Contacts of the helix formed by residues 235 - 243 (chain B) in PDB entry 3LKB
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 GLY 235 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B GLY* 1.3 70.1 - - - -
236B PRO* 1.3 77.6 - - - +
237B ASP 3.0 3.4 - - - -
238B LEU 3.0 11.6 + - - -
239B ILE* 3.3 7.8 + - - +
251B TRP* 3.3 26.9 - - - -
285B VAL* 4.3 3.1 - - - -
366B PHE* 3.4 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B GLY* 1.3 82.7 - - - +
237B ASP* 1.3 59.9 + - - +
239B ILE* 3.4 11.7 + - + +
240B ALA* 2.9 29.8 + - - +
251B TRP* 5.2 1.8 - - + -
257B MET* 5.5 6.5 - - - -
258B ALA* 5.1 8.5 - - + +
280B ASN 5.8 0.9 - - - +
283B GLU* 3.4 42.0 - - + +
284B SER* 5.1 0.2 - - - -
285B VAL* 4.6 10.5 - - + +
366B PHE* 5.2 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASP* 4.5 14.6 - - + +
26B PRO* 5.6 0.8 - - - +
208B ALA* 4.2 13.0 - - + -
234B GLY 4.6 6.5 - - - +
235B GLY 3.0 1.0 + - - -
236B PRO* 1.3 76.9 - - - +
238B LEU* 1.3 62.5 + - - +
240B ALA* 3.5 4.9 + - - +
241B LEU* 2.6 39.1 + - + +
280B ASN* 4.0 20.1 - - - +
284B SER* 2.6 33.2 + - - -
285B VAL* 4.4 2.6 + - - +
286B ASN* 4.3 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ALA* 4.0 13.7 - - + +
211B VAL* 4.4 7.9 - - + -
212B ALA* 5.3 1.3 - - + -
215B LEU* 4.2 4.7 - - + -
233B THR 3.3 28.3 - - - +
234B GLY* 3.8 8.0 + - - -
235B GLY 3.0 9.9 + - - +
237B ASP* 1.3 76.9 - - - +
239B ILE* 1.3 68.0 + - + +
241B LEU* 3.1 4.3 + - - +
242B ALA* 3.0 27.0 + - + +
246B ALA* 3.2 31.6 - - + -
249B PHE* 3.6 43.5 - - + -
366B PHE* 4.1 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 4.6 0.2 - - - +
235B GLY 3.3 10.0 + - - +
236B PRO* 3.6 11.2 - - + +
237B ASP 3.3 0.6 - - - -
238B LEU* 1.3 77.8 - - + +
240B ALA* 1.3 57.8 + - - +
243B GLY* 2.7 42.9 + - - +
246B ALA* 3.7 24.5 - - + -
361B ALA* 4.1 11.7 - - + -
364B GLY* 3.6 42.4 - - - +
365B ARG* 4.9 0.7 - - - -
366B PHE* 3.8 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLY* 4.9 7.6 - - - -
185A LEU* 3.5 19.3 - - - +
236B PRO 2.9 16.0 + - - +
237B ASP* 4.0 8.3 - - - +
238B LEU 3.3 0.2 - - - -
239B ILE* 1.3 77.2 - - - +
241B LEU* 1.3 67.1 + - + +
280B ASN* 6.0 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 3.7 13.1 - - + +
22B ASP* 5.2 12.3 - - - +
208B ALA* 4.7 7.4 - - + +
209B GLY* 4.7 12.8 - - - -
212B ALA* 3.5 22.6 - - + +
216B LYS* 3.6 25.3 + - - +
237B ASP* 2.6 36.9 + - + +
238B LEU* 3.1 3.3 + - - +
240B ALA* 1.3 86.3 - - + +
242B ALA* 1.3 59.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 3.8 6.2 - - - +
212B ALA* 3.6 24.5 - - + +
215B LEU* 4.4 7.0 - - + -
216B LYS* 4.1 10.6 - - - +
238B LEU* 3.0 27.6 + - + +
241B LEU* 1.3 78.1 - - - +
243B GLY* 1.3 64.6 - - - +
244B ASP 3.3 0.7 + - - -
245B ALA* 3.2 17.8 + - + +
246B ALA* 4.0 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 3.5 14.3 - - - +
239B ILE* 2.7 29.1 + - - +
242B ALA* 1.3 75.9 - - - +
244B ASP* 1.3 64.2 + - - -
246B ALA* 3.1 19.2 + - - +
247B GLU 4.3 1.0 + - - -
364B GLY* 5.9 1.8 - - - -
----------------------------------------------------------
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