Contacts of the helix formed by residues 238 - 258 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B GLY 3.4 3.6 + - - +
237B ILE* 1.3 73.6 - - - +
239B ASP* 1.3 65.8 + - - +
240B GLU* 3.3 21.1 - - - +
241B SER* 2.9 36.2 + - - -
242B TYR* 3.0 24.4 + - - +
280B ASN* 3.7 18.8 - - + +
281B LEU* 3.6 5.2 - - - -
352B PRO* 5.8 2.9 - - + -
357B ASN* 3.6 19.9 + - - +
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Residues in contact with ASP 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ASP* 1.3 73.5 - - - +
240B GLU* 1.3 69.2 + - - +
242B TYR* 4.0 0.8 - - - +
243B GLY* 2.9 29.3 + - - -
280B ASN 4.4 1.0 + - - -
281B LEU* 3.3 9.2 - - - +
282B THR* 2.5 56.3 + - - +
284B LYS* 4.8 2.1 - - - +
285B GLY* 3.2 26.4 + - - -
352B PRO* 6.4 0.2 - - - -
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Residues in contact with GLU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ASP* 3.3 27.1 - - - +
239B ASP* 1.3 86.3 + - - +
241B SER* 1.3 57.6 + - - +
243B GLY* 3.9 0.7 - - - -
244B GLN* 3.1 37.2 + - + +
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Residues in contact with SER 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ILE* 3.9 15.9 - - - -
238B ASP* 2.9 18.9 + - - -
240B GLU* 1.3 73.8 - - - +
242B TYR* 1.4 65.8 + - - +
244B GLN* 3.6 6.8 + - - +
245B ILE* 3.5 21.3 + - - +
357B ASN* 3.1 21.2 + - - -
359B ASN 4.5 2.8 + - - -
364B MET* 3.8 18.7 - - - +
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Residues in contact with TYR 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ILE* 3.4 27.8 + - + +
203B PHE* 3.3 25.3 + + + +
233B MET* 3.7 28.9 - - + -
237B ILE* 4.0 15.4 - - + +
238B ASP 3.0 18.5 + - - +
239B ASP* 4.0 2.2 - - - +
241B SER* 1.4 73.9 - - - +
243B GLY* 1.3 53.0 + - - +
245B ILE* 3.2 7.9 + - - +
246B PHE* 2.8 49.9 + + + +
279B PHE* 4.3 10.4 - + - -
281B LEU* 3.7 36.3 - - + -
285B GLY 5.0 4.3 - - - +
289B CYS* 3.5 31.0 - - - -
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Residues in contact with GLY 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ASP 2.9 18.6 + - - -
240B GLU 3.9 0.7 - - - -
242B TYR* 1.3 76.8 - - - +
244B GLN* 1.4 61.2 + - - +
245B ILE 3.4 0.5 + - - -
246B PHE* 4.5 5.2 - - - -
247B LYS* 3.5 25.5 + - - +
248B PRO* 4.2 0.3 - - - +
285B GLY 6.1 0.9 - - - -
288B LYS* 5.4 12.8 - - - -
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Residues in contact with GLN 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B GLU* 3.1 23.6 + - - +
241B SER* 3.9 7.6 - - - +
242B TYR 3.3 0.4 - - - -
243B GLY* 1.4 75.7 - - - +
245B ILE* 1.3 60.8 + - + +
248B PRO* 3.3 13.2 - - - +
365B GLU* 5.1 8.3 - - - +
368B LYS* 3.1 22.9 + - - -
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Residues in contact with ILE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B PHE* 3.5 33.4 - - + -
231B PHE* 3.6 21.8 - - + -
233B MET* 3.6 11.7 - - + -
241B SER 3.5 3.5 + - - +
242B TYR* 3.2 10.0 + - + +
244B GLN* 1.3 81.6 - - + +
246B PHE* 1.4 68.9 + - + +
247B LYS 3.5 0.4 - - - -
248B PRO* 3.4 2.8 - - - +
249B ILE* 3.1 28.0 + - + +
364B MET* 3.4 52.7 - - + +
365B GLU* 4.6 2.0 - - - +
368B LYS* 3.7 22.7 - - - +
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Residues in contact with PHE 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ILE* 3.7 13.0 - - + -
180B ILE* 3.6 22.9 - - + -
203B PHE* 3.6 29.4 - + - -
242B TYR* 2.8 36.6 + + + +
243B GLY* 3.6 4.4 + - - +
245B ILE* 1.4 78.4 - - + +
247B LYS* 1.3 65.1 + - - +
249B ILE* 3.8 0.5 - - - +
250B ILE* 3.0 46.6 + - + +
264B LEU* 4.9 0.4 - - + -
289B CYS* 3.6 51.1 - - + -
292B VAL* 3.9 20.9 - - + -
293B VAL* 4.0 9.0 - - + -
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Residues in contact with LYS 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B GLY 3.5 11.3 + - - +
246B PHE* 1.3 78.0 - - - +
248B PRO* 1.4 64.4 - - + +
250B ILE* 3.8 0.5 - - - +
251B SER* 2.8 43.5 + - - +
288B LYS* 5.5 9.8 - - - +
292B VAL* 4.1 36.2 - - + +
295B THR* 6.2 0.2 - - - -
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Residues in contact with PRO 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B GLY 4.2 0.7 - - - +
244B GLN* 3.3 29.6 - - - +
245B ILE 3.4 7.6 - - - +
247B LYS* 1.4 94.3 - - + +
249B ILE* 1.3 59.9 + - - +
