THR* 3.2 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LEU* 5.6 2.5 - - + -
4A PHE* 3.9 22.2 - + - -
6A LEU* 3.8 22.7 - - + -
212A ILE* 3.8 27.8 - - + +
213A HIS* 3.5 30.6 + + - -
255A LEU* 3.6 22.0 + - + +
258A ALA* 5.2 1.1 - - + -
12D ILE* 3.9 26.9 - - + -
14D PHE* 4.0 20.2 - + + -
175D LEU* 4.2 1.6 - - + -
242D ALA 3.0 18.1 + - - +
243D ASN* 4.1 3.8 - - - +
245D MET* 1.3 74.2 - - - +
247D ALA* 1.3 66.3 + - - +
249D THR* 3.2 26.8 + - + -
250D GLN* 3.0 52.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ILE* 3.9 26.1 - - + +
195D ALA* 4.8 0.7 - - - -
220D ILE* 4.0 8.6 - - + +
223D THR* 4.7 3.8 - - + -
224D LEU* 3.9 27.1 - - + -
243D ASN 3.0 19.6 + - - +
244D VAL 3.6 4.9 - - - +
245D MET 3.3 0.2 - - - -
246D TRP* 1.3 77.0 - - - +
248D ALA* 1.3 56.3 + - - +
250D GLN* 3.2 3.7 + - - +
251D ALA* 3.0 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D PRO* 4.0 8.5 - - + +
141D ALA* 3.8 30.0 - - - +
142D THR 4.7 0.5 - - - -
143D GLY* 3.7 15.1 + - - +
145D GLU* 4.4 3.6 - - - +
191D GLY 5.1 0.7 - - - +
195D ALA* 3.8 23.5 - - + +
198D HIS* 5.4 0.2 + - - -
244D VAL* 3.1 17.7 + - + +
245D MET 3.6 5.2 - - - +
246D TRP 3.3 0.2 - - - -
247D ALA* 1.3 75.1 - - - +
249D THR* 1.3 64.7 + - - +
251D ALA* 3.4 12.0 + - - +
252D LEU* 4.0 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ILE* 4.5 5.6 - - + -
143D GLY* 4.5 2.7 - - - -
145D GLU* 2.6 24.0 + - + +
146D SER* 3.5 22.4 + - - +
175D LEU* 3.4 19.8 - - + +
245D MET* 3.2 14.3 + - - +
246D TRP* 3.5 32.7 - - + -
248D ALA* 1.3 77.1 - - - +
250D GLN* 1.3 66.6 + - - +
251D ALA 3.2 1.2 + - - -
252D LEU 3.5 8.7 + - - -
253D ASN* 3.5 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 5.4 0.5 - - - +
212A ILE* 4.3 10.8 - - + -
216A PHE* 4.0 11.3 - - + -
255A LEU* 3.6 33.9 - - - +
220D ILE* 3.6 20.6 - - + +
246D TRP* 3.0 55.5 + - - +
247D ALA* 3.2 4.9 + - - +
249D THR* 1.3 78.1 - - - +
251D ALA* 1.3 61.3 + - - +
252D LEU 3.3 0.7 + - - -
253D ASN* 3.5 32.9 + - - +
255D LEU* 4.2 6.9 - - - +
256D ILE* 4.1 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D ALA* 3.6 18.4 - - + +
198D HIS* 4.0 10.7 - - + +
199D THR* 3.6 19.7 - - - +
202D GLN* 2.8 26.5 + - - -
220D ILE* 4.0 9.2 - - + -
247D ALA 3.0 16.4 + - - +
248D ALA 3.7 9.0 - - - +
249D THR 3.1 1.2 - - - -
250D GLN* 1.3 78.5 - - - +
252D LEU* 1.3 59.8 + - - +
253D ASN 4.0 0.2 - - - -
256D ILE* 3.7 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D THR 3.6 17.5 - - - +
143D GLY* 4.1 4.7 - - - +
147D ASN* 3.2 31.5 + - + +
198D HIS* 3.5 38.6 - - + +
202D GLN* 3.7 17.5 - - - +
248D ALA 4.0 1.4 + - - -
249D THR 3.5 5.2 + - - -
251D ALA* 1.3 78.6 - - + +
253D ASN* 1.3 60.7 + - - +
254D GLY* 3.4 5.8 + - - +
256D ILE* 5.8 0.2 - - - -
262D GLN* 5.9 0.2 - - - +
264D TRP* 3.6 32.3 - - + -
----------------------------------------------------------
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