Contacts of the helix formed by residues 192 - 206 (chain A) in PDB entry 1J0B
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 GLY 192 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ALA* 4.7 10.8 - - - -
190A GLY 3.1 5.0 - - - -
191A SER* 1.3 79.7 - - - +
193A GLY* 1.3 56.9 + - - -
194A THR 3.3 2.9 - - - -
195A LEU* 3.7 3.9 + - - +
196A ALA* 3.1 28.2 + - - +
223A MET* 6.3 3.6 - - - -
227A LEU* 3.5 18.0 - - - +
230A LEU* 4.3 2.7 - - - -
1011A 5PA 2.8 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LYS* 3.8 11.9 - - - -
159A ALA* 3.7 17.0 - - - -
164A THR* 3.1 22.5 + - - +
167A TYR* 5.7 0.3 - - - +
191A SER* 3.3 6.4 + - - -
192A GLY* 1.3 76.1 - - - +
194A THR* 1.3 64.4 + - - +
196A ALA* 3.3 4.5 - - - +
197A GLY* 3.5 1.6 + - - -
230A LEU* 3.6 17.5 - - - -
1011A 5PA 3.4 7.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ASN* 3.1 12.1 + - - +
57A LYS* 2.9 21.5 + - - +
167A TYR* 3.9 33.6 - - + +
187A VAL* 3.2 35.7 - - + -
188A ALA 4.7 2.2 - - - -
193A GLY* 1.3 73.4 - - - +
195A LEU* 1.3 63.3 + - - +
196A ALA 2.9 5.4 + - - -
197A GLY* 3.0 3.3 + - - -
198A LEU* 3.0 22.0 + - + +
308A THR* 4.7 1.1 - - + -
1011A 5PA 2.7 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A VAL* 3.9 19.2 - - + +
188A ALA 5.0 1.2 + - - +
189A ALA* 4.6 17.5 - - + -
192A GLY* 3.7 7.3 + - - +
193A GLY 3.6 0.2 - - - -
194A THR* 1.3 79.7 - - - +
196A ALA* 1.3 54.2 + - - +
198A LEU* 4.0 6.1 - - + -
199A SER* 2.5 42.5 + - - +
211A PRO* 4.1 13.0 - - + -
212A VAL 4.5 0.2 - - - +
213A GLY* 3.9 29.6 - - - +
227A LEU* 3.6 30.7 - - + -
246A PRO* 3.8 21.8 - - + -
247A GLU 4.4 8.7 - - - +
248A LEU* 4.9 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A THR* 3.7 5.8 - - - +
192A GLY 3.1 19.8 + - - +
193A GLY 3.3 5.2 - - - +
194A THR 2.9 0.8 - - - -
195A LEU* 1.3 81.6 - - - +
197A GLY* 1.3 59.2 + - - +
199A SER* 3.6 0.9 - - - -
200A LEU* 3.5 15.1 + - - +
227A LEU* 4.0 8.7 - - + +
230A LEU* 3.2 28.9 - - + -
231A ILE* 3.5 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A THR* 3.5 33.3 + - - -
167A TYR* 4.3 1.1 - - - -
168A VAL* 3.6 15.2 - - - +
193A GLY 3.5 4.2 + - - -
194A THR 3.0 5.1 + - - -
196A ALA* 1.3 75.1 - - - +
198A LEU* 1.3 57.1 + - - +
199A SER 3.1 1.8 - - - -
200A LEU* 2.8 22.1 + - - +
201A GLY 2.8 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A TYR* 4.1 11.6 - - + +
171A VAL* 3.6 18.8 - - + +
174A ILE* 5.7 1.3 - - + -
185A ILE* 4.1 35.4 - - + +
187A VAL* 3.9 28.5 - - + -
194A THR* 3.0 16.7 + - + +
195A LEU* 3.8 12.6 - - + +
197A GLY* 1.3 75.9 - - - +
199A SER* 1.3 63.0 + - - +
201A GLY 3.5 0.5 + - - -
202A LEU* 3.0 44.9 + - + +
211A PRO* 4.8 3.4 - - + -
306A ILE* 4.7 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU 2.5 24.7 + - - -
196A ALA 3.6 6.2 + - - -
