Contacts of the helix formed by residues 228 - 247 (chain B) in PDB entry 1KCX
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 PRO 228 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208B GLU* 5.4 7.2 - - + +
224B ALA 3.7 5.3 - - - +
225B LEU 3.7 11.7 - - - +
226B SER 3.5 7.6 - - - +
227B ARG* 1.3 94.3 - - - +
229B GLU* 1.3 59.1 + - - +
230B GLU* 3.3 19.3 - - + +
231B LEU* 2.9 46.1 + - + +
232B GLU* 3.8 2.3 + - - +
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Residues in contact with GLU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ARG 3.7 1.7 + - - -
228B PRO* 1.3 72.2 - - - +
230B GLU* 1.3 70.3 + - - +
232B GLU* 3.0 9.9 + - - +
233B ALA* 2.9 31.7 + - - +
257B SER* 3.4 26.3 + - - +
258B LYS* 3.9 6.5 + - - +
259B SER* 2.6 44.0 + - - +
308B SER* 4.0 18.8 + - - +
310B ASP* 4.9 7.8 - - - +
313B THR* 5.2 0.9 + - - -
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Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B PRO* 3.0 23.3 + - + +
229B GLU* 1.3 87.3 + - - +
231B LEU* 1.3 64.7 + - + +
233B ALA* 3.8 6.4 - - - +
234B GLU* 3.1 28.4 + - - +
259B SER* 5.3 5.1 + - - +
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Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B GLU* 3.5 2.1 - - + +
201B ASN* 3.2 30.8 + - + +
204B LEU* 3.9 35.4 - - + +
205B ILE* 3.6 41.3 - - + +
208B GLU* 5.1 4.3 - - + -
226B SER 4.2 1.8 - - - +
227B ARG* 4.6 1.3 - - + -
228B PRO* 2.9 39.6 + - + +
230B GLU* 1.3 83.2 - - + +
232B GLU* 1.3 61.4 + - - +
234B GLU* 4.1 4.8 - - + +
235B ALA 3.5 10.4 + - - -
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Residues in contact with GLU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ALA 3.5 19.5 - - - +
200B GLU* 4.2 8.5 - - + +
227B ARG 6.1 0.4 - - - +
228B PRO 3.8 1.6 + - - +
229B GLU* 3.0 13.3 + - - +
231B LEU* 1.3 76.5 - - - +
233B ALA* 1.3 61.6 + - - +
235B ALA* 3.3 2.9 + - - +
236B VAL* 2.9 38.3 + - + +
252B ILE* 5.8 1.2 - - - +
253B THR 5.4 0.3 - - - +
254B LYS 3.6 9.0 - - - +
255B VAL* 3.7 3.5 - - - -
256B MET* 3.1 27.0 + - - +
257B SER* 2.9 26.0 + - - -
260B ALA* 3.6 19.2 - - + +
305B PRO* 3.8 19.0 - - + +
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Residues in contact with ALA 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 GLU 2.9 15.2 + - - +
230B GLU* 3.8 7.2 - - - +
232B GLU* 1.3 78.2 - - - +
234B GLU* 1.3 57.4 + - - +
236B VAL* 3.2 4.0 + - - +
237B PHE* 2.8 30.1 + - - +
259B SER* 3.9 29.2 - - - -
260B ALA* 4.3 11.6 - - - +
263B ILE* 4.1 13.9 - - + +
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Residues in contact with GLU 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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201B ASN* 2.9 22.9 + - - +
204B LEU* 5.2 3.8 - - + +
230B GLU 3.1 17.0 + - - +
231B LEU* 4.4 5.8 - - + +
233B ALA* 1.3 78.6 - - - +
235B ALA* 1.3 61.3 + - - +
237B PHE* 3.2 8.9 + - + +
238B ARG* 2.7 73.4 + - - +
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Residues in contact with ALA 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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168B MET* 3.2 24.5 - - + +
199B ALA* 3.3 9.0 - - + -
200B GLU* 3.1 47.1 - - - +
201B ASN 3.8 0.9 - - - +
231B LEU 3.5 4.6 + - - +
232B GLU 3.3 0.8 + - - +
233B ALA 3.3 0.4 - - - -
234B GLU* 1.3 83.9 + - - +
236B VAL* 1.3 57.7 + - - +
238B ARG* 3.3 2.4 + - - +
239B ALA* 2.9 26.2 + - - +
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ALA* 3.8 19.1 - - + -
232B GLU* 2.9 26.8 + - + +
233B ALA* 3.5 9.4 - - - +
235B ALA* 1.3 76.4 - - - +
237B PHE* 1.3 62.6 + - - +
239B ALA* 3.2 5.2 + - - +
240B ILE* 3.1 26.6 + - + +
252B ILE* 4.0 22.9 - - + -
260B ALA* 4.2 14.4 - - + +
263B ILE* 4.0 14.6 - - + -
264B ILE* 3.9 28.0 - - + -
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Residues in contact with PHE 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 ALA 2.8 13.7 + - - +
234B GLU* 3.5 12.6 - - + +
236B VAL* 1.3 77.3 - - - +
238B ARG* 1.3 62.7 + - - +
240B ILE* 3.3 10.7 + - + +
241B ALA* 3.0 25.8 + - + +
263B ILE* 3.8 30.9 - - + +
266B LEU* 6.3 3.1 - - + -
270B LYS* 5.9 6.1 - - - -
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Residues in contact with ARG 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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168B MET* 3.2 33.5 + - + +
