Contacts of the helix formed by residues 192 - 205 (chain N) 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 N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189N ALA* 4.9 9.0 - - - -
190N GLY 2.9 8.4 - - - -
191N SER* 1.3 79.4 - - - +
193N GLY* 1.3 64.1 + - - +
194N THR 3.3 3.1 + - - -
195N LEU* 3.6 6.6 + - - +
196N ALA* 3.1 23.1 + - - +
223N MET* 5.9 3.1 - - - -
227N LEU* 3.9 14.9 - - - +
230N LEU* 4.8 1.6 - - - -
1141N 5PA 2.9 10.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 193 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57N LYS* 3.7 21.3 - - - -
159N ALA* 4.6 5.4 - - - +
164N THR* 4.0 10.4 + - - +
191N SER* 3.1 13.0 + - - -
192N GLY* 1.3 75.8 - - - +
194N THR* 1.3 66.1 + - - +
196N ALA* 3.1 3.8 + - - +
197N GLY* 3.0 16.8 + - - -
230N LEU* 4.2 15.0 - - - -
1141N 5PA 3.7 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 194 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53N ASN* 2.8 20.7 + - - +
57N LYS* 3.1 9.7 + - - +
167N TYR* 3.7 35.6 - - + +
187N VAL* 3.7 33.2 - - + -
188N ALA 4.8 2.7 - - - -
192N GLY 3.3 0.4 - - - -
193N GLY* 1.3 73.3 - - - +
195N LEU* 1.3 53.1 + - - +
196N ALA 2.8 2.3 + - - -
197N GLY* 2.8 5.4 + - - -
198N LEU* 2.8 35.2 + - + +
308N THR* 4.7 1.1 - - + -
1141N 5PA 2.5 27.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187N VAL* 4.0 13.7 - - + -
188N ALA 4.8 4.5 - - - +
189N ALA* 4.8 9.0 - - + -
192N GLY* 3.6 7.5 + - - +
193N GLY 3.6 0.4 - - - -
194N THR* 1.3 79.0 - - - +
196N ALA* 1.3 51.8 + - - +
198N LEU* 3.7 11.9 - - + -
199N SER* 2.6 35.4 + - - +
211N PRO* 3.8 16.6 - - + +
212N VAL 4.0 2.2 - - - +
213N GLY* 3.7 31.4 - - - +
227N LEU* 3.7 26.9 - - + -
246N PRO* 3.3 33.2 - - + -
247N GLU 4.4 1.1 - - - +
248N LEU* 5.3 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 196 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164N THR* 3.6 7.4 - - + +
192N GLY 3.1 12.5 + - - +
193N GLY 3.1 10.1 + - - +
194N THR 2.8 0.8 + - - -
195N LEU* 1.3 77.5 - - - +
197N GLY* 1.3 61.4 + - - +
198N LEU 3.1 0.7 - - - -
199N SER* 3.1 1.8 + - - -
200N LEU* 2.8 31.9 + - - +
227N LEU* 4.1 1.6 - - + -
230N LEU* 3.5 26.0 - - + -
231N ILE* 3.5 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 197 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164N THR* 3.0 33.7 - - - +
167N TYR* 4.0 1.8 - - - -
168N VAL* 3.4 19.7 - - - +
193N GLY 3.0 7.0 + - - -
194N THR 2.8 6.8 + - - -
196N ALA* 1.3 75.2 - - - +
198N LEU* 1.3 53.2 + - - +
201N GLY* 2.7 33.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 198 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167N TYR* 3.8 18.1 - - + +
171N VAL* 4.2 18.1 - - + +
174N ILE* 5.3 4.9 - - + -
185N ILE* 3.6 44.9 - - + +
187N VAL* 4.5 12.6 - - + -
194N THR* 2.8 15.6 + - + +
195N LEU* 3.6 11.7 - - + +
197N GLY* 1.3 77.6 - - - +
199N SER* 1.3 55.6 + - - +
201N GLY* 3.6 0.7 - - - -
