Contacts of the helix formed by residues 233 - 251 (chain B) in PDB entry 1K3B
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 SER 233 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B GLN* 3.6 2.9 + - - -
231B CYS* 2.6 18.2 + - - -
232B GLY* 1.3 71.8 - - - -
234B CYS* 1.3 65.2 + - - +
235B TYR* 3.3 10.1 - - - -
236B SER* 2.8 15.6 + - - -
237B PHE* 3.1 26.0 + - - -
261B PRO* 4.7 0.2 - - - +
265B VAL* 3.2 24.1 - - - +
300B TYR* 3.3 26.6 + - - -
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Residues in contact with CYS 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B GLN* 3.1 20.4 + - - +
232B GLY* 4.9 5.6 - - - -
233B SER* 1.3 74.3 - - - +
235B TYR* 1.3 68.5 + - - +
237B PHE* 3.0 4.3 + - - +
238B ALA* 2.8 30.1 + - - +
277B GLY 6.0 0.4 - - - -
380C ASN 4.5 5.4 - - - -
381C HIS* 3.4 34.5 - - + +
382C ALA* 3.5 31.9 - - - +
404C SER* 4.2 3.5 + - - +
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Residues in contact with TYR 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B GLY 3.4 15.3 - - - -
233B SER* 4.0 6.7 - - - -
234B CYS* 1.3 83.7 - - - +
236B SER* 1.3 72.7 + - - +
238B ALA* 3.6 1.7 + - - +
239B SER* 2.8 34.0 + - - -
264B VAL* 3.9 9.1 + - + +
265B VAL* 4.1 11.4 - - + +
271B ALA* 3.4 21.5 - - + +
273B GLY* 2.8 38.9 + - - -
276B GLY* 3.1 22.4 - - - -
277B GLY* 3.1 39.9 - - - +
278B PHE 3.9 1.8 - - - +
279B PRO* 3.9 12.2 - - + +
282B ILE* 3.8 20.6 - - + -
382C ALA* 3.7 13.9 - - + -
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Residues in contact with SER 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B SER* 2.8 18.6 + - - -
235B TYR* 1.3 95.3 - - - +
237B PHE* 1.3 61.1 + - - +
239B SER* 3.3 5.9 + - - -
240B MET* 2.9 36.0 + - - +
261B PRO* 3.0 37.4 + - - +
264B VAL* 3.6 13.3 - - - +
265B VAL* 4.3 2.7 - - - -
282B ILE* 4.8 2.7 - - - -
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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
----------------------------------------------------------
226B ARG* 3.7 43.1 - - + -
227B ASN 3.8 7.2 - - - -
228B GLN* 3.7 15.7 - - + -
233B SER* 3.1 25.8 + - - -
234B CYS 3.0 7.9 + - - +
236B SER* 1.3 77.4 - - - +
238B ALA* 1.3 56.1 + - - +
240B MET* 3.3 5.5 + - - +
241B GLY* 2.8 28.9 + - - -
261B PRO* 3.8 19.1 - - + -
300B TYR* 3.4 50.0 - + - -
404C SER* 3.7 27.1 - - - +
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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
----------------------------------------------------------
234B CYS 2.8 19.0 + - - +
235B TYR 3.9 3.8 - - - +
237B PHE* 1.3 71.1 - - - +
239B SER* 1.3 63.8 + - - +
241B GLY* 3.2 1.7 + - - -
242B MET* 2.9 24.9 + - - +
279B PRO* 4.5 0.4 - - + -
347B ALA* 4.3 10.9 - - + +
382C ALA* 3.9 9.6 + - + +
383C VAL* 3.6 43.1 - - - +
384C LEU* 4.2 9.0 - - - +
404C SER* 5.5 0.4 + - - -
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Residues in contact with SER 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B TYR 2.8 23.4 + - - -
236B SER 3.5 4.3 - - - -
237B PHE 3.2 0.2 - - - -
238B ALA* 1.3 80.3 - - - +
240B MET* 1.3 67.5 + - - +
242B MET* 3.3 4.5 + - - +
243B LEU* 3.1 26.0 + - - +
279B PRO* 3.3 17.8 - - - +
282B ILE* 3.6 15.1 - - - +
283B ALA* 3.3 36.0 + - - +
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Residues in contact with MET 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B SER* 2.9 26.9 + - - +
237B PHE* 3.9 3.8 - - - +
239B SER* 1.3 83.7 - - - +
241B GLY* 1.3 58.0 + - - +
243B LEU* 3.2 2.5 + - + +
244B GLU* 2.8 51.2 + - - +
259B LEU* 3.6 28.0 - - + +
260B SER 4.0 9.4 - - - +
261B PRO* 4.0 26.5 - - + -
264B VAL* 3.8 19.7 - - + -
282B ILE* 3.9 4.5 - - + +
292B LEU* 3.8 34.5 - - + -
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Residues in contact with GLY 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B VAL* 5.9 0.3 - - - +
223B SER* 4.8 1.4 + - - -
237B PHE 2.8 17.6 + - - -
238B ALA 3.6 1.8 - - - -
240B MET* 1.3 77.9 - - - +
242B MET* 1.3 62.4 + - - +
244B GLU* 3.9 12.5 + - - +
245B ALA* 3.1 25.1 + - - +
384C LEU* 3.9 17.3 - - - +
402C LYS* 4.6 11.8 + - - -
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Residues in contact with MET 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ALA 2.9 12.8 + - - +
239B SER* 3.6 4.9 - - - +
241B GLY* 1.3 78.2 - - - +
243B LEU* 1.3 66.3 + - + +