176B MET 5.8 0.6 + - - -
178B ASP* 3.1 40.2 + - - +
181B LEU* 4.5 3.0 - - - +
200B GLU 5.3 0.2 + - - -
201B ASN* 3.2 21.7 - - - +
234B GLU* 2.7 56.2 + - - +
235B ALA* 3.8 5.4 - - - +
237B PHE* 1.3 77.1 - - - +
239B ALA* 1.3 62.9 + - - +
241B ALA* 3.2 8.2 + - + +
242B ILE* 3.1 32.4 + - + +
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Residues in contact with ALA 239 (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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168B MET* 4.1 16.4 - - - +
185B PHE* 3.6 14.7 - - + -
197B VAL* 4.4 14.1 - - + -
199B ALA* 5.0 0.4 - - + -
235B ALA 2.9 14.5 + - - +
236B VAL* 3.2 10.7 + - - +
238B ARG* 1.3 78.9 - - - +
240B ILE* 1.3 62.3 + - - +
242B ILE* 3.3 7.6 + - - +
243B ALA* 3.1 19.1 + - - +
250B VAL* 4.7 4.3 - - + -
252B ILE* 4.3 18.2 - - + -
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Residues in contact with ILE 240 (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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236B VAL* 3.1 23.7 + - + +
237B PHE* 3.7 11.7 - - + +
239B ALA* 1.3 74.2 - - + +
241B ALA* 1.3 62.4 + - - +
243B ALA* 3.3 7.2 + - - +
244B GLY* 2.8 26.5 + - - -
250B VAL* 4.6 5.6 - - + -
252B ILE* 5.0 2.0 - - + -
263B ILE* 4.0 20.2 - - + -
264B ILE* 4.2 4.5 - - - -
267B ALA* 3.8 34.8 - - + -
272B PRO* 4.0 21.5 - - + +
274B VAL* 4.1 26.7 - - + -
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Residues in contact with ALA 241 (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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237B PHE* 3.0 20.4 + - + +
238B ARG* 3.2 14.1 + - + +
240B ILE* 1.3 75.8 - - - +
242B ILE* 1.3 64.5 + - + +
244B GLY* 3.2 2.6 + - - -
245B ARG* 3.2 28.5 + - + +
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Residues in contact with ILE 242 (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 ASP* 4.4 13.9 - - + +
181B LEU* 3.9 34.3 - - + -
182B TYR* 4.0 19.3 - - + -
185B PHE* 3.5 24.9 - - + -
238B ARG* 3.1 26.8 + - + +
239B ALA* 3.6 9.6 - - - +
241B ALA* 1.3 76.6 - - + +
243B ALA* 1.3 62.8 + - - +
245B ARG* 3.3 8.0 + - - +
246B ILE* 3.1 36.4 + - + +
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Residues in contact with ALA 243 (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 PHE* 4.2 3.6 - - + -
239B ALA 3.1 13.6 + - - +
240B ILE* 3.3 8.0 + - + +
242B ILE* 1.3 78.4 - - - +
244B GLY* 1.3 52.2 + - - +
247B ASN* 2.6 36.0 + - - -
248B CYS* 3.2 36.4 + - - +
250B VAL* 3.9 26.0 - - + -
272B PRO* 5.8 2.9 - - + -
273B LEU 6.3 0.2 - - - +
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Residues in contact with GLY 244 (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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240B ILE 2.8 16.5 + - - -
241B ALA* 3.2 2.7 + - - -
242B ILE 3.2 0.2 - - - -
243B ALA* 1.3 76.5 - - - +
245B ARG* 1.3 75.0 + - - +
247B ASN* 3.2 13.9 + - - +
272B PRO* 4.7 18.6 - - - +
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Residues in contact with ARG 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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182B TYR* 4.9 13.0 - - + -
241B ALA 3.2 17.4 + - - +
242B ILE* 3.7 7.9 - - - +
244B GLY* 1.3 85.1 + - - +
246B ILE* 1.3 65.1 + - + +
247B ASN* 4.7 1.0 - - - +
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Residues in contact with ILE 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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182B TYR* 3.4 38.6 - - + +
185B PHE* 3.4 28.9 - - + -
186B THR* 3.5 22.4 - - + +
189B LYS* 2.9 42.4 + - + +
242B ILE* 3.1 27.2 + - + +
243B ALA 4.0 2.0 - - - +
245B ARG* 1.3 75.4 - - - +
247B ASN* 1.3 65.9 + - - +
248B CYS* 3.9 12.1 - - - -
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Residues in contact with ASN 247 (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 LYS* 3.1 19.6 + - - +
243B ALA 2.6 15.7 + - - -
244B GLY* 3.2 11.3 + - - +
245B ARG 4.7 1.3 - - - +
246B ILE* 1.3 76.3 - - - +
248B CYS* 1.3 56.6 + - - +
273B LEU* 5.2 1.6 - - - +
482B VAL* 3.4 20.8 + - - +
485B ARG* 3.6 31.9 + - - +
486B SER* 3.0 35.8 + - - +
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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
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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