Contacts of the helix formed by residues 229 - 251 (chain B) in PDB entry 1KI6
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 LEU 229 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B GLU* 5.3 1.4 - - - +
214B ILE* 4.1 46.2 - - + +
217B LEU* 5.4 1.6 - - + -
227B LEU* 3.8 32.6 + - + +
228B ASP* 1.3 70.5 + - - +
230B ALA* 1.3 59.6 + - - +
232B LEU* 3.5 11.6 - - + +
233B ALA* 3.0 27.0 + - - +
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Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B MET* 3.6 19.1 - - + +
228B ASP* 3.1 10.5 + - - +
229B LEU* 1.3 78.2 - - - +
231B MET* 1.3 58.9 + - - +
233B ALA* 3.4 6.2 + - - +
234B ALA* 3.1 26.7 + - - +
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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
----------------------------------------------------------
58B HIS* 4.8 10.1 - - + +
101B TYR* 4.7 7.9 - - + +
172B TYR* 4.0 27.1 - - + -
175B ALA* 3.6 28.0 - - + -
176B ARG* 3.4 41.5 - - + +
179B MET* 3.5 28.7 - - + +
228B ASP* 3.1 32.8 + - + +
230B ALA* 1.3 74.3 - - - +
232B LEU* 1.3 63.4 + - - +
234B ALA* 4.4 0.7 - - - -
235B ILE* 3.1 26.3 + - + +
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Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B HIS* 4.1 9.0 - - - +
210B GLU* 4.8 1.3 - - + +
213B HIS* 3.5 32.1 - - + +
214B ILE* 3.2 33.0 - - + -
217B LEU* 3.5 30.1 - - + -
228B ASP 3.1 7.6 + - - +
229B LEU* 3.5 21.3 - - + +
230B ALA 3.1 0.4 - - - -
231B MET* 1.3 77.2 - - - +
233B ALA* 1.3 62.7 + - - +
235B ILE* 3.2 11.3 - - + +
236B ARG* 3.0 56.6 + - - +
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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
----------------------------------------------------------
210B GLU* 4.3 15.2 + - - +
229B LEU 3.0 16.0 + - - +
230B ALA* 3.8 6.5 - - - +
231B MET 3.3 0.2 - - - -
232B LEU* 1.3 77.6 - - - +
234B ALA* 1.3 57.0 + - - +
236B ARG* 3.4 9.8 + - - +
237B ARG* 2.8 31.1 + - - +
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Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ALA* 3.9 25.1 - - + +
178B LEU* 4.0 17.9 - - + +
179B MET* 4.2 10.8 - - + -
230B ALA 3.1 16.6 + - - +
231B MET* 3.9 4.5 - - - +
232B LEU 3.4 0.2 - - - -
233B ALA* 1.3 74.5 - - - +
235B ILE* 1.3 57.0 + - - +
237B ARG* 3.2 5.7 + - - +
238B VAL* 2.8 34.8 + - - +
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Residues in contact with ILE 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PRO* 3.7 17.3 - - + -
58B HIS* 3.7 20.0 - - + -
171B CYS* 3.7 15.0 - - + +
172B TYR* 3.8 41.7 - - + +
175B ALA* 3.5 23.1 - - + +
231B MET* 3.1 16.4 + - + +
232B LEU* 3.2 15.0 - - + +
234B ALA* 1.3 75.7 - - - +
236B ARG* 1.3 70.9 + - - +
238B VAL* 3.3 2.2 + - + +
239B TYR* 3.0 40.5 + - + -
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Residues in contact with ARG 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PRO* 3.9 13.5 - - + -
208B LEU 2.4 32.3 + - - +
209B PRO* 3.5 1.2 - - - +
210B GLU* 3.2 38.1 - - - +
213B HIS* 3.3 29.5 + - + +
232B LEU* 3.0 46.6 + - + +
233B ALA* 3.6 7.2 - - - +
235B ILE* 1.3 76.6 - - - +
237B ARG* 1.3 64.8 + - - +
239B TYR* 3.4 1.9 + - - +
240B GLY* 3.1 19.8 + - - -
