Contacts of the helix formed by residues 238 - 258 (chain C) in PDB entry 4LXZ
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 ASP 238 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C GLY 3.3 4.2 + - - +
237C ILE* 1.3 74.7 - - - +
239C ASP* 1.4 66.3 + - - +
240C GLU* 3.6 18.3 - - - +
241C SER* 2.8 33.0 + - - -
242C TYR* 3.0 24.6 + - - +
280C ASN* 3.8 19.1 - - + +
281C LEU* 3.6 5.4 - - - -
352C PRO* 6.0 2.0 - - + -
357C ASN* 4.0 13.8 + - - +
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Residues in contact with ASP 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C ASP* 1.4 73.2 - - - +
240C GLU* 1.3 58.3 + - - +
242C TYR* 4.0 0.7 - - - +
243C GLY* 3.0 27.9 + - - -
280C ASN 4.3 1.9 + - - -
281C LEU* 3.3 9.8 - - - +
282C THR* 2.5 55.5 + - - +
284C LYS* 4.9 1.0 - - - +
285C GLY* 3.3 24.5 + - - +
352C PRO* 6.3 0.4 - - - -
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Residues in contact with GLU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C ASP* 3.6 20.4 - - - +
239C ASP* 1.3 75.5 - - - +
241C SER* 1.3 71.7 + - - +
243C GLY* 4.0 1.0 - - - -
244C GLN* 3.1 48.4 + - - +
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Residues in contact with SER 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C ILE* 3.8 8.7 - - - -
238C ASP* 2.8 22.5 + - - -
240C GLU* 1.3 83.8 + - - +
242C TYR* 1.3 63.1 + - - +
244C GLN* 3.5 7.9 + - - +
245C ILE* 3.3 28.6 + - - +
357C ASN* 3.1 19.7 + - - -
364C MET* 3.7 30.7 - - - +
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Residues in contact with TYR 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ILE* 3.4 28.4 + - + +
203C PHE* 3.3 24.9 + + + +
233C MET* 3.9 26.2 - - + -
237C ILE* 3.8 26.6 - - + +
238C ASP 3.0 17.1 + - - +
239C ASP 4.0 1.6 - - - +
241C SER* 1.3 76.1 - - - +
243C GLY* 1.3 52.5 + - - +
245C ILE* 3.0 8.3 + - + +
246C PHE* 2.8 48.1 + + + +
279C PHE* 4.2 11.4 - + - -
281C LEU* 3.6 31.4 - - + -
285C GLY 5.1 3.8 - - - +
289C CYS* 3.6 30.1 - - - -
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Residues in contact with GLY 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C ASP 3.0 17.9 + - - -
240C GLU* 4.1 0.9 - - - -
242C TYR* 1.3 76.6 - - - +
244C GLN* 1.3 55.9 + - - +
245C ILE 3.2 0.2 - - - -
246C PHE* 4.5 5.8 - - - -
247C LYS* 3.2 32.1 + - - +
285C GLY 6.1 1.3 - - - -
288C LYS* 5.5 12.3 - - - -
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Residues in contact with GLN 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C GLU* 3.1 39.7 + - - +
241C SER* 3.9 7.6 - - - +
242C TYR 3.3 0.4 - - - -
243C GLY* 1.3 74.4 - - - +
245C ILE* 1.3 57.5 + - + +
248C PRO* 3.2 24.0 - - - +
368C LYS* 3.2 17.2 + - - +
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Residues in contact with ILE 245 (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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203C PHE* 3.7 23.6 - - + -
231C PHE* 3.5 46.2 - - + -
233C MET* 4.0 5.4 - - + -
237C ILE* 4.1 11.7 - - + -
241C SER 3.3 18.3 + - - +
242C TYR* 3.0 7.1 + - + +
244C GLN* 1.3 80.1 - - - +
246C PHE* 1.3 66.1 + - + +
247C LYS 3.5 0.2 - - - -
248C PRO* 3.3 2.3 - - - +
249C ILE* 3.2 29.3 + - - +
364C MET* 3.6 31.0 - - + +
368C LYS* 4.5 12.8 - - + +
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Residues in contact with PHE 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C ILE* 3.7 13.7 - - + -
180C ILE* 3.5 21.5 - - + -
203C PHE* 3.6 30.5 - + - -
242C TYR* 2.8 36.3 + + + +
243C GLY* 4.3 5.2 - - - +
245C ILE* 1.3 76.6 - - + +
247C LYS* 1.4 60.5 + - - +
249C ILE* 4.0 0.2 - - - +
250C ILE* 3.0 52.2 + - + +
264C LEU* 4.9 0.7 - - + -
288C LYS 5.4 0.4 - - - -
289C CYS* 3.6 51.8 - - + -
292C VAL* 3.8 20.9 - - + -
293C VAL* 4.1 8.3 - - + -
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Residues in contact with LYS 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C GLY 3.2 12.6 + - - +
246C PHE* 1.4 78.2 - - - +
248C PRO* 1.4 70.0 - - + +
250C ILE* 4.1 0.5 - - - +
251C SER* 2.9 39.8 + - - +
292C VAL* 4.2 36.3 - - + +
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Residues in contact with PRO 248 (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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243C GLY 4.1 0.2 - - - +
244C GLN* 3.2 30.7 - - - +
245C ILE 3.3 7.0 - - - +
247C LYS* 1.4 92.5 - - + +
249C ILE* 1.3 59.6 + - - +
251C SER* 3.7 5.8 - - - -
252C LYS* 3.0 26.0 + - - +
368C LYS* 4.3 14.1 - - + +
372C PHE* 3.5 21.3 - - + -
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Residues in contact with ILE 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C VAL* 4.5 7.4 - - + -
