Contacts of the helix formed by residues 226 - 239 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A THR* 6.5 0.4 - - + -
274A ARG* 6.2 1.6 - - - +
224C PRO 4.0 3.6 + - - -
225C SER* 1.3 72.5 + - - +
227C ARG* 1.3 62.6 + - - +
229C LEU* 4.1 4.3 - - - +
230C LYS* 3.0 25.8 + - - +
265C VAL* 4.6 22.1 - - + +
266C LEU* 6.4 1.8 - - + -
269C ASP* 6.2 3.8 - - + -
272C THR* 5.4 0.2 + - - -
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Residues in contact with ARG 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ARG* 4.2 32.1 - - - +
176C GLU* 2.5 36.0 + - - +
177C LEU* 4.1 20.2 - - - +
180C THR* 4.1 18.6 + - + +
225C SER* 3.5 8.1 - - - +
226C ALA* 1.3 81.0 - - - +
228C LEU* 1.3 64.0 + - - +
230C LYS* 3.6 6.2 + - - +
231C HIS* 3.0 30.8 + - - -
802D GLU* 3.9 19.8 + - - -
806D VAL* 3.5 29.2 - - - +
809D VAL* 5.8 1.1 - - + -
810D ASP* 4.7 9.4 - - - +
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Residues in contact with LEU 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C GLU* 4.4 12.3 - - + +
179C LYS* 4.1 28.3 - - + +
180C THR* 3.8 29.4 - - - +
183C THR* 3.8 24.2 - - - +
216C MET* 4.8 9.4 - - + +
219C GLN* 6.1 0.2 - - - +
220C LEU* 4.0 20.2 - - + -
225C SER* 3.2 21.4 + - - +
227C ARG* 1.3 76.8 - - - +
229C LEU* 1.3 65.2 + - - +
231C HIS* 3.1 4.1 + - + -
232C VAL* 3.0 37.1 + - + +
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Residues in contact with LEU 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C VAL* 5.6 0.7 - - + -
220C LEU* 3.9 26.8 - - + +
225C SER 3.0 19.7 + - - +
226C ALA* 4.1 3.6 - - - +
228C LEU* 1.3 76.8 - - - +
230C LYS* 1.3 62.6 + - - +
232C VAL* 4.3 4.9 - - + -
233C VAL* 2.9 49.5 + - + +
257C LEU* 4.2 15.9 - - + -
262C PHE* 3.6 43.3 - - + -
265C VAL* 5.1 8.3 - - + -
266C LEU* 4.0 22.4 - - + -
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Residues in contact with LYS 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A THR* 3.1 37.1 + - - +
275A TRP* 5.5 1.2 - - - -
226C ALA 3.0 19.2 + - - +
227C ARG* 3.7 7.9 - - - +
228C LEU 3.2 0.2 - - - -
229C LEU* 1.3 77.2 - - - +
231C HIS* 1.3 72.9 + - + +
233C VAL* 3.6 2.1 + - - +
234C ARG* 3.0 25.5 + - - +
269C ASP* 4.3 4.9 - - - +
271C THR* 4.2 6.7 - - - -
272C THR* 3.4 29.1 - - - +
275C TRP* 3.6 32.3 - - + -
810D ASP* 5.0 19.1 + - - +
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Residues in contact with HIS 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C THR* 4.0 20.4 - - + -
183C THR* 3.7 21.5 - - + -
184C PHE* 3.9 16.5 - + - +
187C GLN* 2.5 35.5 + - - +
227C ARG 3.0 23.7 + - - -
228C LEU* 3.1 6.0 + - + +
230C LYS* 1.3 88.1 - - + +
232C VAL* 1.3 65.7 + - - +
234C ARG* 3.7 2.3 - - - +
235C CYS* 3.0 28.9 + - - -
275C TRP* 6.0 1.5 - + - -
809D VAL* 3.1 33.7 + - - +
810D ASP* 3.7 11.9 + - - -
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Residues in contact with VAL 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C THR* 4.3 7.2 - - + -
213C LEU* 4.2 12.5 - - + +
216C MET* 4.1 25.6 - - + -
217C VAL* 4.0 17.7 - - + -
220C LEU* 4.1 15.7 - - + -
228C LEU* 3.0 27.5 + - + +
229C LEU* 3.3 10.1 + - + +
231C HIS* 1.3 73.7 - - - +
233C VAL* 1.3 66.7 + - + +
235C CYS* 3.2 7.1 + - - +
236C TYR* 3.0 49.9 + - + -
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Residues in contact with VAL 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C LEU* 2.9 41.0 + - + +
