Contacts of the helix formed by residues 192 - 202 (chain A) in PDB entry 3ONC
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 GLN 192 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ILE* 3.8 22.9 - - + +
185A GLU 2.9 30.5 + - - +
186A CYS* 4.3 2.0 - - + -
190A LEU* 3.4 32.2 - - + +
191A THR* 1.3 78.6 + - - +
193A GLU* 1.3 66.0 + - - +
194A LYS* 3.2 3.5 + - - +
195A LEU* 3.4 21.9 + - - +
196A ILE* 3.0 36.1 + - + +
292A ASN* 4.8 0.8 + - - -
296A ARG* 4.0 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A THR* 2.6 32.4 + - - -
192A GLN* 1.3 71.8 + - - +
194A LYS* 1.3 66.6 + - + +
196A ILE* 4.0 1.4 - - - +
197A GLN* 3.0 27.0 + - - +
255A ARG* 4.0 15.0 - - - +
289A LEU* 3.7 29.0 - - + +
292A ASN* 5.1 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A HIS* 4.9 6.9 + - - +
192A GLN* 3.3 1.6 - - - +
193A GLU* 1.3 83.1 - - + +
195A LEU* 1.3 62.1 + - - +
197A GLN* 3.4 3.5 + - - +
198A TYR* 3.1 23.4 + - - +
294A ASN* 5.5 4.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
161A PHE 3.6 19.1 - - - +
162A ASN* 4.0 7.6 - - - +
163A HIS* 3.7 37.0 - - + +
166A VAL* 4.6 1.1 - - + -
182A ASN* 4.2 0.4 - - - +
184A ILE* 3.9 31.0 - - + -
192A GLN* 3.4 24.3 + - - +
194A LYS* 1.3 79.7 - - - +
196A ILE* 1.3 62.3 + - - +
198A TYR* 3.3 5.8 + - + +
199A CYS* 2.9 41.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ILE* 4.2 3.6 - - + -
186A CYS* 3.8 12.8 - - - -
191A THR 3.6 7.4 - - - +
192A GLN* 3.0 30.8 + - + +
193A GLU* 4.0 3.6 - - - +
195A LEU* 1.3 77.0 - - - +
197A GLN* 1.3 57.8 + - - +
199A CYS* 3.3 0.7 + - - -
200A GLN* 2.9 58.6 + - + +
206A VAL* 4.1 23.8 - - + -
255A ARG* 3.6 31.4 - - + +
257A LEU* 3.9 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A GLU 3.0 19.5 + - - +
194A LYS* 4.0 4.0 - - - +
196A ILE* 1.3 77.6 - - - +
198A TYR* 1.3 64.9 + - - +
200A GLN* 4.5 12.2 - - - +
201A SER* 2.9 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A HIS* 3.3 55.4 - + + +
166A VAL* 3.7 33.4 - - + -
167A GLU* 3.5 33.0 + - + +
170A LEU* 3.7 10.7 - - - +
194A LYS 3.1 17.6 + - - +
195A LEU* 3.7 4.7 - - + +
197A GLN* 1.3 78.6 - - - +
199A CYS* 1.3 67.9 + - - +
201A SER* 2.7 25.1 + - - -
202A LYS* 3.3 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A VAL* 4.2 15.5 - - - -
182A ASN* 3.7 34.3 - - - -
195A LEU* 2.9 32.4 + - - +
196A ILE 3.9 0.2 - - - +
198A TYR* 1.3 79.5 - - - +
200A GLN* 1.3 62.7 + - - +
202A LYS* 3.0 11.9 + - - -
204A ILE* 3.0 35.7 + - + +
206A VAL* 3.6 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ILE* 2.9 32.7 + - + +
197A GLN* 4.1 12.2 - - - +
199A CYS* 1.3 75.5 - - - +
201A SER* 1.3 62.3 + - - +
203A GLY* 3.0 14.8 + - - -
204A ILE 3.8 12.3 - - - +
205A VAL* 5.8 0.9 - - - -
206A VAL* 4.8 6.6 - - + +
255A ARG 3.1 25.8 + - - +
256A ASN* 3.7 18.0 + - - +
257A LEU* 3.6 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A GLN* 2.9 29.8 + - - +
198A TYR* 2.7 22.7 + - - -
200A GLN* 1.3 75.6 - - - +
202A LYS* 1.3 73.0 + - - +
203A GLY 3.4 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASN* 5.0 1.2 + - - -
170A LEU* 3.6 31.2 - - + +
178A LYS* 4.8 17.2 + - - +
198A TYR* 3.5 44.4 - - + +
199A CYS* 3.0 9.6 + - - +
201A SER* 1.3 85.5 - - - +
203A GLY* 1.3 61.2 + - - +
204A ILE* 3.5 10.9 + - + +
----------------------------------------------------------
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