Contacts of the helix formed by residues 235 - 249 (chain B) in PDB entry 3LXA
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 235 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A TRP* 5.7 2.7 - - - -
279A GLN* 5.8 0.2 - - - +
358A GLU* 3.2 27.4 - - - -
233B ASP* 2.7 31.2 + - - +
234B ASP* 1.3 74.1 - - - +
236B TRP* 1.3 61.9 + - - +
237B LYS* 3.6 11.8 + - - +
238B SER* 2.8 25.6 + - - -
239B ILE* 3.2 17.0 + - - +
274B GLY 4.2 3.1 - - - -
275B LEU* 3.4 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A SER* 5.8 1.6 - - - -
274A GLY 5.5 0.9 - - - +
235B SER* 1.3 69.8 - - - +
237B LYS* 1.3 66.7 + - - +
239B ILE* 3.3 19.3 + - + +
240B LYS* 3.0 62.6 + - + +
243B LEU* 5.2 2.7 - - + -
274B GLY 4.3 2.9 + - - +
275B LEU* 3.3 8.0 - - - +
279B GLN* 3.3 41.3 - - + +
282B THR* 3.7 30.1 - - + -
354B ILE* 4.7 2.9 - - + -
356B ARG* 4.3 15.9 - - - -
358B GLU* 2.9 29.1 + - + -
410B THR* 3.2 45.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A TRP* 6.5 1.3 - - + -
237A LYS* 3.4 41.6 - - + +
240A LYS* 5.9 6.3 - - - +
358A GLU* 5.3 3.1 - - - +
235B SER* 3.7 11.9 - - - +
236B TRP* 1.3 81.5 - - - +
238B SER* 1.3 65.9 + - - +
240B LYS* 3.6 24.4 + - - +
241B SER* 3.1 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ASP 4.9 3.4 - - - -
232B ILE* 3.2 16.7 - - - +
233B ASP* 3.1 48.2 + - - -
235B SER* 2.8 8.4 + - - -
237B LYS* 1.3 78.4 - - - +
239B ILE* 1.3 66.3 + - - +
241B SER* 3.2 8.6 + - - -
242B ILE* 2.9 26.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
232B ILE* 3.9 10.5 - - + -
235B SER 3.2 15.0 - - - +
236B TRP* 3.3 26.4 + - + +
238B SER* 1.3 77.6 + - - +
240B LYS* 1.3 54.3 + - - +
242B ILE* 2.9 11.5 + - - +
243B LEU* 2.8 45.9 + - + +
269B VAL* 4.0 14.4 - - + -
275B LEU* 4.2 12.1 - - + -
279B GLN 5.4 0.9 - - - +
282B THR* 4.9 0.4 - - + -
283B GLN* 3.7 42.4 - - + +
287B TRP* 4.1 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LYS* 6.1 4.2 - - - +
236B TRP* 3.0 57.2 + - + +
237B LYS* 3.7 21.5 - - - +
239B ILE* 1.3 79.1 - - - +
241B SER* 1.3 57.8 + - - +
243B LEU* 3.7 7.8 - - + +
244B ASP* 2.8 38.1 + - - +
356B ARG* 3.4 36.6 - - - +
358B GLU* 2.5 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B PHE* 2.9 28.1 - - - -
237B LYS* 3.1 20.8 + - - -
238B SER* 3.2 8.1 + - - -
240B LYS* 1.3 78.9 - - - +
242B ILE* 1.3 56.5 + - - +
244B ASP* 3.8 5.8 - - - +
245B TRP* 2.8 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B PHE* 3.6 30.3 - - + -
230B ALA 4.4 6.5 - - - +
231B ASP 5.1 0.7 - - - +
232B ILE* 3.6 45.1 - - + -
238B SER* 2.9 18.5 + - - +
239B ILE* 2.9 9.1 + - - +
241B SER* 1.3 73.9 - - - +
243B LEU* 1.3 66.4 + - - +
245B TRP* 3.2 1.8 + - - +
246B THR* 2.8 35.1 + - - +
265B PRO* 3.7 38.1 - - + +
287B TRP* 3.8 11.7 - - + -
290B MET* 5.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B TRP* 5.2 4.0 - - + -
239B ILE* 2.8 32.7 + - + +
240B LYS* 3.8 8.3 - - - +
242B ILE* 1.3 72.4 - - - +
244B ASP* 1.3 61.4 + - - +
246B THR* 3.5 3.6 + - - -
247B SER* 2.9 30.5 + - - -
282B THR* 4.1 20.0 - - + -
286B LEU* 3.6 45.5 - - + -
287B TRP* 4.1 11.7 - - + -
290B MET* 4.1 8.5 - - + -
338B GLU* 5.3 1.6 - - - +
340B TRP* 3.6 20.1 - - + -
354B ILE* 4.2 10.8 - - + -
356B ARG* 4.9 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B LYS* 2.8 24.2 + - - +
241B SER* 3.8 5.1 - - - +
243B LEU* 1.3 71.5 - - - +
245B TRP* 1.3 68.2 + - - +
247B SER* 3.0 8.7 + - - -
248B PHE* 2.9 26.6 + - - +
338B GLU* 4.0 5.9 - - - +
356B ARG* 2.7 43.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B TRP* 3.4 43.4 - + - +
216B TYR* 4.2 2.5 - - - -
228B ASN* 3.4 41.7 - - + -
229B PHE* 3.4 44.4 - + + -
241B SER 2.8 19.3 + - - +
242B ILE 3.8 3.4 - - - +
244B ASP* 1.3 76.9 - - - +
246B THR* 1.3 68.6 + - - +
248B PHE* 3.3 4.4 + + + +
249B ASN* 3.0 63.9 + - + +
253B ILE* 4.2 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ILE* 2.8 25.5 + - - +
243B LEU 3.5 4.3 - - - -
245B TRP* 1.3 89.2 - - - +
247B SER* 1.3 57.3 + - - +
249B ASN 2.9 5.0 + - - -
250B GLN* 2.8 38.0 + - + -
253B ILE* 3.9 19.5 - - + +
254B VAL* 5.8 1.1 - - + -
263B ASN* 6.5 0.2 - - + -
265B PRO* 5.1 3.1 - - - +
290B MET* 4.0 25.3 - - - -
327B GLN* 4.5 10.5 - - - +
340B TRP* 4.5 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LEU 2.9 19.8 + - - -
244B ASP* 3.0 21.8 + - - -
246B THR* 1.3 71.5 - - - +
248B PHE* 1.3 62.8 + - - +
250B GLN* 3.3 31.4 - - - +
330B GLN* 3.8 32.5 + - - +
338B GLU* 4.6 0.2 + - - -
340B TRP* 3.7 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ASP 2.9 19.4 + - - +
245B TRP* 3.4 7.0 - + - +
247B SER* 1.3 79.1 + - - +
249B ASN* 1.3 77.5 + - - +
250B GLN* 3.4 1.3 + - - +
251B GLU* 5.0 2.3 + - - +
252B ARG* 6.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B TRP* 3.7 10.2 - - + -
245B TRP* 3.0 68.9 + - + +
246B THR 2.9 6.3 + - - +
248B PHE* 1.3 92.7 - - - +
250B GLN* 1.3 63.4 + - - +
251B GLU* 3.0 5.3 + - - -
252B ARG* 3.0 44.1 + - - +
253B ILE* 3.5 14.9 + - + +
----------------------------------------------------------
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