Contacts of the helix formed by residues 207 - 222 (chain B) in PDB entry 1JPP
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 ASP 207 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ASN* 3.2 32.5 + - - +
205B THR* 3.3 8.1 + - - +
206B ASN* 1.3 83.3 - - - +
208B VAL* 1.3 82.2 + - - +
209B GLU* 4.0 9.9 + - - +
210B THR* 3.6 13.3 + - - +
211B ALA* 3.9 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ASN 5.6 1.3 - - - +
207B ASP* 1.3 79.9 + - - +
209B GLU* 1.3 70.3 + - + +
210B THR 3.2 1.6 - - - -
211B ALA* 2.8 24.2 + - - +
212B ARG* 2.9 14.5 + - + +
248B VAL* 4.5 34.3 - - + -
251B VAL* 4.9 1.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B VAL* 6.3 2.2 - - + -
207B ASP* 4.0 7.7 + - - +
208B VAL* 1.3 83.8 - - + +
210B THR* 1.3 60.5 + - - +
212B ARG* 3.5 39.6 + - + +
213B CYS* 2.8 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B VAL* 4.8 1.8 - - + +
169B ASN* 2.8 42.3 + - - +
172B ALA* 4.3 16.2 - - + -
173B VAL* 6.2 1.3 - - - -
201B THR* 4.1 19.5 - - + -
205B THR* 3.5 29.8 - - - +
207B ASP* 3.6 9.3 + - - -
208B VAL 3.2 0.8 - - - -
209B GLU* 1.3 77.6 - - - +
211B ALA* 1.3 57.4 + - - +
213B CYS* 3.8 4.9 - - - +
214B THR* 2.9 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B MET* 5.0 5.0 - - - +
205B THR* 4.3 12.3 - - + +
207B ASP 3.9 10.5 + - - +
208B VAL* 2.8 11.9 + - - +
210B THR* 1.3 77.2 - - - +
212B ARG* 1.3 56.6 + - - +
213B CYS 2.9 10.2 + - - -
214B THR* 3.1 7.5 + - - -
215B ALA* 2.9 30.9 + - - +
243B MET* 5.2 7.2 - - - -
251B VAL* 4.6 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B HIS* 4.5 13.1 + - - -
208B VAL* 2.9 19.0 + - + +
209B GLU* 3.5 32.8 + - - +
211B ALA* 1.3 75.0 - - - +
213B CYS* 1.3 89.0 + - - +
215B ALA* 4.5 3.6 - - - -
216B GLY* 4.2 10.0 + - - -
248B VAL* 5.3 0.4 - - + -
250B SER* 3.3 34.1 - - - +
251B VAL* 4.0 16.1 - - + +
254B TYR* 4.7 16.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ALA* 4.7 12.5 - - + +
173B VAL* 4.5 24.7 - - + +
176B HIS* 3.7 29.0 + - + +
209B GLU* 2.8 20.9 + - - +
210B THR* 3.9 5.8 - - - +
212B ARG* 1.3 107.6 - - - +
214B THR* 1.3 62.4 + - - +
215B ALA 3.4 1.6 - - - -
216B GLY 3.8 1.7 + - - -
217B THR* 2.8 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B LEU* 6.1 0.9 - - + -
172B ALA* 4.2 15.3 - - + -
198B ILE* 4.4 13.9 - - + +
201B THR* 4.2 25.6 - - + -
202B MET* 3.1 33.8 - - - +
210B THR* 2.9 25.8 + - + +
211B ALA* 3.1 9.9 + - - -
213B CYS* 1.3 76.4 - - - +
215B ALA* 1.3 63.7 + - - +
217B THR* 3.4 7.3 + - - -
218B LEU* 3.4 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B MET* 4.1 17.5 - - + -
211B ALA 2.9 17.7 + - - +
212B ARG* 4.9 3.4 - - - -
214B THR* 1.3 79.8 + - - +
216B GLY* 1.3 61.5 + - - +
218B LEU* 3.4 5.4 + - - +
219B HIS* 3.2 21.3 + - - +
240B LEU* 6.3 0.7 - - - -
243B MET* 6.0 1.8 - - + -
