Contacts of the helix formed by residues 212 - 227 (chain A) in PDB entry 2J86
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 212 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A GLU* 2.7 26.5 + - - +
211A PRO* 1.3 73.1 - - - +
213A VAL* 1.3 65.9 + - - +
214A GLN* 3.3 17.0 - - - +
215A LYS* 3.0 32.8 + - + +
216A ALA* 2.8 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ASP* 3.6 36.1 - - + +
3A VAL 4.2 1.8 - - - +
4A ALA* 3.8 13.3 - - + +
187A ARG* 4.4 7.9 - - - +
210A GLU 5.1 0.2 - - - -
211A PRO 3.5 2.7 + - - +
212A ASN* 1.3 77.6 - - - +
214A GLN* 1.3 61.2 + - + +
216A ALA* 3.8 3.0 - - - +
217A ALA* 2.9 32.1 + - - +
237A VAL* 3.5 35.4 - - + +
239A SER* 3.6 30.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ALA* 3.9 14.6 - - + -
212A ASN* 3.2 14.9 - - - +
213A VAL* 1.3 83.8 - - + +
215A LYS* 1.3 61.4 + - - +
217A ALA* 4.1 2.2 - - - +
218A ALA* 3.3 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A GLU* 3.5 20.4 - - + +
212A ASN* 3.0 38.1 + - + +
214A GLN* 1.3 76.0 - - - +
216A ALA* 1.3 58.8 + - - +
218A ALA* 3.4 5.0 + - - +
219A ALA* 2.8 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A TYR 3.4 24.2 - - - +
208A LEU* 4.4 8.1 - - - +
210A GLU* 3.4 16.1 - - + +
212A ASN 2.8 14.8 + - - +
213A VAL* 3.8 7.2 - - - +
215A LYS* 1.3 74.2 - - - +
217A ALA* 1.3 57.6 + - - +
219A ALA* 2.8 5.2 + - - +
220A LEU* 2.7 41.3 + - + +
237A VAL* 4.6 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ALA* 4.4 17.3 - - + +
5A GLY 5.1 0.2 - - - -
6A LEU* 4.1 13.0 - - + -
213A VAL 2.9 22.4 + - - +
214A GLN* 4.1 3.8 - - - +
216A ALA* 1.3 72.8 - - - +
218A ALA* 1.3 62.0 + - - +
220A LEU* 3.4 4.2 + - - +
221A VAL* 3.1 27.5 + - - +
235A VAL* 3.8 20.4 - - + +
237A VAL* 4.1 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.8 16.3 - - + +
214A GLN 3.3 16.3 + - - +
215A LYS* 3.7 5.2 - - - +
216A ALA 3.1 0.4 - - - -
217A ALA* 1.3 76.6 - - - +
219A ALA* 1.3 61.3 + - - +
221A VAL* 3.2 1.9 + - - +
222A ASP* 2.8 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A TYR* 3.6 30.0 - - + +
210A GLU* 5.7 2.5 - - + -
215A LYS 2.8 18.1 + - - +
216A ALA* 3.3 11.4 - - - +
218A ALA* 1.3 73.4 - - - +
220A LEU* 1.3 53.5 + - - +
222A ASP* 3.8 5.0 - - - +
223A ALA* 2.8 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 4.2 15.0 - - + -
195A LEU* 3.9 24.0 - - + +
199A LEU* 3.8 9.1 - - + +
204A ILE* 4.2 26.0 - - + +
207A TYR* 3.9 21.1 - - + -
208A LEU* 4.4 11.9 - - + +
216A ALA* 2.7 21.7 + - + +
217A ALA* 3.4 9.4 - - - +
219A ALA* 1.3 73.3 - - - +
221A VAL* 1.3 57.3 + - - +
223A ALA* 3.6 3.6 - - - +
224A ALA* 2.9 29.6 + - - +
235A VAL* 4.5 7.9 - - + -
237A VAL* 3.8 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.5 43.3 - - + +
8A ASP* 4.0 17.9 - - + +
217A ALA 3.1 7.1 + - - +
218A ALA 3.9 1.3 - - - +
220A LEU* 1.3 73.6 - - - +
222A ASP* 1.3 67.2 + - - +
224A ALA* 3.3 6.5 + - - +
225A LYS* 2.9 43.4 + - + +
233A VAL* 4.3 20.2 - - + +
235A VAL* 4.1 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ALA 2.8 22.3 + - - +
219A ALA* 3.8 5.7 - - - +
221A VAL* 1.3 74.5 - - - +
223A ALA* 1.3 60.1 + - - +
225A LYS* 3.2 6.8 + - - +
226A THR* 2.7 38.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LEU* 3.7 19.2 - - + +
203A VAL* 5.0 0.2 - - + -
207A TYR* 3.4 33.4 - - + +
219A ALA 2.8 22.9 + - - +
220A LEU 3.6 3.6 - - - +
222A ASP* 1.3 75.2 + - - +
224A ALA* 1.3 63.8 + - - +
226A THR* 2.9 19.3 + - - -
227A HIS* 3.2 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A GLY 4.6 9.9 - - - +
195A LEU* 4.7 3.8 - - + -
198A GLU* 3.5 12.8 - - + +
199A LEU* 3.8 19.4 - - + +
220A LEU 2.9 18.9 + - - +
221A VAL* 3.4 9.4 - - - +
223A ALA* 1.3 77.0 - - - +
225A LYS* 1.3 53.9 + - - +
227A HIS 3.3 5.5 + - - -
228A GLY 2.5 23.1 - - - +
233A VAL* 4.3 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ASP* 3.2 39.3 + - + +
10A GLY* 4.0 21.0 + - - -
11A LEU* 2.8 53.0 - - + +
221A VAL* 2.9 29.6 + - + +
222A ASP* 3.8 6.3 - - - +
224A ALA* 1.3 77.3 - - - +
226A THR* 1.3 56.8 + - - +
228A GLY 3.0 15.3 + - - +
229A GLY* 4.5 1.6 - - - -
233A VAL* 4.5 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 5.0 2.2 - - - +
222A ASP* 2.7 32.0 + - - -
223A ALA* 2.9 9.9 + - - -
225A LYS* 1.3 72.8 - - - +
227A HIS* 1.3 60.8 + - - +
228A GLY* 2.9 6.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A GLU 5.2 1.6 + - - -
198A GLU* 3.0 49.7 + - + +
199A LEU* 4.4 6.8 - - + +
223A ALA 3.2 9.0 + - - +
224A ALA 3.7 9.0 - - - +
225A LYS 3.3 0.4 - - - -
226A THR* 1.3 75.5 - - - +
228A GLY* 1.3 56.7 + - - +
51B ASP* 5.4 3.3 - - - +
----------------------------------------------------------
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