Contacts of the helix formed by residues 183 - 194 (chain D) in PDB entry 2X86
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 SER 183 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D VAL 4.2 5.6 - - - -
171D TYR* 3.5 23.9 - - - +
175D GLU* 2.7 34.7 + - - -
181D MET 3.9 0.6 + - - -
182D ALA* 1.3 78.2 - - - +
184D VAL* 1.3 65.0 + - - +
185D ALA* 3.5 9.5 - - - +
186D PHE* 3.0 16.5 + - - +
187D HIS* 3.1 18.4 + - - -
211D PHE* 6.5 0.7 - - - -
401D ADP 5.3 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D ALA 3.7 0.2 + - - -
183D SER* 1.3 69.5 - - - +
185D ALA* 1.3 66.6 + - - +
187D HIS* 3.1 9.5 + - + +
188D LEU* 2.9 44.8 + - + +
199D LYS 4.8 0.4 - - - +
200D LEU* 3.9 23.1 - - + -
211D PHE* 5.6 6.0 - - + -
243D PHE* 3.6 32.8 - - + -
246D VAL* 4.9 7.9 - - + -
401D ADP 3.6 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D TYR* 4.6 10.5 - - + -
183D SER* 3.5 11.0 - - - +
184D VAL* 1.3 79.7 - - - +
186D PHE* 1.3 63.6 + - - +
188D LEU* 3.3 3.2 + - - +
189D ASN* 3.0 24.1 + - - +
246D VAL* 4.2 21.8 - - + +
250D THR* 4.6 3.4 - - - +
299D VAL* 4.7 4.7 - - + -
302D TYR* 4.0 19.5 - - + -
303D MET* 3.6 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D GLU* 3.6 8.1 - - + +
176D GLY* 3.5 38.8 - - - -
179D GLY* 5.6 2.2 - - - -
182D ALA* 3.8 20.4 - - + -
183D SER* 3.0 16.0 + - - +
185D ALA* 1.3 80.0 - - - +
187D HIS* 1.3 71.4 + + - +
189D ASN* 3.2 5.5 + - - +
190D THR* 3.1 54.6 + - + +
302D TYR* 3.3 28.6 - - - +
306D LEU* 4.1 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D GLY 2.9 27.0 + - - -
180D SER* 3.8 14.0 - - - -
182D ALA* 3.1 24.0 + - - +
183D SER 3.1 13.3 + - - -
184D VAL* 3.1 10.8 + - + +
186D PHE* 1.3 89.5 - + - +
188D LEU* 1.3 59.2 + - + +
190D THR* 3.3 9.0 + - - -
191D GLN* 2.9 47.5 + - - +
199D LYS 6.1 0.7 - - - +
401D ADP 3.2 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D VAL* 2.9 35.4 + - + +
185D ALA* 3.7 3.8 - - - +
187D HIS* 1.3 76.9 - - + +
189D ASN* 1.3 63.9 + - - +
191D GLN* 3.4 15.9 + - - +
192D LEU* 2.9 30.8 + - + +
198D PRO* 3.8 14.1 - - + -
199D LYS 3.4 33.2 - - - +
200D LEU* 5.0 2.0 - - + -
246D VAL* 4.6 2.5 - - + -
247D ALA* 3.8 36.1 - - + +
250D THR* 4.1 19.3 - - + +
251D LEU* 5.5 1.1 - - + -
259D ILE* 4.7 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 189 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D ALA 3.0 17.1 + - - +
186D PHE 3.6 4.0 - - - +
188D LEU* 1.3 78.6 - - - +
190D THR* 1.3 67.6 + - - +
192D LEU* 3.3 2.9 + - - +
193D ASN* 3.0 42.9 + - - +
250D THR* 4.5 1.7 - - - +
254D HIS* 2.8 34.3 + - - -
303D MET* 3.6 10.1 - - - +
306D LEU* 3.6 39.0 + - + +
307D ASN* 3.4 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 190 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D PHE* 3.1 48.3 + - + +
187D HIS* 3.4 13.0 + - - -
189D ASN* 1.3 84.8 - - - +
191D GLN* 1.3 67.6 + - - +
193D ASN* 3.4 7.7 + - - +
194D ASN* 3.1 36.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 191 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D HIS* 2.9 32.1 + - - +
188D LEU* 3.4 15.2 - - - +
190D THR* 1.3 80.5 + - - +
192D LEU* 1.3 58.5 + - - +
194D ASN* 3.3 5.9 + - - +
196D GLU* 2.9 55.0 + - - +
197D SER 3.9 13.9 - - - +
198D PRO* 3.3 6.9 - - + +
199D LYS* 3.0 49.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D LEU* 2.9 21.1 + - + +
189D ASN 3.7 3.6 - - - +
191D GLN* 1.3 73.2 - - - +
193D ASN* 1.3 62.9 + - - +
194D ASN 3.1 4.7 - - - -
195D GLY* 3.2 6.9 + - - -
196D GLU 4.2 5.8 - - - +
198D PRO* 3.9 31.4 - - + -
250D THR* 3.9 7.9 - - + -
251D LEU* 3.8 21.8 - - + -
254D HIS* 3.8 37.9 - - + +
256D LYS* 2.8 43.3 + - - +
257D GLY* 4.1 18.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 193 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D ASN* 3.0 40.6 + - - +
190D THR* 3.9 7.0 - - - +
192D LEU* 1.3 75.0 - - - +
194D ASN* 1.3 62.7 + - - +
195D GLY 3.3 1.2 + - - -
254D HIS* 3.4 17.9 + - - -
256D LYS* 5.2 0.2 - - - +
306D LEU 5.2 1.4 + - - -
307D ASN* 3.4 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 194 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D THR* 3.1 27.9 + - - +
191D GLN* 3.6 7.1 - - - +
192D LEU 3.1 1.2 - - - -
193D ASN* 1.3 81.1 - - - +
195D GLY* 1.3 54.7 + - - +
196D GLU* 3.0 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