Contacts of the helix formed by residues 218 - 232 (chain B) in PDB entry 1JS3
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 ARG 218 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B PRO 5.1 0.6 + - - -
212B ASP* 3.3 36.3 + - + +
216B ALA* 3.6 9.6 + - - +
217B MET* 1.3 85.6 - - - +
219B ALA* 1.3 66.9 + - - +
220B SER* 3.3 14.6 + - - +
221B ALA* 3.3 10.8 + - + +
222B LEU* 3.0 22.2 + - - +
253B ASN* 3.9 17.4 - - - +
256B GLU* 2.9 36.7 + - - +
257B VAL* 4.5 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ARG* 1.3 70.0 - - - +
220B SER* 1.3 59.6 + - - +
222B LEU* 3.1 4.7 + - - +
223B GLN* 2.8 37.8 + - - +
256B GLU* 2.9 40.7 + - + +
257B VAL* 4.6 1.1 - - - +
260B ILE* 3.6 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ARG* 4.3 11.8 + - - +
219B ALA* 1.3 78.8 - - - +
221B ALA* 1.3 65.1 + - - +
223B GLN* 3.8 6.3 - - - +
224B GLU* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ILE* 3.6 13.3 - - + +
210B PRO* 3.6 33.8 - - + +
218B ARG* 3.3 12.9 + - + +
219B ALA 3.3 0.4 - - - -
220B SER* 1.3 80.8 + - - +
222B LEU* 1.3 65.2 + - - +
224B GLU* 3.6 10.1 + - - +
225B ALA* 3.2 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B TYR* 4.4 7.4 - - + -
209B ILE* 3.9 29.1 - - + +
217B MET* 4.7 7.4 - - + -
218B ARG 3.0 14.0 + - - +
219B ALA* 3.6 7.4 - - - +
221B ALA* 1.3 76.6 - - - +
223B GLN* 1.3 58.6 + - - +
225B ALA* 3.0 6.4 + - - +
226B LEU* 2.8 46.8 + - + +
239B VAL* 4.3 17.9 - - + -
257B VAL* 3.7 34.5 - - + -
260B ILE* 4.1 22.0 - - + -
261B CYS* 4.5 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ALA* 2.8 22.7 + - - +
220B SER* 3.8 5.9 + - - +
222B LEU* 1.3 72.9 - - - +
224B GLU* 1.3 65.2 + - - +
226B LEU* 3.2 11.8 + - + +
227B GLU* 2.9 44.8 + - + +
260B ILE* 3.3 42.5 - - + +
263B GLU* 4.9 8.5 + - - -
264B GLU* 5.6 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B SER 3.0 18.9 + - - +
221B ALA* 3.7 9.2 - - - +
222B LEU 3.2 0.2 - - - -
223B GLN* 1.3 76.6 - - - +
225B ALA* 1.3 63.0 + - - +
227B GLU* 3.5 7.7 + - - +
228B ARG* 3.1 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B TYR* 4.1 7.2 - - + -
209B ILE* 3.4 30.1 - - + -
210B PRO* 6.1 0.9 - - + -
221B ALA 3.2 5.2 + - - +
222B LEU* 3.0 9.9 + - + +
224B GLU* 1.3 76.9 - - - +
226B LEU* 1.3 66.3 + - - +
228B ARG* 3.3 31.8 + - - +
229B ASP* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B TYR* 3.4 21.1 - - + -
222B LEU* 2.8 25.0 + - + +
223B GLN* 3.2 12.3 + - + +
225B ALA* 1.3 77.0 - - - +
227B GLU* 1.3 57.7 + - + +
229B ASP* 3.2 1.0 + - - +
230B LYS* 2.8 46.2 + - - +
236B PRO* 3.4 35.2 - - + -
260B ILE* 3.5 31.9 - - + -
264B GLU* 3.8 19.5 - - + -
266B ILE* 3.6 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B GLN* 2.9 35.7 + - + +
224B GLU* 3.9 5.7 + - - +
226B LEU* 1.3 77.5 - - + +
228B ARG* 1.3 63.9 + - - +
230B LYS* 4.1 14.8 - - - +
231B ALA* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B TYR* 4.6 0.4 - - - -
207B LYS* 3.7 21.5 - - - +
210B PRO* 5.9 4.6 - - - +
224B GLU* 3.1 20.8 + - + +
225B ALA* 3.7 26.5 + - - +
227B GLU* 1.3 79.4 - - - +
229B ASP* 1.3 107.9 + - - +
231B ALA* 3.5 6.7 + - - +
232B ALA* 3.1 21.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B VAL* 4.5 2.0 - - + -
186B TYR* 2.6 37.8 + - - +
207B LYS* 2.9 30.5 + - - +
225B ALA 2.9 8.8 + - - +
226B LEU 4.0 0.9 - - - +
228B ARG* 1.3 106.5 + - - +
230B LYS* 1.3 64.1 + - - +
232B ALA* 3.1 11.6 + - - +
233B GLY 3.2 0.2 + - - -
234B LEU* 2.9 42.6 + - + +
236B PRO* 5.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B LEU* 2.8 33.9 + - - +
227B GLU* 4.1 12.6 - - - +
229B ASP* 1.3 72.5 - - - +
231B ALA* 1.3 56.0 + - - +
233B GLY* 2.7 25.8 + - - -
234B LEU 3.5 9.8 - - - +
236B PRO* 3.7 26.5 - - + -
264B GLU* 2.9 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B GLU 3.0 19.6 + - - +
228B ARG* 3.6 6.7 - - - +
230B LYS* 1.3 76.7 - - - +
232B ALA* 1.3 58.1 + - - +
233B GLY* 3.1 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ARG* 3.1 14.1 + - + +
229B ASP* 3.1 13.6 + - - +
230B LYS 3.1 0.8 - - - -
231B ALA* 1.3 76.4 - - - +
233B GLY* 1.3 61.1 + - - +
234B LEU* 3.4 12.8 + - + +
----------------------------------------------------------
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