Contacts of the helix formed by residues 235 - 240 (chain A) in PDB entry 1L8A
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 GLU 235 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A MET* 3.7 14.4 - - + +
195A GLY* 3.8 5.8 - - - -
232A GLU 2.9 16.7 + - - +
233A MET 3.4 3.1 - - - +
234A ASP* 1.3 77.6 - - - +
236A PRO* 1.3 76.6 - - - +
237A GLU* 3.6 7.9 - - - +
238A SER* 2.9 25.3 + - - +
239A LYS 4.0 1.2 + - - -
240B GLY 4.4 0.9 - - - +
569B ILE* 3.1 33.3 + - + +
570B ASN* 3.4 9.2 - - - -
571B GLU* 2.5 31.9 + - - +
572B LEU 4.9 0.3 + - - -
606B ARG* 3.6 13.8 + - - -
887B TPP 3.2 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ASP 3.6 1.3 - - - +
235A GLU* 1.3 87.1 - - - +
237A GLU* 1.3 69.8 + - - +
240A GLY* 2.8 32.1 + - - -
199B ILE* 4.9 6.5 - - + -
236B PRO* 3.5 8.7 - - + +
237B GLU* 4.4 13.9 - - + +
240B GLY* 3.3 27.7 - - - +
241B ALA* 4.9 1.6 - - + -
570B ASN* 3.1 28.0 - - - +
572B LEU* 3.9 26.0 - - + -
573B GLY 4.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLY* 3.4 25.1 - - - +
196A LEU* 4.3 4.0 - - + +
199A ILE* 3.6 26.6 + - + +
202A ILE* 5.8 0.3 - - - +
235A GLU* 3.6 1.4 - - - +
236A PRO* 1.3 94.8 - - - +
238A SER* 1.3 63.4 + - - +
239A LYS 3.5 0.2 - - - -
240A GLY 4.1 3.2 + - - -
241A ALA* 4.7 3.3 + - - +
572A LEU* 3.7 31.6 - - + +
236B PRO* 4.2 11.4 - - + +
237B GLU* 5.3 5.7 - - - +
572B LEU* 5.6 3.9 - - - +
606B ARG* 3.1 45.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLY* 3.3 18.2 - - - -
198A PRO* 3.5 28.7 - - - +
202A ILE* 5.2 1.7 - - - +
232A GLU* 2.8 27.6 + - - +
233A MET* 3.6 21.9 - - - +
235A GLU 2.9 12.0 + - - -
237A GLU* 1.3 81.4 - - - +
239A LYS* 1.3 61.2 + - - +
241A ALA 5.1 0.3 + - - -
242A ILE* 3.7 13.0 - - - +
255A PHE* 4.0 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A MET* 2.7 46.0 + - + +
234A ASP* 4.4 4.9 + - - +
235A GLU 4.0 1.4 + - - -
236A PRO 3.7 1.6 + - - -
238A SER* 1.3 77.7 - - - +
240A GLY* 1.3 66.1 + - - +
241A ALA 3.0 4.8 + - - -
242A ILE* 3.2 31.6 - - + +
277A GLU* 4.5 7.0 + - - -
278A LEU* 4.3 10.9 - - + +
281A ILE* 4.0 29.8 - - + -
282A PHE* 4.2 13.2 - - + -
239B LYS* 5.1 2.2 - - - +
240B GLY* 4.0 21.2 + - - +
243B THR* 4.0 33.3 + - - -
247B ARG* 5.3 0.4 - - - +
281B ILE* 4.8 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A PRO 2.8 21.3 + - - -
237A GLU 4.1 0.6 - - - -
238A SER 3.6 0.4 - - - -
239A LYS* 1.3 77.9 - - - +
241A ALA* 1.3 58.4 + - - +
234B ASP 4.3 3.6 - - - +
235B GLU 4.3 1.6 - - - +
236B PRO* 3.3 33.8 - - - +
239B LYS* 4.0 22.8 + - - +
240B GLY* 3.7 9.5 - - - -
----------------------------------------------------------
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