Contacts of the helix formed by residues 188 - 201 (chain J) in PDB entry 3SWD
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 GLU 188 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161J VAL* 4.6 0.3 - - - +
163J VAL* 3.4 32.3 - - + +
186J ALA* 3.4 21.6 - - - +
187J ARG* 1.3 78.6 + - - +
189J PRO* 1.3 77.5 - - + +
190J GLU* 3.2 12.6 - - + +
191J ILE* 3.1 28.1 + - + +
192J VAL* 3.6 7.1 - - - +
232J ARG* 3.9 12.5 + - - +
298J PRO* 4.3 9.3 - - - +
299J HIS* 3.1 33.4 + - + +
303J PRO* 6.1 0.5 - - - +
501J EPZ 4.8 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 189 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187J ARG 4.5 0.2 - - - +
188J GLU* 1.3 91.4 - - + +
190J GLU* 1.3 70.6 + - - +
191J ILE 3.2 1.0 + - - -
192J VAL* 3.3 15.5 + - + +
193J ASP* 3.2 19.1 + - - +
229J LEU* 4.3 16.1 - - + +
232J ARG* 3.9 15.5 - - - +
255J GLN* 5.5 1.3 - - - +
258J THR* 3.5 26.7 - - - +
299J HIS* 3.5 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 190 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J ALA* 4.4 12.9 - - + +
23J ASN* 3.8 28.0 - - + +
24J ALA* 3.7 28.9 - - + +
27J PRO* 5.2 1.1 - - + +
163J VAL* 6.2 3.1 - - + -
167J VAL* 6.2 0.2 - - - -
188J GLU* 3.2 4.2 - - + +
189J PRO* 1.3 81.2 - - - +
191J ILE* 1.3 53.8 + - + +
193J ASP* 3.7 8.5 - - - +
194J THR* 2.6 35.2 + - - -
229J LEU* 4.5 4.4 - - + +
230J PRO 5.3 0.3 - - - +
231J ASP* 5.5 1.9 - - - +
232J ARG* 2.7 53.6 + - - +
233J ILE* 5.7 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 191 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163J VAL* 4.1 21.1 - - + +
166J THR* 4.1 24.7 - - + -
167J VAL* 4.0 14.4 - - + -
170J MET* 3.5 23.7 - - + +
186J ALA* 3.8 38.4 - - + +
188J GLU* 3.1 16.0 + - + +
190J GLU* 1.3 77.3 - - + +
192J VAL* 1.3 58.2 + - + +
193J ASP 3.1 0.2 - - - -
194J THR* 3.3 4.8 + - - -
195J ALA* 2.7 32.1 + - - +
208J GLN* 5.2 3.4 - - + -
209J GLY 5.5 2.0 - - - +
213J ILE* 4.5 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 192 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187J ARG 4.7 0.7 - - - +
188J GLU 3.6 13.7 - - - +
189J PRO* 3.3 19.3 - - + +
191J ILE* 1.3 77.0 - - - +
193J ASP* 1.3 51.8 + - - +
195J ALA* 2.9 9.9 + - - +
196J ASN* 2.6 52.8 + - - +
208J GLN* 4.0 22.9 - - + +
209J GLY* 4.2 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 193 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J ALA* 3.8 10.0 - - + +
28J ILE* 4.6 4.7 - - + +
189J PRO 3.2 8.3 + - - +
190J GLU* 3.7 12.8 - - - +
192J VAL* 1.3 79.1 - - - +
194J THR* 1.3 57.0 + - - +
196J ASN* 2.7 24.9 + - - +
197J PHE* 2.9 13.5 + - - +
226J TYR* 2.9 29.7 + - - -
227J ARG 4.3 1.9 - - - +
228J VAL* 3.7 5.7 - - - -
229J LEU* 2.8 49.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 194 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J ALA 4.6 0.7 + - - -
27J PRO* 3.7 39.7 - - + +
28J ILE* 4.1 16.5 - - + +
31J ALA* 4.8 3.8 - - + -
167J VAL* 4.3 8.3 - - + +
170J MET* 4.2 7.4 - - + -
171J CYS* 4.2 24.2 - - - -
190J GLU 2.6 22.6 + - - -
