Contacts of the helix formed by residues 197 - 208 (chain A) in PDB entry 1W45
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 197 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ASP 5.3 1.4 - - - +
189A ALA* 3.3 42.9 + - + +
192A LYS* 3.5 28.9 - - - +
193A ILE 5.6 1.3 - - - +
195A GLY* 3.2 1.8 - - - +
196A THR* 1.3 81.6 + - - +
198A GLU* 1.3 65.2 + - - +
199A MET* 3.1 3.6 - - - -
200A LYS* 3.1 29.3 + - + +
201A PHE* 3.3 18.7 + - + -
235A GLU* 5.0 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR* 2.9 36.1 - - + -
195A GLY* 3.4 32.4 + - - +
196A THR 3.7 1.2 - - - -
197A ASP* 1.3 78.6 - - - +
199A MET* 1.3 61.0 + - - +
201A PHE* 3.4 12.1 + - - +
202A ILE* 3.2 27.9 + - - +
235A GLU* 3.3 19.3 - - + +
236A THR* 3.6 26.6 - - + +
237A HIS* 5.5 5.5 + - - -
240A LEU* 3.9 10.5 - - + +
244A MET* 4.1 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR* 4.2 23.0 - - + +
157A ARG* 3.4 42.8 - - + +
196A THR 5.4 0.4 - - - -
197A ASP 3.1 1.2 + - - -
198A GLU* 1.3 76.6 - - - +
200A LYS* 1.3 58.8 + - - +
202A ILE* 3.4 21.9 + - + +
203A THR* 2.8 47.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ASP* 3.3 35.7 + - + +
186A LEU* 4.9 2.9 - - + -
189A ALA* 6.4 0.4 - - + -
197A ASP* 3.1 24.2 + - - +
199A MET* 1.3 76.8 - - - +
201A PHE* 1.3 66.1 + - + +
203A THR* 3.8 7.5 - - - +
204A ILE* 3.3 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 3.9 35.9 - - + -
189A ALA* 3.8 23.3 - - + -
197A ASP* 3.3 25.6 + - + -
198A GLU* 3.6 9.4 - - - +
199A MET 3.3 0.6 - - - -
200A LYS* 1.3 78.7 - - + +
202A ILE* 1.3 57.4 + - - +
204A ILE* 4.0 1.0 - - - +
205A LEU* 2.9 40.6 + - + +
228A ILE* 4.8 1.3 - - + -
231A SER* 3.8 26.5 - - - -
232A ILE* 3.7 28.9 - - + -
235A GLU* 3.7 34.5 - - + -
236A THR* 6.1 0.2 - - + -
244A MET* 3.7 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR* 3.8 47.8 - - + +
157A ARG* 4.5 7.4 - - + +
158A ILE* 3.9 36.3 - - + +
161A CYS* 4.8 0.9 - - + -
198A GLU 3.2 17.6 + - - +
199A MET* 3.7 20.9 - - + +
200A LYS 3.4 0.2 - - - -
201A PHE* 1.3 76.4 - - - +
203A THR* 1.3 54.9 + - - +
205A LEU* 3.2 4.7 + - - +
206A CYS* 2.8 50.2 + - - +
240A LEU* 4.5 2.9 - - + -
244A MET* 3.9 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A MET* 2.8 33.6 + - + +
200A LYS* 3.8 11.5 - - + +
201A PHE 3.4 0.2 - - - -
202A ILE* 1.3 76.1 - - - +
204A ILE* 1.3 55.6 + - + +
206A CYS* 4.4 2.5 - - - -
207A THR* 2.7 60.4 + - + +
208A ARG* 4.7 6.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
182A ASP* 4.0 48.9 - - + +
185A ASP* 4.6 6.3 - - + +
186A LEU* 3.7 28.5 - - + -
200A LYS* 3.3 31.6 + - + +
201A PHE 4.0 2.2 - - - +
203A THR* 1.3 77.5 - - + +
205A LEU* 1.3 65.7 + - + +
206A CYS 3.4 0.5 + - - -
208A ARG* 3.3 37.3 + - + +
213A LEU* 3.4 19.1 - - + +
216A VAL* 4.8 7.6 - - + -
217A PHE* 6.4 0.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
158A ILE* 5.0 6.3 - - + -
162A LEU* 5.2 0.9 - - - +
167A ARG* 5.7 3.8 - - - +
186A LEU* 6.2 3.8 - - + -
201A PHE* 2.9 25.5 + - + +
202A ILE* 3.9 3.8 - - - +
204A ILE* 1.3 79.5 - - + +
206A CYS* 1.3 59.4 + - - +
208A ARG 4.8 1.1 - - - +
213A LEU* 3.7 17.4 - - + +
217A PHE* 4.3 28.0 - - + -
228A ILE* 5.7 2.9 - - + -
232A ILE* 4.0 12.8 - - + -
244A MET* 3.7 45.1 - - + +
247A VAL* 3.5 33.4 - - + +
248A VAL* 4.3 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ILE* 4.7 6.5 - - + -
161A CYS* 2.0 53.9 - - + +
162A LEU* 4.1 28.5 - - + +
166A SER* 3.3 20.5 + - - +
167A ARG* 5.1 3.5 - - - +
202A ILE* 2.8 38.2 + - - +
203A THR* 4.4 1.1 - - - -
205A LEU* 1.3 76.4 - - - +
207A THR* 1.3 63.3 + - - +
208A ARG 3.7 2.4 - - - +
247A VAL* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A CYS* 4.2 6.5 - - - -
166A SER* 3.5 14.5 - - - +
170A VAL* 3.4 20.4 - - - +
203A THR* 2.7 43.1 + - + +
206A CYS* 1.3 85.2 - - - +
208A ARG* 1.3 84.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A SER 3.7 9.0 - - - +
167A ARG* 4.5 6.4 - - - +
170A VAL* 4.9 2.0 - - - -
178A LEU* 3.9 23.9 - - - +
182A ASP* 2.8 36.7 + - - +
203A THR* 4.4 10.3 + - - +
204A ILE* 3.3 34.1 + - + +
205A LEU 4.8 0.5 - - - +
206A CYS 4.5 2.6 - - - -
207A THR* 1.3 104.5 + - - +
209A SER* 1.3 65.8 + - - +
212A HIS* 3.5 33.4 + - + +
213A LEU* 4.0 15.4 - - + +
----------------------------------------------------------
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