251B VAL* 4.6 15.9 - - + +
254B TYR* 4.4 21.5 - - + +
255B ALA* 5.3 4.9 - - + +
258B THR* 4.8 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B HIS* 4.3 15.0 - - - -
212B ARG 4.2 6.5 + - - -
213B CYS 3.8 6.0 + - - -
214B THR 3.3 0.4 - - - -
215B ALA* 1.3 80.5 - - - +
217B THR* 1.3 60.2 + - - +
219B HIS* 3.3 3.5 + - - +
220B ASN* 3.3 27.5 + - - -
254B TYR* 3.8 28.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ALA 5.0 0.7 + - - -
175B VAL* 4.3 12.7 - - + +
176B HIS* 3.5 19.3 + - - +
179B SER* 4.1 22.0 - - - -
188B ILE* 5.3 2.5 - - + -
198B ILE* 4.1 29.4 - - + -
213B CYS 2.8 20.4 + - - -
214B THR* 3.7 11.1 - - - -
215B ALA 3.2 0.8 - - - -
216B GLY* 1.3 75.9 - - - +
218B LEU* 1.3 61.8 + - + +
220B ASN* 3.4 4.3 + - - +
221B LEU* 3.0 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B VAL* 5.1 6.5 - - + +
198B ILE* 3.9 24.9 - - + -
199B VAL* 4.5 23.1 - - + -
202B MET* 3.7 37.0 - - + -
214B THR 3.4 8.9 + - - +
215B ALA* 3.4 6.1 + - - +
216B GLY 3.4 0.2 - - - -
217B THR* 1.3 74.7 - - + +
219B HIS* 1.3 63.9 + - - +
221B LEU* 3.1 20.9 + - + +
222B SER* 3.2 10.9 + - - -
231B ILE* 3.6 32.0 - - + +
236B GLY* 5.6 1.6 - - - +
240B LEU* 4.1 12.6 - - + -
258B THR* 4.3 9.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ALA 3.2 13.1 + - - +
216B GLY 3.5 9.4 - - - +
217B THR 3.3 0.4 - - - -
218B LEU* 1.3 78.0 - - - +
220B ASN* 1.3 71.5 + - - +
222B SER* 2.7 24.1 + - - -
223B HIS* 3.5 34.0 + + - -
254B TYR* 4.0 26.7 - + + +
257B THR* 3.1 32.2 + - - -
258B THR* 3.5 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B HIS* 4.9 4.7 - - - -
179B SER* 3.4 36.8 + - - +
180B LYS* 4.1 14.2 - - - +
185B ARG* 3.6 23.4 + - - +
189B MET* 5.5 0.9 - - - +
216B GLY* 3.3 13.3 + - - +
217B THR 3.7 7.9 - - - +
218B LEU 3.2 0.4 - - - -
219B HIS* 1.3 94.7 + - - +
221B LEU* 1.3 66.0 + - - +
222B SER 3.2 1.2 + - - -
223B HIS* 3.6 18.8 + - - +
224B HIS 5.0 0.3 + - - -
254B TYR* 5.7 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B SER* 4.2 17.7 - - - -
185B ARG* 4.9 9.2 - - + +
188B ILE* 3.6 30.1 - - + -
189B MET* 3.7 34.7 - - + +
195B VAL* 5.2 7.6 - - + -
198B ILE* 6.2 1.1 - - + -
217B THR* 3.0 29.4 - - + +
218B LEU* 3.1 16.2 + - + +
220B ASN* 1.3 79.2 - - + +
222B SER* 1.3 59.7 + - - +
223B HIS 3.3 0.9 + - - -
224B HIS* 3.7 5.8 + - - +
227B GLY* 3.3 28.9 - - - +
230B ALA* 6.1 0.7 - - + -
231B ILE* 4.1 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LEU 3.2 9.9 + - - -
219B HIS* 2.7 23.4 + - - -
220B ASN 3.2 0.2 - - - -
221B LEU* 1.3 74.6 - - - +
223B HIS* 1.3 57.2 + - - +
224B HIS 3.1 9.9 + - - -
228B LEU* 3.2 37.9 - - - +
231B ILE* 4.4 2.7 - - - -
258B THR* 4.2 19.1 - - - +
261B ASN* 3.4 29.1 + - - -
----------------------------------------------------------
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