Contacts of the helix formed by residues 226 - 239 (chain A) in PDB entry 5LSW
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 ALA 226 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A PRO 4.3 0.4 - - - -
225A SER* 1.3 73.2 + - - +
227A ARG* 1.3 63.0 + - - +
229A LEU* 3.4 7.5 + - - +
230A LYS* 3.2 22.0 + - - +
265A VAL* 4.5 22.8 - - + +
266A LEU* 6.6 0.2 - - - -
269A ASP* 5.3 9.4 - - + +
272A THR* 5.2 1.4 + - - +
274C ARG* 5.5 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A GLU* 2.6 32.8 + - - +
177A LEU* 3.6 28.9 - - - +
180A THR* 4.2 16.7 + - + +
225A SER* 3.7 7.2 - - - +
226A ALA* 1.3 80.0 - - - +
228A LEU* 1.3 63.5 + - - +
230A LYS* 3.4 11.2 + - - +
231A HIS* 3.1 27.1 - - - -
802B GLU* 3.0 27.2 + - - -
806B VAL* 3.5 26.5 - - - +
809B VAL* 5.7 0.9 - - + -
810B ASP* 4.5 8.5 - - - +
274C ARG* 4.3 27.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A GLU* 4.4 13.0 - - + +
179A LYS* 3.9 29.6 - - + -
180A THR* 3.7 35.4 - - - +
183A THR* 3.9 8.1 - - - +
216A MET* 3.8 27.8 - - + -
220A LEU* 4.1 20.6 - - + -
225A SER* 3.3 18.7 + - - +
226A ALA 3.3 0.4 - - - -
227A ARG* 1.3 80.4 - - - +
229A LEU* 1.3 65.8 + - - +
230A LYS 3.3 0.2 + - - -
231A HIS* 3.3 3.1 + - + -
232A VAL* 3.2 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A VAL* 5.7 1.3 - - + -
220A LEU* 3.8 24.1 - - + +
225A SER 3.1 19.1 + - - +
226A ALA* 3.8 7.4 - - - +
228A LEU* 1.3 76.5 - - - +
230A LYS* 1.3 62.2 + - - +
232A VAL* 3.4 6.0 + - + -
233A VAL* 3.0 41.8 + - + +
257A LEU* 4.3 15.9 - - + -
262A PHE* 3.8 35.4 - - + -
265A VAL* 6.0 4.5 - - + -
266A LEU* 3.8 30.7 - - + -
272A THR* 4.7 0.4 - - + -
276A LEU* 6.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ALA 3.2 12.5 + - - +
227A ARG* 3.5 12.1 - - - +
228A LEU 3.2 1.0 - - - -
229A LEU* 1.3 78.2 - - - +
231A HIS* 1.3 66.7 + - + +
233A VAL* 3.5 2.3 + - - +
234A ARG* 3.1 25.5 + - - +
269A ASP* 4.6 2.2 - - - +
271A THR* 4.5 5.6 - - - +
272A THR* 3.7 27.8 - - - +
275A TRP* 3.6 34.3 - - + -
810B ASP* 3.8 34.9 + - - +
271C THR* 3.5 32.9 - - + +
275C TRP* 5.8 4.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A THR* 4.1 7.9 - - + +
183A THR* 3.6 21.5 - - + -
184A PHE* 3.7 18.2 - + + +
187A GLN* 2.6 32.1 + - - +
227A ARG 3.1 25.1 - - - -
228A LEU* 3.3 6.3 + - + +
229A LEU 3.3 0.2 - - - -
230A LYS* 1.3 87.4 - - + +
232A VAL* 1.3 65.2 + - - +
234A ARG* 3.4 2.8 + - - +
235A CYS* 3.1 27.9 + - - -
275A TRP* 6.2 0.6 - + - -
809B VAL* 3.1 49.5 - - + +
810B ASP* 3.2 11.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A THR* 4.3 7.0 - - + -
213A LEU* 4.2 14.3 - - + +
216A MET* 3.7 32.5 - - + -
217A VAL* 4.2 15.0 - - + -
220A LEU* 4.4 11.2 - - + -
228A LEU* 3.2 22.4 + - + +
229A LEU* 3.8 9.0 - - + +
231A HIS* 1.3 73.9 - - - +
233A VAL* 1.3 68.3 + - + +
235A CYS* 3.2 7.3 + - - +
