Contacts of the strand formed by residues 192 - 197 (chain A) in PDB entry 3QLE
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 LEU 192 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ARG* 3.2 3.9 - - - +
191A PRO* 1.3 96.7 - - + +
193A THR* 1.3 64.3 + - - +
231A TYR 4.7 1.8 - - - +
232A TYR* 3.4 43.1 - - + +
233A GLU* 2.9 25.1 + - - +
288A LYS* 3.4 20.4 - - + +
290A ILE* 6.2 0.2 - - + -
330A LEU* 4.0 12.3 - - + +
331A ALA* 3.9 24.5 - - + +
335A THR 3.9 18.2 - - - +
338A VAL* 3.7 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 5.4 0.4 - - + -
190A ARG 5.7 0.2 + - - -
192A LEU* 1.3 74.1 + - - +
194A LEU* 1.3 62.1 + - - +
195A VAL* 4.2 13.0 - - + -
232A TYR* 4.1 3.0 - - - -
233A GLU* 2.7 37.0 + - - +
235A VAL* 4.0 20.0 - - + -
282A LEU* 5.4 1.1 - - + -
284A ARG* 3.7 20.0 - - + +
288A LYS 2.9 11.5 + - - +
289A VAL* 3.4 14.3 - - + +
290A ILE* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A THR* 1.3 72.4 - - - +
195A VAL* 1.3 62.3 + - - +
196A ILE* 3.6 18.7 + - + -
224A PHE* 4.4 5.2 - - + -
228A LEU* 4.1 26.9 - - + -
232A TYR* 3.6 29.0 - - + -
233A GLU 2.8 8.8 + - - +
234A ILE* 3.4 17.1 - - + +
235A VAL 2.9 25.6 + - - +
290A ILE* 3.7 22.4 - - + +
292A ILE* 3.9 24.9 - - + -
327A LEU* 4.3 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A THR* 4.2 5.4 - - + -
194A LEU* 1.3 73.3 - - - +
196A ILE* 1.3 64.3 + - - +
235A VAL* 3.3 16.2 - - + +
237A PHE* 3.8 36.1 - - + -
279A LEU* 4.2 3.8 - - + -
282A LEU* 3.6 28.3 - - + -
289A VAL* 4.0 17.9 - - + -
290A ILE 2.8 12.7 + - - +
291A ILE* 3.2 22.1 - - + +
292A ILE* 2.8 26.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
194A LEU* 3.6 30.1 - - + -
195A VAL* 1.3 80.8 - - - +
197A THR* 1.3 62.5 + - - +
201A PHE* 3.9 21.5 - - + -
202A LEU* 3.9 15.5 - - + -
224A PHE* 4.1 11.4 - - + -
225A LEU* 3.5 31.9 - - + -
234A ILE* 4.0 11.9 - - + -
235A VAL 2.9 15.3 + - - +
236A LEU* 3.5 10.5 - - + -
237A PHE* 2.8 29.6 + - - -
291A ILE* 5.9 0.4 - - - -
292A ILE* 3.7 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ILE* 1.3 78.0 - - - +
198A LEU* 1.3 65.1 + - - +
199A GLU* 3.8 16.3 + - - +
201A PHE* 3.4 39.7 - - + -
202A LEU* 4.1 1.9 - - - +
236A LEU* 4.0 4.6 - - - +
237A PHE 3.3 8.3 + - - -
239A SER* 3.5 9.5 + - - -
277A LYS* 2.9 25.4 + - - +
291A ILE* 5.8 0.4 - - - +
292A ILE 3.1 16.1 + - - +
293A ASP* 3.5 27.5 + - - +
294A THR* 4.1 4.7 + - + +
----------------------------------------------------------
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