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Residues in contact with ARG 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LEU* 4.4 19.3 - - + +
233B ALA 2.8 18.4 + - - +
234B ALA* 3.4 7.6 - - - +
236B ARG* 1.3 77.5 - - - +
238B VAL* 1.3 62.0 + - - +
240B GLY* 3.2 3.0 + - - -
241B LEU* 3.0 49.5 + - + +
285B GLY 5.1 3.0 + - - -
290B THR* 4.0 25.1 + - - +
291B LEU* 4.1 14.8 - - - +
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Residues in contact with VAL 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B CYS* 3.5 40.4 - - + +
174B ALA* 4.0 13.9 - - + -
175B ALA* 3.7 19.5 - - - +
178B LEU* 3.6 22.2 - - + -
234B ALA 2.8 23.9 + - - +
235B ILE* 3.7 6.5 - - - +
237B ARG* 1.3 72.3 - - - +
239B TYR* 1.3 57.8 + - - +
241B LEU* 3.3 11.5 + - - +
242B LEU* 2.8 25.5 + - - +
288B LEU* 3.8 10.6 - - + +
291B LEU* 4.5 3.4 - - + -
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Residues in contact with TYR 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASP* 2.6 26.0 + - - -
56B GLY* 3.5 42.2 + - - -
57B PRO* 4.0 11.4 - - + -
163B ARG* 4.0 1.6 + - - -
166B ILE* 6.1 0.2 - - + -
167B ALA* 3.4 21.1 - - - +
171B CYS* 3.6 29.2 - - + +
172B TYR* 4.1 3.3 - + - -
205B LEU* 3.8 27.2 - - + +
235B ILE* 3.0 43.1 + - + +
236B ARG 4.1 2.7 - - - +
238B VAL* 1.3 73.9 - - - +
240B GLY* 1.3 67.5 + - - +
242B LEU* 3.5 16.1 - - + +
243B ALA* 3.1 21.3 + - - +
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Residues in contact with GLY 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ARG 3.1 15.1 + - - -
237B ARG 3.7 3.4 - - - -
239B TYR* 1.3 76.6 - - - +
241B LEU* 1.3 62.9 + - - +
243B ALA* 3.1 15.3 + - - +
244B ASN* 3.1 20.7 + - - +
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Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LEU* 5.8 0.2 - - + -
237B ARG* 3.0 53.2 + - + +
238B VAL* 3.5 9.0 - - + +
240B GLY* 1.3 75.0 - - - +
242B LEU* 1.3 64.0 + - - +
244B ASN* 2.8 5.5 + - - +
245B THR* 2.8 27.5 + - - -
285B GLY 5.1 0.4 - - - +
286B ASP* 3.6 34.8 - - - +
287B THR* 3.9 8.7 - - - +
288B LEU* 3.9 14.4 - - + +
290B THR* 4.7 1.1 - - + -
291B LEU* 4.1 32.3 - - + -
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Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ILE* 4.0 18.4 - - + -
170B LEU* 4.3 4.9 - - + -
171B CYS* 3.9 15.0 - - - -
203B ILE* 5.5 1.6 - - + -
205B LEU* 4.0 16.2 - - + -
238B VAL 2.8 15.4 + - - +
239B TYR* 3.5 33.4 - - + +
240B GLY 3.2 0.2 - - - -
241B LEU* 1.3 78.6 - - - +
243B ALA* 1.3 63.3 + - - +
245B THR* 3.3 1.4 + - - -
246B VAL* 3.3 27.4 + - + +
288B LEU* 3.8 17.4 - - + +
319B LEU* 3.8 36.6 - - + -
322B MET* 5.7 0.4 - - - -
324B VAL* 5.9 0.9 - - + -
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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
----------------------------------------------------------
205B LEU* 4.1 17.3 - - + -
239B TYR 3.1 12.5 + - - +
240B GLY* 3.1 10.7 + - - +
242B LEU* 1.3 76.2 - - - +
244B ASN* 1.3 64.2 + - - +
246B VAL* 3.3 9.0 + - - +
247B ARG* 3.3 27.9 + - - +
324B VAL* 4.8 7.2 - - + +
326B ILE* 4.6 14.6 - - + -
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Residues in contact with ASN 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B GLY 3.1 13.0 + - - +
241B LEU* 2.8 8.8 + - - +
243B ALA* 1.3 75.6 - - - +