203C PHE* 3.9 21.5 - - + -
229C VAL* 4.8 2.2 - - + -
231C PHE* 4.5 9.9 - - + -
245C ILE 3.2 21.9 + - - +
246C PHE 4.0 1.8 - - - +
248C PRO* 1.3 78.0 - - - +
250C ILE* 1.4 58.3 + - + +
252C LYS* 3.2 5.0 + - - +
253C VAL* 2.8 43.6 + - + +
368C LYS* 3.9 15.7 - - + -
371C LEU* 3.8 38.4 - - + -
372C PHE* 3.6 29.6 - - + -
375C LEU* 4.2 4.6 - - + +
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Residues in contact with ILE 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C LEU* 5.1 1.1 - - + -
178C ILE* 3.8 38.1 - - + -
201C VAL* 3.9 31.2 - - + -
203C PHE* 4.0 6.1 - - + -
246C PHE* 3.0 46.1 + - + +
247C LYS 4.4 0.9 - - - +
249C ILE* 1.4 71.3 - - + +
251C SER* 1.4 56.3 + - - +
253C VAL* 3.1 7.1 + - + +
254C MET* 2.8 56.7 + - + +
292C VAL* 4.5 9.2 - - + -
293C VAL* 4.5 4.9 - - + -
296C PHE* 4.3 9.4 - - + -
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Residues in contact with SER 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C LYS* 2.9 35.9 + - - +
248C PRO* 3.7 6.7 - - - -
250C ILE* 1.4 76.2 - - - +
252C LYS* 1.3 56.4 + - - +
254C MET* 3.4 2.6 + - - +
255C GLU* 3.1 27.4 + - - +
292C VAL* 5.4 0.2 - - - +
296C PHE* 3.8 26.1 - - - -
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Residues in contact with LYS 252 (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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248C PRO 3.0 18.1 + - - +
249C ILE 3.6 3.8 - - - +
251C SER* 1.3 73.0 - - - +
253C VAL* 1.4 65.8 + - - +
255C GLU* 3.3 24.4 + - - +
256C MET* 3.0 49.5 + - - +
372C PHE* 3.4 57.2 + - + -
375C LEU* 3.7 22.1 - - + +
376C ARG* 3.4 20.2 - - - +
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Residues in contact with VAL 253 (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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176C LEU* 3.5 41.3 - - + -
199C MET* 3.7 12.3 - - - -
201C VAL* 4.2 18.2 - - + -
229C VAL* 5.0 2.0 - - + -
249C ILE* 2.8 27.4 + - + +
250C ILE* 3.1 11.4 + - + +
252C LYS* 1.4 75.1 - - - +
254C MET* 1.3 54.8 + - - +
256C MET* 5.0 0.2 - - - -
257C TYR* 2.7 41.6 + - + +
259C PRO* 5.8 0.2 - - + -
375C LEU* 3.8 28.7 - - + -
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Residues in contact with MET 254 (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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176C LEU* 3.7 22.7 - - + -
178C ILE* 4.8 0.7 - - + -
250C ILE* 2.8 32.0 + - + +
251C SER 3.7 2.0 - - - +
252C LYS 3.3 0.2 - - - -
253C VAL* 1.3 73.0 - - - +
255C GLU* 1.3 56.5 + - - +
258C GLN* 2.9 30.8 + - - +
259C PRO* 3.8 25.7 - - - +
262C VAL* 3.9 17.5 - - + -
293C VAL* 4.7 11.0 - - + +
296C PHE* 3.6 57.2 - - + -
298C LEU* 3.9 9.4 - - - -
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Residues in contact with GLU 255 (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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251C SER 3.1 17.1 + - - +
252C LYS* 3.5 31.5 - - - +
253C VAL 3.3 0.2 - - - -
254C MET* 1.3 78.3 - - - +
256C MET* 1.3 66.3 + - - +
258C GLN* 3.0 24.7 - - - +
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Residues in contact with MET 256 (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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252C LYS* 3.0 46.4 + - + +
253C VAL* 4.2 2.0 - - - +
255C GLU* 1.3 90.3 - - - +
257C TYR* 1.3 60.9 + - - +
258C GLN* 3.8 7.4 - - - +
375C LEU* 3.5 28.3 - - + +
376C ARG* 4.2 9.9 - - + +
378C LEU* 3.7 24.6 - - + +
379C PRO* 3.6 32.5 - - + -
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Residues in contact with TYR 257 (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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174C ARG* 2.9 49.8 + - + +
175C VAL 3.6 21.1 - - - -
176C LEU* 4.4 4.7 - - + -
196C ASP 2.8 29.3 + - - -
197C ARG 3.0 23.4 + - - -
198C VAL* 3.2 3.8 + - - -
199C MET* 3.7 29.8 - - + -
227C TYR* 3.5 30.3 - + - -
253C VAL* 2.7 22.2 + - + +
256C MET* 1.3 74.7 - - - +
258C GLN* 1.3 66.8 + - - +
259C PRO* 3.8 17.5 - - + -
378C LEU* 3.8 9.9 - - + -
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Residues in contact with GLN 258 (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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174C ARG* 2.8 32.3 + - - +
254C MET 2.9 16.1 + - - +
255C GLU* 3.0 23.6 - - - +
256C MET* 3.8 9.1 - - - +
257C TYR* 1.3 72.5 - - - +
259C PRO* 1.3 72.0 - - - +
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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