Contacts of the helix formed by residues 220 - 238 (chain B) in PDB entry 1LT8
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 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219B PHE* 1.3 73.2 - - - +
221B PRO* 1.3 74.2 - - + +
222B THR* 3.0 6.4 + - - -
223B ILE* 2.8 27.6 + - - +
224B SER* 2.8 23.1 + - - -
248B PRO* 3.9 0.2 - - - -
249B LEU 4.1 1.3 - - - -
251B TYR 3.0 24.1 + - - +
252B HIS* 3.8 5.8 - - + -
253B THR* 2.9 30.8 + - - +
702B CIT 2.4 30.7 - - - +
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Residues in contact with PRO 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ASP* 1.3 90.0 - - + +
222B THR* 1.3 58.2 + - - +
224B SER* 3.5 0.9 + - - -
225B LEU* 3.0 35.4 + - - +
248B PRO* 3.6 20.4 - - + -
249B LEU 3.2 21.1 - - - +
250B ALA* 5.0 2.7 - - - -
251B TYR 4.6 2.5 - - - +
252B HIS* 6.2 2.7 - - + +
276B ALA* 5.7 3.6 - - + -
280B ASP* 5.6 1.1 - - + +
281B ILE* 4.4 15.3 - - + -
284B TYR* 3.5 36.3 - - + -
287B GLU* 5.9 0.4 - - - -
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Residues in contact with THR 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ASP* 3.0 7.6 + - - -
221B PRO* 1.3 78.4 - - - +
223B ILE* 1.3 66.9 + - + +
225B LEU* 3.4 5.5 + - - +
226B LYS* 3.3 35.9 + - + +
283B LYS* 4.1 18.2 + - - -
287B GLU* 4.9 7.1 + - - +
702B CIT 4.4 26.2 + - + +
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Residues in contact with ILE 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B PRO* 3.6 25.6 - - + -
219B PHE* 3.7 30.5 - - + -
220B ASP* 2.8 24.3 + - - +
222B THR* 1.3 76.6 - - + +
224B SER* 1.3 60.6 + - - +
226B LYS* 3.2 16.2 + - + +
227B THR* 2.9 26.0 + - - +
253B THR* 3.3 31.6 - - - +
254B PRO* 4.5 5.4 - - + +
256B ALA* 5.5 3.4 - - + +
702B CIT 4.1 7.0 - - - +
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Residues in contact with SER 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B VAL* 3.9 19.3 - - - +
216B ASN 6.0 0.2 - - - -
217B CYS 4.6 3.8 + - - -
219B PHE* 3.3 19.6 + - - +
220B ASP 2.8 21.1 + - - -
221B PRO 3.5 5.8 - - - -
223B ILE* 1.3 78.0 - - - +
225B LEU* 1.3 60.8 + - - +
227B THR* 3.0 10.2 + - - -
228B VAL* 2.9 29.4 + - - +
246B SER* 5.6 0.7 - - - -
248B PRO* 3.3 21.3 - - - +
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Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B PRO 3.0 19.1 + - - +
222B THR* 3.4 4.7 + - - +
223B ILE 3.3 0.2 - - - -
224B SER* 1.3 74.6 - - - +
226B LYS* 1.3 66.2 + - - +
228B VAL* 3.7 4.3 - - + -
229B LYS* 3.0 23.4 + - - +
246B SER* 4.1 16.6 - - - +
284B TYR* 3.9 23.3 - - + +
287B GLU* 3.7 23.6 - - + +
288B ALA* 3.5 44.0 - - + +
291B LEU* 3.7 19.9 - - + +
293B VAL* 4.4 3.1 - - + -
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Residues in contact with LYS 226 (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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189B PRO* 4.0 16.6 - - + -
222B THR* 3.3 29.7 + - + +
223B ILE* 3.2 19.0 + - + +
224B SER 3.1 0.2 - - - -
225B LEU* 1.3 77.1 - - - +
227B THR* 1.3 63.5 + - - +
229B LYS* 3.3 10.3 + - + +
230B LEU* 3.1 28.3 + - + +
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Residues in contact with THR 227 (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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187B ILE* 3.6 23.0 + - + +
188B GLY* 3.4 18.9 - - - +
189B PRO* 3.2 18.0 - - - +
198B PRO* 4.1 12.8 - - + -
215B VAL* 3.7 17.5 - - + -
219B PHE* 5.5 0.3 - - - -
223B ILE 2.9 13.5 + - - -
224B SER* 3.3 9.7 - - - -
226B LYS* 1.3 76.5 - - - +
228B VAL* 1.3 64.5 + - - +
230B LEU* 3.1 11.9 + - - +
231B MET* 3.0 26.7 + - + +
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Residues in contact with VAL 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ILE* 6.4 0.2 - - + -
214B GLY* 4.8 3.8 - - - -
215B VAL* 3.7 24.9 - - + +
224B SER 2.9 19.6 + - - +
225B LEU* 3.8 6.7 - - + +
226B LYS 3.4 0.4 - - - -
227B THR* 1.3 75.5 - - - +
229B LYS* 1.3 58.4 + - - +
231B MET* 3.2 9.6 + - + +
232B LYS* 2.8 27.9 + - - +
244B LEU* 4.3 22.7 - - + -
245B MET 4.1 13.0 - - - +
246B SER* 4.3 10.5 - - - -
291B LEU* 3.7 19.7 - - + -
293B VAL* 4.1 13.2 - - + -
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Residues in contact with LYS 229 (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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225B LEU 3.0 18.8 + - - +
