Contacts of the helix formed by residues 189 - 196 (chain A) in PDB entry 4JU5
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 ASN 189 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU 4.6 0.7 - - - +
141A PRO* 2.5 33.1 + - + +
142A ASP* 3.9 5.1 - - - +
187A THR* 3.4 10.0 + - - +
188A SER* 1.3 76.1 - - - +
190A SER* 1.3 62.5 + - - +
191A ASP* 3.1 28.3 + - - +
192A VAL* 2.9 32.9 + - + +
193A PHE* 3.3 11.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LYS* 3.7 22.0 - - - +
188A SER 3.5 4.8 + - - -
189A ASN* 1.3 72.2 + - - +
191A ASP* 1.3 64.6 + - - +
192A VAL 3.4 0.2 - - - -
193A PHE* 3.4 14.9 - - - +
194A SER* 3.1 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLY* 6.0 1.8 - - - +
189A ASN* 3.0 22.2 + - - +
190A SER* 1.3 80.0 + - - +
192A VAL* 1.3 60.8 + - + +
194A SER* 3.4 5.8 + - - -
195A LYS* 3.0 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 4.6 0.7 - - + +
142A ASP* 3.6 32.5 - - - +
143A GLY* 3.8 4.0 - - - +
146A ALA* 4.1 11.9 - - + -
158A ILE* 5.4 1.6 - - + -
160A PHE* 3.7 3.7 - - + -
187A THR* 3.7 35.4 - - + +
189A ASN* 2.9 21.7 + - + +
191A ASP* 1.3 74.4 - - + +
193A PHE* 1.3 64.0 + - - +
195A LYS* 3.2 9.9 + - - -
196A TYR* 3.1 47.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A PHE* 3.5 38.6 - + + -
161A PHE 3.7 1.1 - - - -
162A LYS* 3.3 34.3 - - + +
187A THR* 3.8 17.7 - - + -
188A SER* 4.2 10.8 - - - -
189A ASN 3.3 15.7 + - - -
190A SER* 3.4 11.7 - - - +
192A VAL* 1.3 79.0 - - - +
194A SER* 1.3 55.5 + - - +
196A TYR* 3.2 2.3 + - - +
197A GLN 2.9 9.2 + - - -
198A LEU* 2.8 44.9 + - + +
199A ASP 4.1 4.5 - - - -
200A LYS 3.3 34.1 - - - -
201A ASP* 3.5 19.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A SER 3.1 16.6 + - - -
191A ASP* 3.9 5.8 - - - -
193A PHE* 1.3 74.4 - - - +
195A LYS* 1.3 67.1 + - - +
197A GLN* 3.1 19.1 + - - +
198A LEU 4.2 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLY* 3.9 25.1 - - - -
147A GLU* 3.2 46.0 + - - +
191A ASP 3.0 15.2 + - - +
192A VAL* 3.3 12.6 - - - +
193A PHE 3.2 0.2 - - - -
194A SER* 1.3 78.5 - - - +
196A TYR* 1.3 83.6 + - + +
197A GLN* 3.8 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ALA* 3.4 24.1 + - + +
147A GLU* 3.6 22.9 + - - +
150A VAL* 4.1 4.8 - - + +
158A ILE* 4.6 4.9 - - + -
160A PHE* 3.9 26.5 - + + -
192A VAL* 3.1 34.5 + - + +
193A PHE 3.2 3.3 + - - +
194A SER 3.1 0.2 - - - -
195A LYS* 1.3 102.8 - - + +
197A GLN* 1.3 70.3 + - - +
198A LEU* 3.2 11.3 - - + +
204A VAL* 5.4 0.2 - - + -
206A PHE* 3.5 34.1 - + + -
213A ARG* 2.6 34.4 + - - +
----------------------------------------------------------
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