236A TYR* 3.0 43.1 + - + -
257A LEU* 5.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LEU* 3.0 39.4 + - + +
230A LYS 3.9 3.1 - - - +
232A VAL* 1.3 75.4 - - + +
234A ARG* 1.3 52.7 + - - +
236A TYR* 3.1 9.2 + - - +
237A LEU* 2.7 33.6 + - - +
257A LEU* 4.5 15.3 - - + -
272A THR* 4.4 11.9 - - + +
275A TRP* 4.0 13.9 - - + +
276A LEU* 3.7 44.6 - - + +
279A LEU* 5.0 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLN* 3.6 35.5 - - + +
191A LEU* 3.3 28.2 - - + +
230A LYS 3.1 17.4 + - - +
231A HIS 3.6 5.8 - - - +
232A VAL 3.2 0.2 - - - -
233A VAL* 1.3 77.8 - - - +
235A CYS* 1.3 56.5 + - - +
237A LEU* 3.3 32.8 + - - +
238A ARG* 2.9 39.3 + - + +
275A TRP* 3.5 43.1 - - + -
148C LYS* 5.1 13.7 - - - +
810D ASP* 5.6 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A THR* 3.9 17.7 - - - -
186A LEU* 4.3 7.6 - - - -
187A GLN* 3.8 33.4 - - - +
190A LEU* 3.8 20.2 - - + +
213A LEU* 4.1 17.0 - - + -
231A HIS 3.1 23.2 + - - -
232A VAL 3.2 8.0 + - - +
234A ARG* 1.3 73.3 - - - +
236A TYR* 1.3 59.4 + - - +
238A ARG* 3.5 3.6 + - - +
239A LEU* 2.9 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ALA* 4.0 6.4 + - - -
213A LEU* 3.2 22.5 - - + +
214A GLY* 3.0 32.9 + - - -
217A VAL* 4.0 4.3 - - + -
232A VAL* 3.0 38.0 + - + -
233A VAL* 3.5 9.2 - - - +
235A CYS* 1.3 76.1 - - - +
237A LEU* 1.3 62.5 + - - +
239A LEU* 3.2 8.1 + - + +
240A SER 3.1 17.0 + - - -
249A LEU* 3.6 38.6 - - + +
252A CYS* 4.9 2.4 + - - -
253A LEU* 4.4 5.6 - - + -
254A PRO* 3.8 13.0 - - + +
257A LEU* 3.8 28.7 - - + -
279A LEU* 3.6 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A VAL 2.7 20.1 + - - +
234A ARG* 3.3 29.6 - - - +
236A TYR* 1.3 73.5 - - - +
238A ARG* 1.3 60.6 + - - +
240A SER* 2.4 28.4 + - - +
241A ASP* 3.7 7.8 - - - +
275A TRP* 4.1 46.4 - - + +
278A GLN* 4.3 18.2 - - + +
279A LEU* 3.9 17.4 - - + +
282A ASN* 4.1 22.4 - - - +
810D ASP 5.9 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLN* 6.5 0.4 - - + -
190A LEU* 2.6 44.2 + - + +
191A LEU* 3.2 37.9 + - + +
192A ASP 3.7 6.7 + - - -
193A ASP* 3.0 29.3 + - - +
196A LEU* 3.7 23.5 - - + +
234A ARG* 2.9 28.5 + - + +
235A CYS* 4.0 3.6 - - - +
237A LEU* 1.3 77.3 - - - +
239A LEU* 1.3 62.9 + - - +
241A ASP* 2.9 46.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A LEU* 3.8 27.1 - - + -
196A LEU* 4.1 2.9 - - + -
199A ILE* 4.9 6.3 - - + -
200A CYS* 3.9 24.5 - - - -
206A PHE* 3.9 24.5 - - + -
209A VAL* 4.2 10.1 - - + -
210A ALA* 5.5 2.0 - - - +
213A LEU* 4.0 24.0 - - + -
235A CYS 2.9 21.6 + - - +
236A TYR* 3.5 13.2 - - + +
238A ARG* 1.3 76.4 - - - +
240A SER* 1.3 57.4 + - - +
242A ASN* 3.0 19.1 + - - +
245A ALA* 3.3 20.3 - - + +
249A LEU* 4.2 8.5 - - + -
----------------------------------------------------------
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