226B LYS* 3.4 9.2 - - + +
227B THR 3.2 0.2 - - - -
228B VAL* 1.3 78.4 - - - +
230B LEU* 1.3 62.0 + - + +
232B LYS* 3.2 9.2 + - + +
233B GLU* 2.8 58.4 + - + +
291B LEU* 4.1 26.4 - - + +
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Residues in contact with LEU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B PRO* 3.8 38.8 - - + +
198B PRO* 3.8 17.9 - - + -
199B GLY* 3.7 9.0 - - - +
226B LYS* 3.1 19.4 + - + +
227B THR* 3.1 8.4 + - - +
229B LYS* 1.3 80.8 - - + +
231B MET* 1.3 62.0 + - - +
233B GLU* 3.0 23.0 + - - +
234B GLY 2.9 18.4 + - - -
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Residues in contact with MET 231 (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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185B MET* 4.1 23.1 - - + -
187B ILE* 4.2 13.5 - - + -
198B PRO* 3.6 31.6 - - + +
199B GLY* 3.9 0.9 - - - -
201B ALA* 4.7 2.5 - - + -
202B ALA* 3.6 20.3 - - + +
205B LEU* 5.3 1.3 - - + -
213B ILE* 4.1 14.4 - - + -
214B GLY* 3.5 35.9 - - - +
215B VAL* 3.9 18.2 - - + -
227B THR* 3.0 14.4 + - + +
228B VAL* 3.5 9.0 - - + +
230B LEU* 1.3 75.2 - - - +
232B LYS* 1.3 57.7 + - - +
234B GLY* 3.1 2.3 + - - -
235B LEU* 2.9 29.7 + - - +
244B LEU* 5.6 0.2 - - + -
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Residues in contact with LYS 232 (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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228B VAL 2.8 17.1 + - - +
229B LYS* 3.5 6.6 - - + +
231B MET* 1.3 76.3 - - - +
233B GLU* 1.3 61.3 + - + +
235B LEU* 3.7 7.3 - - - +
236B GLU* 3.0 63.4 + - + +
244B LEU* 3.4 36.5 - - + +
291B LEU* 3.4 34.0 - - + +
292B GLY* 5.2 1.8 - - - -
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Residues in contact with GLU 233 (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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229B LYS* 2.8 50.4 + - + +
230B LEU* 3.0 29.1 + - - +
232B LYS* 1.3 78.8 - - + +
234B GLY* 1.3 61.5 + - - +
235B LEU 3.2 0.2 - - - -
236B GLU* 4.0 12.4 - - - +
237B ALA* 3.0 29.3 + - - +
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Residues in contact with GLY 234 (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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199B GLY* 3.8 21.1 - - - -
203B VAL* 3.5 18.5 - - - +
230B LEU 2.9 10.3 + - - -
231B MET 3.1 3.1 + - - -
233B GLU* 1.3 75.6 - - - +
235B LEU* 1.3 62.4 + - - +
237B ALA* 3.6 6.5 + - - +
238B ALA* 3.4 15.4 + - - +
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Residues in contact with LEU 235 (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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202B ALA* 3.7 33.0 - - + -
203B VAL* 3.8 9.9 - - + +
206B VAL* 3.7 19.5 - - + -
213B ILE* 4.4 13.7 - - + -
231B MET 2.9 11.1 + - - +
232B LYS* 3.7 7.0 - - - +
234B GLY* 1.3 75.3 - - - +
236B GLU* 1.3 65.1 + - + +
238B ALA* 3.1 7.6 + - - +
240B LEU* 3.0 45.5 + - + +
241B LYS* 4.8 0.2 - - - -
242B ALA* 3.9 39.9 - - + +
244B LEU* 4.7 7.0 - - + -
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Residues in contact with GLU 236 (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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232B LYS* 3.0 51.9 + - + +
233B GLU* 4.0 13.0 - - - +
234B GLY 3.4 0.2 - - - -
235B LEU* 1.3 77.2 - - + +
237B ALA* 1.3 62.7 + - - +
238B ALA 3.0 4.7 - - - -
239B GLN* 3.0 19.4 + - - +
240B LEU 4.4 6.7 - - - +
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Residues in contact with ALA 237 (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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233B GLU 3.0 19.4 + - - +
234B GLY* 3.9 7.9 - - - +
235B LEU 3.3 0.4 - - - -
236B GLU* 1.3 75.8 - - - +
238B ALA* 1.3 55.9 + - - +
239B GLN* 3.0 12.4 + - - +
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Residues in contact with ALA 238 (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 VAL* 4.3 12.6 - - + -
207B LYS* 5.7 2.7 - - - -
234B GLY 3.4 14.1 + - - +
235B LEU 3.1 5.5 + - - +
236B GLU 3.0 1.4 - - - -
237B ALA* 1.3 78.8 - - - +
239B GLN* 1.3 70.3 + - - +
240B LEU* 2.9 28.4 + - + +
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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