197A GLY 3.1 0.2 - - - -
198A LEU* 1.3 74.7 - - - +
200A LEU* 1.3 60.5 + - - +
202A LEU* 3.4 0.9 + - - +
203A SER* 2.8 32.0 + - - -
211A PRO* 3.7 20.1 - - - +
231A ILE* 4.2 13.5 - - - +
244A VAL 5.8 1.6 - - - -
245A ARG 5.4 2.2 - - - -
246A PRO* 3.2 31.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A THR* 4.1 5.6 - - + -
165A LEU* 4.7 1.1 - - + -
168A VAL* 3.5 21.8 - - + -
196A ALA 3.5 4.8 + - - +
197A GLY* 2.8 18.4 + - - +
199A SER* 1.3 79.1 - - - +
201A GLY* 1.3 55.0 + - - +
203A SER* 3.0 10.1 + - - +
204A ILE* 2.9 38.9 + - + +
231A ILE* 4.2 15.9 - - + +
234A ALA* 3.8 29.6 - - + -
235A ALA* 4.4 9.4 - - + -
238A LEU* 4.1 13.0 - - + -
240A VAL* 3.7 29.4 - - + -
241A LYS 5.5 0.2 - - - +
242A VAL* 6.0 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 3.7 9.0 - - - +
168A VAL* 4.3 9.7 - - - +
171A VAL* 3.2 28.3 - - - -
197A GLY 2.8 14.7 + - - -
198A LEU 3.5 0.2 + - - -
200A LEU* 1.3 74.3 - - - +
202A LEU* 1.3 57.0 + - - +
204A ILE* 4.5 1.8 - - - -
205A LEU* 2.8 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A VAL* 4.0 16.2 - - + -
185A ILE* 4.0 12.3 - - + -
198A LEU* 3.0 38.6 + - + +
199A SER 3.7 3.1 - - - +
201A GLY* 1.3 75.5 - - - +
203A SER* 1.3 59.0 + - - +
205A LEU* 4.2 9.6 - - + +
206A ASN* 3.0 25.1 + - - -
207A GLU* 4.3 4.4 + - + +
209A ILE* 3.5 66.1 + - + +
210A ARG 4.3 2.0 - - - +
211A PRO* 4.1 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS* 5.2 0.2 + - - -
199A SER 2.8 18.8 + - - -
200A LEU* 3.1 12.0 - - - +
202A LEU* 1.3 78.6 - - - +
204A ILE* 1.3 64.0 + - - +
206A ASN* 3.6 19.6 + - - +
240A VAL* 5.8 0.2 - - - +
241A LYS 3.5 11.1 + - - -
242A VAL* 4.3 3.8 - - - -
243A GLU* 3.4 43.9 + - - +
244A VAL 6.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS* 2.5 50.2 + - + +
5A ILE* 4.3 11.7 - - + -
8A LEU* 3.1 39.0 - - + -
168A VAL* 4.8 7.0 - - + -
200A LEU* 2.9 23.5 + - + +
201A GLY* 4.1 3.4 - - - +
203A SER* 1.3 76.4 - - - +
205A LEU* 1.3 65.4 + - - +
206A ASN* 4.0 1.2 - - - +
238A LEU* 3.8 19.3 - - + -
240A VAL* 3.7 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HIS* 3.8 37.7 + - + +
4A LYS* 4.9 4.1 + - + +
5A ILE* 3.5 25.4 - - + -
171A VAL* 3.5 22.4 - - + +
175A ALA* 3.5 25.6 - - + -
201A GLY 2.8 22.7 + - - +
202A LEU* 4.2 13.9 - - + +
204A ILE* 1.3 75.8 - - - +
206A ASN* 1.3 69.5 + - - +
207A GLU* 3.2 25.5 - - + +
209A ILE* 5.4 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS* 5.1 5.9 - - - +
202A LEU 3.0 16.2 + - - -
203A SER 3.9 12.3 + - - +
204A ILE 3.3 6.0 + - - +
205A LEU* 1.3 80.4 - - - +
207A GLU* 1.3 70.7 + - - +
208A ASP* 4.5 3.1 - - - +
243A GLU* 4.3 15.6 + - - +
37Q ASP* 5.6 2.9 + - - +
301Q GLU* 5.1 13.6 + - - +
----------------------------------------------------------
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