230C LYS 3.8 3.6 - - - +
232C VAL* 1.3 75.1 - - + +
234C ARG* 1.3 57.7 + - - +
236C TYR* 3.0 10.3 + - - +
237C LEU* 2.8 27.3 + - + +
257C LEU* 4.3 16.6 - - + -
266C LEU* 6.0 0.7 - - + -
272C THR* 4.3 12.8 - - + +
275C TRP* 3.9 14.8 - - + +
276C LEU* 3.7 42.2 - - + +
279C LEU* 4.8 4.6 - - + +
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Residues in contact with ARG 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LYS* 4.7 19.2 - - - +
810B ASP* 5.7 1.6 + - - -
187C GLN* 3.7 33.6 - - + +
191C LEU* 3.4 28.8 - - + +
230C LYS 3.0 17.9 + - - +
231C HIS* 3.7 5.6 - - - +
232C VAL 3.2 0.4 - - - -
233C VAL* 1.3 77.2 - - - +
235C CYS* 1.3 57.0 + - - +
237C LEU* 3.3 32.1 + - - +
238C ARG* 3.0 40.5 + - + +
241C ASP* 5.7 0.4 + - - -
275C TRP* 3.5 45.9 - - + +
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Residues in contact with CYS 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C THR* 3.8 17.5 - - - -
186C LEU* 4.2 7.6 - - - -
187C GLN* 3.7 33.9 - - - +
190C LEU* 4.0 18.8 - - + +
213C LEU* 4.1 17.3 - - + -
231C HIS 3.0 20.5 + - - +
232C VAL 3.5 8.1 - - - +
234C ARG* 1.3 76.0 - - - +
236C TYR* 1.3 57.7 + - - +
238C ARG* 4.0 3.5 - - - +
239C LEU* 3.0 35.6 + - - +
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Residues in contact with TYR 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C ALA* 4.0 5.4 + - + -
213C LEU* 3.1 22.5 + - + +
214C GLY* 3.0 34.0 + - - -
217C VAL* 4.0 3.4 - - + -
232C VAL* 3.0 46.1 + - + -
233C VAL* 3.0 8.3 + - - +
235C CYS* 1.3 74.8 - - - +
237C LEU* 1.3 64.2 + - - +
239C LEU* 3.4 7.9 + - + +
240C SER* 3.0 17.0 + - - -
249C LEU* 3.8 35.4 - - + +
252C CYS 5.2 1.4 + - - -
253C LEU* 4.0 12.8 - - + -
254C PRO* 3.8 14.0 - - + +
257C LEU* 3.9 19.5 - - + -
279C LEU* 3.5 26.8 - - + +
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Residues in contact with LEU 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C VAL 2.8 16.2 + - - +
234C ARG* 3.4 25.6 - - - +
236C TYR* 1.3 76.3 - - - +
238C ARG* 1.3 61.7 + - - +
240C SER* 2.3 35.6 + - - +
241C ASP* 3.6 9.2 + - - +
275C TRP* 3.9 40.4 - - + +
278C GLN* 4.0 26.0 - - + +
279C LEU* 3.8 32.2 - - + +
282C ASN* 4.8 2.7 - - - +
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Residues in contact with ARG 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C GLN* 6.6 0.2 - - + -
190C LEU* 2.8 40.8 + - + +
191C LEU* 3.3 37.2 + - + +
192C ASP 3.8 0.2 + - - -
193C ASP* 2.8 37.2 + - - +
196C LEU* 3.6 23.2 - - + +
234C ARG* 3.0 27.9 + - + +
235C CYS* 4.2 3.6 - - - +
237C LEU* 1.3 75.3 - - - +
239C LEU* 1.3 63.1 + - - +
241C ASP* 3.0 52.5 + - - +
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Residues in contact with LEU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C LEU* 3.8 27.4 - - + -
196C LEU* 4.2 3.6 - - + -
199C ILE* 4.6 5.8 - - + -
200C CYS* 4.1 22.7 - - - -
206C PHE* 4.2 22.7 - - + -
209C VAL* 4.2 10.8 - - + -
210C ALA* 5.5 1.8 - - - +
213C LEU* 3.8 25.1 - - + -
235C CYS 3.0 26.1 + - - +
236C TYR* 3.5 11.2 - - + +
237C LEU 3.3 0.2 - - - -
238C ARG* 1.3 75.8 - - - +
240C SER* 1.3 57.6 + - - +
242C ASN* 3.1 17.8 + - - +
245C ALA* 3.3 19.3 - - + +
249C LEU* 4.0 14.1 - - + -
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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) + - + + + + + -
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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