Contacts of the helix formed by residues 187 - 201 (chain A) in PDB entry 1ZYB
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 THR 187 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ALA* 4.6 0.2 - - - -
186A ASP* 1.3 93.4 + - - +
188A ARG* 1.3 66.0 + - - +
189A LEU* 3.5 8.4 + - - +
190A ASN* 3.2 29.5 + - - +
191A ILE* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A MSE 3.0 52.8 - - + +
178A ASP* 5.2 7.6 - - - +
181A ALA* 4.3 7.2 - - + +
187A THR* 1.3 73.7 - - - +
189A LEU* 1.3 56.5 + - - +
191A ILE* 3.8 1.0 - - - +
192A SER* 2.7 56.7 + - - -
225A GOL 5.3 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A THR* 3.2 8.1 + - - +
188A ARG* 1.3 83.4 - - - +
190A ASN* 1.3 70.9 + - - +
192A SER* 3.4 5.2 + - - -
193A LYS* 3.0 33.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU* 3.5 14.3 - - + +
186A ASP* 2.8 30.2 + - - +
187A THR* 3.2 17.5 + - - +
189A LEU* 1.3 85.7 - - - +
191A ILE* 1.3 66.3 + - - +
193A LYS* 3.3 9.0 + - - +
194A THR* 3.0 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU* 4.0 14.8 - - + -
156A ILE* 4.6 2.9 - - + +
177A MSE 3.7 20.0 - - - -
180A LEU* 3.8 11.0 - - + -
181A ALA* 3.2 39.9 - - + +
184A LEU* 3.8 21.3 - - + -
186A ASP* 4.0 12.1 - - + -
187A THR 3.0 21.8 + - - +
188A ARG 3.8 2.5 - - - +
190A ASN* 1.3 76.5 - - - +
192A SER* 1.3 57.6 + - - +
194A THR* 3.4 2.0 + - - -
195A LEU* 2.9 49.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A MSE 4.3 13.7 - - - +
188A ARG* 2.7 41.4 + - - -
189A LEU* 3.6 6.3 - - - -
191A ILE* 1.3 75.0 - - - +
193A LYS* 1.3 60.9 + - - +
195A LEU* 3.5 3.8 + - - +
196A ASN* 2.8 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 3.0 18.9 + - + +
190A ASN* 3.3 13.4 + - - +
192A SER* 1.3 73.7 - - - +
194A THR* 1.3 65.5 + - - +
196A ASN* 3.2 7.9 + - - +
197A GLU* 3.0 49.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU* 3.4 13.9 - - - +
153A LYS* 3.5 47.6 - - + +
156A ILE* 3.7 20.6 - - + -
190A ASN 3.0 15.6 + - - -
191A ILE 3.9 0.2 - - - -
193A LYS* 1.3 75.7 - - - +
195A LEU* 1.3 66.1 + - - +
197A GLU* 3.3 12.3 + - - +
198A LEU* 3.1 24.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ILE* 4.2 27.1 - - + -
160A PHE* 4.3 1.8 - - + -
177A MSE 4.1 14.8 - - + -
180A LEU* 4.0 13.9 - - + -
191A ILE* 2.9 40.5 + - + +
192A SER* 3.9 3.6 - - - +
194A THR* 1.3 77.1 - - - +
196A ASN* 1.3 57.6 + - - +
198A LEU* 3.4 2.4 + - + -
199A GLN* 3.0 24.8 + - - +
204A ILE* 3.6 28.6 - - + +
206A LEU* 4.0 21.0 - - + +
211A ILE* 4.1 21.8 - - + -
225A GOL 4.4 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A SER* 2.8 41.0 + - - +
193A LYS* 3.2 6.2 + - - +
195A LEU* 1.3 73.8 - - - +
197A GLU* 1.3 54.5 + - - +
199A GLN* 3.3 22.0 + - - +
200A ASP* 2.8 48.9 + - - +
206A LEU* 4.0 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LYS* 2.4 43.7 + - - +
193A LYS* 3.0 51.8 + - + +
194A THR* 3.3 12.3 + - - +
196A ASN* 1.3 74.3 - - - +
198A LEU* 1.3 64.5 + - - +
200A ASP* 3.2 8.2 + - - +
201A ASN* 2.9 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LYS* 4.0 29.8 - - + -
156A ILE* 4.1 26.0 - - + -
157A ILE* 4.3 17.0 - - + -
160A PHE* 4.6 5.6 - - + -
194A THR* 3.1 23.0 + - + +
195A LEU* 3.6 8.5 - - - +
196A ASN 3.4 0.2 - - - -
197A GLU* 1.3 77.8 - - - +
199A GLN* 1.3 60.5 + - - +
201A ASN* 3.3 9.8 + - - +
203A LEU* 2.9 50.3 + - + +
204A ILE* 3.6 27.4 - - + -
219A LEU* 5.1 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU 3.0 16.7 + - - +
196A ASN* 3.7 16.6 + - - +
198A LEU* 1.3 72.7 - - - +
200A ASP* 1.3 72.0 + - - +
202A GLY* 3.0 14.4 + - - -
204A ILE* 3.4 26.3 - - + +
205A GLU* 3.6 5.6 - - + +
206A LEU* 2.9 49.5 + - + +
226A GOL 4.9 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ASN* 2.8 32.0 + - - +
197A GLU* 3.2 7.9 + - - +
199A GLN* 1.3 87.2 + - - +
201A ASN* 1.3 61.6 + - - +
202A GLY* 3.2 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LYS* 4.3 13.5 - - - +
197A GLU* 2.9 25.4 + - - +
198A LEU* 3.3 5.4 + - - +
199A GLN 3.2 0.4 - - - -
200A ASP* 1.3 78.6 - - - +
202A GLY* 1.3 61.2 + - - +
203A LEU* 3.3 24.3 + - + +
----------------------------------------------------------
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