245B THR* 1.3 62.6 + - - +
247B ARG* 2.9 28.8 + - - +
248B TYR* 2.8 30.3 + - - +
282B PRO* 3.6 14.2 - - + +
286B ASP* 2.7 42.8 + - - +
287B THR* 3.9 1.8 - - + -
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Residues in contact with THR 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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241B LEU 2.8 18.6 + - - -
242B LEU 3.7 4.9 - - - -
244B ASN* 1.3 78.2 - - - +
246B VAL* 1.3 58.7 + - - +
248B TYR* 3.3 1.3 + - - +
249B LEU* 2.8 46.8 + - + +
287B THR* 3.4 10.3 - - + -
288B LEU* 2.9 31.7 + - + +
289B PHE* 4.0 24.5 - - + -
315B LEU* 5.2 0.7 - - + -
319B LEU* 3.8 26.0 - - + -
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Residues in contact with VAL 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 3.3 24.4 + - + +
243B ALA 3.7 6.5 - - - +
244B ASN 3.2 0.4 - - - -
245B THR* 1.3 77.2 - - - +
247B ARG* 1.3 58.8 + - + +
249B LEU* 3.3 6.8 + - - +
250B GLN* 2.9 60.3 + - - +
319B LEU* 4.0 31.0 - - + +
322B MET* 4.0 6.1 - - + +
324B VAL* 3.8 34.8 - - + +
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Residues in contact with ARG 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ALA* 3.3 13.0 + - - +
244B ASN* 2.9 34.0 + - - +
246B VAL* 1.3 74.9 - - + +
248B TYR* 1.3 68.2 + - - +
250B GLN* 3.2 9.7 + - - +
251B CYS* 2.9 31.0 + - - -
278B ALA 3.1 37.9 + - - +
279B GLY* 4.2 4.2 - - - +
280B PRO* 3.0 33.3 + - - +
282B PRO* 3.1 26.8 - - + +
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Residues in contact with TYR 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ASN 2.8 16.6 + - - +
245B THR 3.5 3.4 - - - +
247B ARG* 1.3 77.9 - - - +
249B LEU* 1.3 71.4 + - + +
251B CYS* 3.1 7.8 + - - +
252B GLY 3.5 0.2 + - - -
253B GLY* 3.0 46.5 + - - -
254B SER 2.9 22.7 + - - -
255B TRP* 3.3 9.3 + - - -
258B ASP* 2.6 35.0 + - - +
281B ARG* 3.5 14.3 + - - -
282B PRO* 3.3 35.3 - - + +
284B ILE* 4.0 13.0 - - + +
287B THR* 3.7 16.6 - - + -
289B PHE* 4.1 21.3 - + - -
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Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B THR* 2.8 36.9 + - + +
246B VAL* 3.7 3.8 - - - +
248B TYR* 1.3 86.8 - - + +
250B GLN* 1.3 61.3 + - - +
252B GLY* 3.3 13.0 + - - -
253B GLY 3.7 20.8 + - - +
255B TRP* 5.9 1.3 - - + +
289B PHE* 4.6 5.2 - - + -
316B ALA* 3.7 44.2 - - + +
319B LEU* 3.9 16.4 - - + -
320B ARG* 3.7 43.0 + - + +
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Residues in contact with GLN 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B VAL* 2.9 31.6 + - + +
247B ARG* 3.2 8.2 + - - +
249B LEU* 1.3 76.5 - - + +
251B CYS* 1.3 59.1 + - - +
252B GLY 3.1 5.0 + - - -
320B ARG* 3.7 25.8 + - + +
321B SER 5.0 0.6 - - - -
322B MET 3.0 26.7 + - - -
323B HIS* 5.0 6.5 - - - +
324B VAL 5.5 0.5 + - - +
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Residues in contact with CYS 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ARG* 2.9 21.4 + - - +
248B TYR 3.1 2.1 + - - +
250B GLN* 1.3 78.0 - - - +
252B GLY* 1.3 56.3 - - - +
253B GLY 3.4 1.3 - - - -
279B GLY 4.5 7.2 - - - -
280B PRO* 4.3 5.6 - - - -
281B ARG* 3.4 56.6 + - + -
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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