Contacts of the helix formed by residues 193 - 198 (chain A) in PDB entry 1AKZ
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 SER 193 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A MET* 3.4 26.0 - - - +
154A HIS* 4.2 6.4 - - - -
156A LEU* 4.2 10.2 - - - +
161A GLN* 4.6 3.5 + - - -
191A ASP* 2.6 27.6 + - - -
192A LEU* 1.3 76.5 - - - +
194A GLY* 1.3 55.9 + - - +
196A ALA* 3.1 4.7 + - - +
197A LYS* 2.9 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ASP 4.7 1.4 + - - -
192A LEU 3.1 1.6 + - - -
193A SER* 1.3 80.4 - - - +
195A TRP* 1.3 58.5 + - - +
197A LYS* 3.7 9.1 - - - +
198A GLN* 3.2 27.2 + - - +
303A GLU* 3.5 21.7 - - - +
304A LEU* 4.3 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ILE* 4.8 9.6 - - + -
173A ILE* 3.9 19.7 - - + -
174A TYR* 4.7 1.8 - + - -
177A LEU* 3.4 33.9 - - + -
192A LEU* 2.9 40.6 + - + +
194A GLY* 1.3 76.0 - - - +
196A ALA* 1.3 62.1 + - - +
198A GLN* 2.9 25.4 + - - +
199A GLY 3.5 0.2 + - - -
200A VAL* 3.2 33.2 + - + +
202A LEU* 4.6 11.9 - - + -
245A TRP* 5.9 0.7 - + - -
284A PHE* 4.5 4.5 - + - -
299A ILE* 4.9 1.1 - - + -
301A TRP* 2.8 65.5 + + - +
303A GLU 4.1 4.3 - - - -
304A LEU* 3.3 32.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A TRP* 6.0 0.7 - - - -
131A MET* 3.6 27.5 - - + +
132A CYS* 3.6 18.4 - - - +
156A LEU* 4.2 17.7 - - + -
192A LEU 3.2 6.5 + - - +
193A SER 3.1 8.9 + - - +
195A TRP* 1.3 80.2 - - - +
197A LYS* 1.3 60.9 + - - +
199A GLY* 3.1 10.9 + - - -
200A VAL 3.3 18.6 + - - +
202A LEU* 4.2 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLN 4.3 5.1 + - - -
131A MET* 3.3 45.2 + - - +
132A CYS* 4.1 9.4 - - - +
193A SER* 2.9 22.1 + - - +
194A GLY* 3.7 11.0 - - - +
195A TRP 3.2 0.2 - - - -
196A ALA* 1.3 75.8 - - - +
198A GLN* 1.3 60.4 + - + +
199A GLY 3.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ASP* 6.0 1.3 - - - -
138A LYS* 2.9 29.6 + - - -
194A GLY 3.2 20.1 + - - +
195A TRP* 2.9 11.6 + - - +
197A LYS* 1.3 78.8 - - + +
199A GLY* 1.3 58.2 + - - +
200A VAL 3.6 0.4 - - - -
297A LYS* 6.0 2.3 - - - -
298A PRO 4.4 2.1 - - - +
299A ILE* 3.6 20.4 - - + +
300A ASP* 2.7 54.0 + - - +
303A GLU* 3.7 17.9 + - + +
----------------------------------------------------------
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