251B SER* 3.9 5.8 - - - -
252B LYS* 3.1 24.8 + - - +
368B LYS* 4.0 12.6 - - + +
372B PHE* 3.6 21.5 - - + -
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Residues in contact with ILE 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B VAL* 4.5 8.5 - - + -
203B PHE* 3.9 22.9 - - + -
229B VAL* 4.8 3.1 - - + -
231B PHE* 4.4 12.1 - - + -
245B ILE 3.1 24.3 + - - +
246B PHE 3.9 2.2 - - - +
248B PRO* 1.3 76.6 - - - +
250B ILE* 1.3 58.6 + - - +
252B LYS* 3.3 2.6 + - - +
253B VAL* 2.9 44.0 + - + +
368B LYS* 3.8 20.2 - - + +
371B LEU* 3.9 37.2 - - + -
372B PHE* 3.7 23.1 - - + -
375B LEU* 4.3 3.0 - - + +
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Residues in contact with ILE 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LEU* 5.1 2.2 - - + -
178B ILE* 3.8 40.2 - - + -
201B VAL* 4.0 23.3 - - + -
203B PHE* 4.1 6.5 - - + -
246B PHE* 3.0 43.8 + - + +
247B LYS 4.2 1.3 - - - +
249B ILE* 1.3 72.6 - - + +
251B SER* 1.3 60.2 + - - +
253B VAL* 3.3 6.4 + - + +
254B MET* 2.9 50.1 + - + +
292B VAL* 4.5 4.7 - - + -
293B VAL* 4.5 7.9 - - + -
296B PHE* 4.1 20.0 - - + -
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Residues in contact with SER 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B LYS* 2.8 42.3 + - - +
248B PRO* 3.9 6.1 - - - -
250B ILE* 1.3 72.9 - - - +
252B LYS* 1.3 56.6 + - - +
254B MET* 3.4 2.9 + - - +
255B GLU* 3.0 29.0 + - - +
296B PHE* 3.8 25.0 - - - -
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Residues in contact with LYS 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B PRO 3.1 18.1 + - - +
249B ILE 3.7 3.6 - - - +
251B SER* 1.3 72.5 - - - +
253B VAL* 1.3 60.7 + - - +
255B GLU* 3.2 30.9 + - - +
256B MET* 2.9 58.6 + - - +
372B PHE* 3.8 22.0 - - + -
375B LEU* 3.8 22.0 - - + -
376B ARG* 4.3 34.4 - - - +
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Residues in contact with VAL 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B LEU* 3.7 32.1 - - + -
199B MET* 3.6 24.2 - - - -
201B VAL* 4.2 13.7 - - + -
229B VAL* 5.0 2.5 - - + -
249B ILE* 2.9 29.4 + - + +
250B ILE* 3.6 8.1 - - + +
252B LYS* 1.3 75.8 - - - +
254B MET* 1.4 55.8 + - - +
256B MET* 5.0 0.2 - - - -
257B TYR* 2.7 43.0 + - + +
375B LEU* 3.8 29.4 - - + -
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Residues in contact with MET 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B LEU* 3.7 22.4 - - + -
178B ILE* 4.9 0.2 - - + -
250B ILE* 2.9 32.5 + - + +
251B SER 3.7 4.9 - - - +
252B LYS 3.3 0.2 - - - -
253B VAL* 1.4 72.1 - - - +
255B GLU* 1.3 58.6 + - - +
258B GLN* 2.9 29.6 + - - +
259B PRO* 3.7 25.8 - - - -
262B VAL* 3.9 17.7 - - + -
293B VAL* 4.7 8.7 - - + +
296B PHE* 3.6 55.6 - - + -
298B LEU* 3.8 9.9 - - + -
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Residues in contact with GLU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B SER 3.0 16.5 + - - +
252B LYS* 3.2 39.1 + - - +
254B MET* 1.3 79.3 - - - +
256B MET* 1.3 69.6 + - - +
258B GLN* 3.4 16.2 + - - +
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Residues in contact with MET 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B LYS* 2.9 52.6 + - + +
253B VAL* 4.2 1.6 - - - +
255B GLU* 1.3 90.7 - - - +
257B TYR* 1.3 59.3 + - - +
258B GLN* 4.5 6.2 + - - +
375B LEU* 3.6 28.3 - - + +
376B ARG* 4.3 10.8 - - - +
378B LEU* 3.9 42.8 - - + +
379B PRO 4.9 7.4 - - - +
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Residues in contact with TYR 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B ARG* 3.1 49.0 + - + +
175B VAL 3.6 17.5 - - - -
176B LEU* 4.3 4.3 - - + -
196B ASP 2.7 29.3 + - - -
197B ARG 3.0 23.2 + - - -
198B VAL 3.2 2.6 + - - -
199B MET* 3.5 30.3 + - + -
227B TYR* 3.5 29.2 - + - -
253B VAL* 2.7 24.1 + - + +
256B MET* 1.3 72.9 - - - +
258B GLN* 1.3 67.4 + - - +
259B PRO* 3.8 21.5 - - + -
378B LEU* 4.0 9.6 - - + -
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Residues in contact with GLN 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B ARG* 3.2 26.7 + - - +
254B MET 2.9 17.0 + - - +
255B GLU* 3.4 21.9 + - - +
256B MET 4.5 4.8 + - - +
257B TYR* 1.3 77.7 - - - +
259B PRO* 1.3 72.0 - - - +
260B SER* 5.2 0.5 - - - -
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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