Contacts of the helix formed by residues 235 - 240 (chain C) in PDB entry 2X1L
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 THR 235 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C HIS* 3.8 0.9 - - - -
103C ALA* 3.7 39.9 - - + +
104C SER* 3.8 8.7 - - - +
107C ILE* 3.4 24.2 - - + +
231C VAL 2.8 19.0 + - - -
232C ASP* 3.5 12.8 + - - -
233C ALA 3.2 0.6 - - - -
234C LEU* 1.3 75.6 - - - +
236C ASN* 1.3 64.5 + - - +
237C TYR 3.2 0.4 - - - -
238C LEU* 3.0 15.2 + - + +
239C THR* 3.0 18.7 + - - +
243C PHE* 4.9 0.2 - - + -
274C TRP* 4.3 8.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 236 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C THR 5.1 0.2 - - - +
11C ILE* 3.6 29.2 - - + +
46C LEU* 3.3 23.6 - - - +
93C ILE* 3.5 21.1 - - + +
95C THR* 4.7 1.8 - - + -
100C HIS* 3.3 23.8 - - + +
233C ALA 2.7 25.0 + - - +
234C LEU 3.1 1.4 + - - -
235C THR* 1.3 76.9 - - - +
237C TYR* 1.3 92.4 + - - +
239C THR* 3.5 3.0 - - - -
240C GLY 2.9 27.4 + - - -
600C MET* 4.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 237 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C TYR* 2.7 34.8 + - - +
8C THR* 3.3 33.7 - - + -
9C THR 3.4 21.7 + - - -
10C ALA* 3.7 4.0 + - - -
46C LEU* 4.0 0.7 - - + -
234C LEU* 3.2 26.2 - - + +
235C THR 3.2 0.6 - - - -
236C ASN* 1.3 100.1 - - - +
238C LEU* 1.3 60.1 + - - +
240C GLY 4.0 0.5 + - - -
241C VAL* 3.6 4.3 - - - +
255C TRP* 4.0 10.1 - - + -
260C HIS* 3.4 29.3 - + + -
262C ILE* 4.3 2.3 - - - +
270C HIS* 2.8 40.8 + + - -
274C TRP* 4.0 10.1 - + + -
600C MET* 3.6 12.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 238 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ILE* 3.7 30.5 - - + -
235C THR* 3.0 12.1 + - + +
237C TYR* 1.3 76.9 - - - +
239C THR* 1.3 65.4 + - - +
240C GLY 3.3 0.2 - - - -
241C VAL* 3.2 14.9 + - - +
243C PHE* 3.2 41.9 + - + +
251C PHE* 3.7 21.8 - - + -
255C TRP* 3.6 34.8 - - + +
274C TRP* 3.7 21.5 - - + -
278C LEU* 3.9 4.7 - - + -
283C LEU* 4.0 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ARG* 3.6 8.4 + - - -
93C ILE* 3.7 16.2 - - + -
99C ASP* 3.7 23.8 - - + +
100C HIS* 3.0 43.4 + - - +
103C ALA* 3.3 12.9 - - + +
235C THR 3.0 14.7 + - - -
236C ASN 3.1 7.2 + - - -
238C LEU* 1.3 76.8 - - - +
240C GLY* 1.3 57.4 + - - +
241C VAL 3.0 5.7 + - - -
242C GLY* 3.2 12.0 + - - -
243C PHE* 4.1 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 240 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C TYR* 4.2 2.0 - - - -
44C ARG* 3.6 19.1 + - - +
46C LEU* 3.8 34.8 - - - +
91C ARG* 4.2 15.3 + - - +
93C ILE* 4.1 0.9 - - - +
236C ASN 2.9 10.3 + - - -
237C TYR 4.0 0.2 + - - -
238C LEU 3.3 0.6 - - - -
239C THR* 1.3 75.9 - - - +
241C VAL* 1.3 65.5 + - - +
242C GLY 3.8 0.2 - - - -
----------------------------------------------------------
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