202N LEU* 3.0 43.7 + - + +
211N PRO* 4.4 15.5 - - + -
306N ILE* 4.2 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 199 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195N LEU* 2.6 21.0 + - - +
196N ALA* 3.1 7.9 + - - -
198N LEU* 1.3 75.3 - - - +
200N LEU* 1.3 69.1 + - - +
201N GLY 3.0 0.7 - - - -
202N LEU* 3.5 1.4 + - - +
203N SER* 3.0 25.3 + - - -
211N PRO* 3.4 15.7 - - - +
231N ILE* 4.7 11.7 - - - -
243N GLU 5.4 3.5 - - - +
245N ARG* 5.4 1.6 - - - -
246N PRO* 3.1 37.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164N THR* 4.7 0.7 - - + -
165N LEU* 4.6 1.1 - - + -
168N VAL* 3.8 18.8 - - + -
196N ALA 2.8 18.7 + - - +
197N GLY 3.7 2.9 - - - +
199N SER* 1.3 71.8 - - - +
201N GLY* 1.3 70.4 + - - +
203N SER* 3.1 9.5 - - - +
204N ILE* 3.0 45.0 + - + +
231N ILE* 4.6 10.4 - - + +
234N ALA* 3.7 32.5 - - + -
235N ALA* 3.7 18.6 - - + +
238N LEU* 3.7 14.1 - - + -
240N VAL* 4.0 11.0 - - + -
242N VAL* 6.0 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 201 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5N ILE* 5.0 1.8 - - - -
168N VAL* 4.1 15.4 - - - +
171N VAL* 3.7 20.0 - - - -
197N GLY 2.7 19.5 + - - -
198N LEU 3.6 0.9 - - - -
199N SER 3.0 0.4 - - - -
200N LEU* 1.3 80.4 - - - +
202N LEU* 1.3 52.2 + - - -
203N SER 2.5 15.1 + - - -
204N ILE* 2.6 16.1 + - - +
205N LEU* 3.4 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171N VAL* 4.0 19.0 - - + +
185N ILE* 3.6 28.0 - - + -
198N LEU* 3.0 29.1 + - + +
199N SER 4.1 1.8 - - - +
201N GLY* 1.3 67.5 - - - -
203N SER* 1.3 58.0 + - - +
205N LEU* 3.7 4.2 + - - +
206N ASN 3.2 1.9 + - - -
207N GLU* 3.0 38.2 + - + +
209N ILE* 3.4 49.8 - - + +
211N PRO* 3.5 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 203 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199N SER 3.0 13.4 + - - -
200N LEU* 3.1 15.1 + - - +
201N GLY 2.5 6.7 + - - -
202N LEU* 1.3 70.3 - - - +
204N ILE* 1.3 61.7 + - - +
206N ASN* 2.5 29.8 + - - +
241N LYS 3.5 15.9 + - - -
242N VAL* 4.5 1.3 - - - -
243N GLU* 2.9 49.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 204 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4N LYS* 3.1 49.0 + - + +
5N ILE* 4.1 15.7 - - + -
8N LEU* 3.5 30.7 - - + -
168N VAL* 4.3 10.5 - - + -
200N LEU* 3.0 36.7 + - + +
201N GLY 2.6 12.1 + - - +
203N SER* 1.3 78.0 + - - +
205N LEU* 1.3 57.0 + - - +
206N ASN* 3.3 4.2 + - - +
238N LEU* 3.5 20.4 - - + -
240N VAL* 3.7 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2N HIS* 3.3 49.6 - - + +
4N LYS* 4.7 4.9 - - + -
5N ILE* 4.0 20.4 - - + -
171N VAL* 3.7 21.8 - - + +
175N ALA* 3.7 30.5 - - + -
201N GLY 3.4 2.9 + - - +
202N LEU* 4.1 3.8 - - - +
203N SER 3.1 0.6 - - - -
204N ILE* 1.3 77.1 - - - +
206N ASN* 1.3 71.2 + - - +
207N GLU* 3.0 29.2 + - + +
----------------------------------------------------------
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