191J ILE* 3.5 9.0 - - - -
193J ASP* 1.3 76.2 - - - +
195J ALA* 1.3 57.0 + - - +
197J PHE* 3.6 3.0 - - - +
198J LEU* 3.1 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 195 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170J MET* 3.9 14.6 - - + +
191J ILE 2.7 14.9 + - - +
192J VAL 3.0 11.9 - - - +
193J ASP 2.8 0.4 + - - -
194J THR* 1.3 76.6 - - - +
196J ASN* 1.3 63.6 + - - +
197J PHE 3.2 0.2 - - - -
198J LEU* 3.3 2.9 + - - +
199J ILE* 2.9 27.9 + - - +
205J ILE* 3.9 20.4 - - + +
208J GLN* 3.9 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 196 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192J VAL* 2.6 36.1 + - - +
193J ASP* 2.7 5.8 + - - +
195J ALA* 1.3 66.8 - - - +
197J PHE* 1.3 63.0 + - - -
199J ILE* 3.2 11.4 + - - +
200J THR* 2.8 24.4 + - - -
208J GLN* 3.6 19.6 + - - -
226J TYR* 3.0 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 197 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J ILE* 3.7 46.0 - - + -
31J ALA* 4.3 12.8 - - + -
32J ALA* 4.2 14.1 - - - -
39J VAL* 3.5 34.3 - - + -
41J ILE* 4.4 4.9 - - + -
193J ASP 2.9 10.7 + - - +
194J THR 3.6 9.9 - - - +
196J ASN* 1.3 72.2 - - - +
198J LEU* 1.3 58.4 + - + +
200J THR* 2.6 34.4 + - + +
201J LEU* 3.0 37.3 + - + +
224J GLY 5.2 0.4 - - - -
226J TYR* 3.3 44.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 198 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J ALA* 4.1 20.9 - - + +
34J LEU* 4.2 8.3 - - + -
170J MET* 4.6 2.7 - - + -
171J CYS* 3.6 32.8 - - + +
174J THR* 3.6 24.2 - - + +
194J THR* 3.1 18.7 + - + +
195J ALA 3.3 0.4 + - - +
197J PHE* 1.3 80.9 - - + +
199J ILE* 1.3 56.8 + - - +
201J LEU* 3.3 17.0 + - + +
202J GLY 3.7 1.0 + - - -
203J ALA* 2.6 26.3 + - + +
205J ILE* 3.6 20.4 - - + -
221J LEU* 3.6 29.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 199 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195J ALA 2.9 16.9 + - - +
196J ASN* 3.5 12.6 - - - +
198J LEU* 1.3 73.9 - - - +
200J THR* 1.3 56.4 + - - +
202J GLY* 2.2 36.6 + - - -
203J ALA* 2.8 24.0 + - - +
205J ILE* 3.5 34.3 - - + +
208J GLN* 3.7 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 200 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196J ASN* 2.8 14.6 + - - +
197J PHE* 2.6 19.7 + - + +
199J ILE* 1.3 73.3 - - - +
201J LEU* 1.3 61.4 + - + +
202J GLY 2.9 2.9 + - - -
223J GLY 3.9 13.8 - - - +
224J GLY* 5.1 2.5 - - - -
225J VAL 3.8 22.2 - - - +
226J TYR* 3.5 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 201 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J ALA 5.1 2.2 - - - +
35J ALA* 4.1 22.2 - - + +
39J VAL* 4.5 2.5 - - + -
197J PHE* 3.0 53.0 + - + +
198J LEU* 3.3 11.2 + - + +
199J ILE 2.8 1.4 + - - -
200J THR* 1.3 77.9 - - + +
202J GLY* 1.3 62.6 + - - +
203J ALA 3.8 0.4 - - - -
220J ARG 4.9 0.5 - - - +
221J LEU* 3.8 25.5 - - + +
222J GLY* 3.2 29.1 + - - +
223J GLY* 3.2 42.0 - - - +
224J GLY 4.2 1.1 - - - +
----------------------------------------------------------
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