245B ALA* 3.9 1.2 - - - +
246B ARG* 3.0 35.8 + - - +
283B ALA* 3.3 32.5 - - + -
345B PRO* 3.4 13.7 - - - +
346B MET* 3.6 13.2 - - - -
347B ALA* 4.1 11.9 - - + +
384C LEU* 3.7 17.8 - - + +
431C VAL* 3.4 28.5 - - + +
432C ALA* 3.8 2.5 - - - -
433C ALA* 3.6 26.2 - - + +
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B SER 3.1 13.0 + - - +
240B MET 3.9 2.0 - - - +
242B MET* 1.3 80.1 - - + +
244B GLU* 1.3 57.6 + - - +
246B ARG 3.5 0.2 + - - -
247B ILE* 3.0 37.4 + - + +
259B LEU* 3.6 16.2 - - + -
283B ALA* 3.8 14.8 - - + +
287B ALA* 4.1 0.7 - - + -
292B LEU* 3.3 33.0 - - + -
316B TYR* 6.4 1.1 - - + -
317B TYR 6.1 1.1 - - - -
318B SER* 3.8 24.9 - - - +
433C ALA* 4.1 20.2 - - + +
435C PRO* 3.8 31.8 - - + +
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Residues in contact with GLU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B SER* 2.7 37.4 + - - +
226B ARG* 5.2 4.9 + - - -
240B MET* 2.8 34.7 + - - +
241B GLY* 3.9 6.8 - - - +
243B LEU* 1.3 73.5 - - - +
245B ALA* 1.3 62.1 + - - +
247B ILE* 3.5 8.1 + - - +
248B ARG* 3.1 29.4 + - - +
257B PRO* 3.4 21.9 - - - +
258B ILE* 3.4 15.3 - - - +
259B LEU* 2.6 44.5 + - + +
402C LYS* 4.8 0.9 + - - -
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Residues in contact with ALA 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B PHE 3.3 22.1 - - - +
222B VAL* 4.3 10.3 - - + +
223B SER* 5.0 1.5 + - - +
241B GLY 3.1 16.6 + - - +
242B MET 3.9 2.2 - - - +
244B GLU* 1.3 74.6 - - - +
246B ARG* 1.3 59.2 + - - +
248B ARG* 2.9 7.3 + - - +
249B ILE* 2.9 32.3 + - + +
345B PRO* 3.7 29.8 - - + -
384C LEU* 5.0 2.0 - - + -
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Residues in contact with ARG 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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242B MET* 3.0 24.7 + - - +
245B ALA* 1.3 76.5 - - - +
247B ILE* 1.3 56.5 + - - +
249B ILE* 4.0 6.5 - - - +
250B LEU* 2.9 37.6 + - + +
339B GLU* 2.7 36.3 + - - +
343B HIS* 3.4 32.1 + - - +
344B GLY* 3.2 24.4 + - - -
345B PRO* 3.0 20.1 + - + +
346B MET* 4.1 2.6 - - - +
432C ALA* 3.8 9.2 - - - +
433C ALA 3.0 36.8 + - - +
434C THR* 4.2 8.5 + - - +
435C PRO* 3.7 20.4 - - + -
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Residues in contact with ILE 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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243B LEU 3.0 26.1 + - - +
244B GLU 3.8 4.0 - - - +
245B ALA 3.2 0.2 - - - -
246B ARG* 1.3 75.9 - - - +
248B ARG* 1.3 62.0 + - - +
250B LEU* 3.5 5.7 + - - +
251B THR* 2.8 30.0 + - - +
255B GLN* 4.0 22.2 - - + +
257B PRO* 3.8 35.0 - - + -
259B LEU* 4.8 9.2 - - + -
316B TYR* 3.8 29.8 - - + -
435C PRO* 3.6 24.0 - - + -
437C PRO* 4.3 14.8 - - + -
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Residues in contact with ARG 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ASN* 4.8 6.9 + - - +
221B PHE* 3.4 25.9 - - + +
222B VAL 3.9 5.7 + - - -
223B SER* 3.2 40.5 - - - +
224B PRO* 4.0 5.9 - - - +
244B GLU 3.1 15.0 + - - +
245B ALA 2.9 9.9 + - - +
247B ILE* 1.3 76.8 - - + +
249B ILE* 1.3 57.1 + - - +
252B ASN 2.8 9.7 + - - -
253B ASN* 2.7 47.1 + - - +
255B GLN 3.7 18.8 - - - +
256B THR* 3.5 40.0 + - + +
257B PRO 4.3 1.6 + - - -
258B ILE* 3.5 12.5 - - - +
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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
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213B TRP* 3.3 57.0 - - + -
221B PHE* 3.6 21.5 - - + -
245B ALA 2.9 20.7 + - - +
246B ARG* 4.0 7.4 - - - +
248B ARG* 1.3 71.4 - - - +
250B LEU* 1.3 67.3 + - + +
252B ASN* 3.0 13.5 + - - +
343B HIS 4.5 4.9 - - - +
344B GLY* 3.7 18.6 - - - -
345B PRO* 3.9 7.9 - - + -
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Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ARG* 2.9 26.4 + - + +
247B ILE 3.7 3.8 - - - +
248B ARG 3.3 0.2 - - - -
249B ILE* 1.3 81.4 - - + +
251B THR* 1.3 58.7 + - - +
252B ASN* 3.8 0.5 + - - +
434C THR* 4.8 8.7 - - + -
435C PRO* 3.5 35.2 - - + +
437C PRO* 3.6 22.7 - - + -
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Residues in contact with THR 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 ILE 2.8 21.3 + - - +
248B ARG 3.4 2.8 + - - -
250B LEU* 1.3 78.2 - - - +
252B ASN* 1.3 68.5 + - - +
254B SER* 2.9 30.3 + - - -
255B GLN* 3.1 39.7 + - + +
437C PRO* 3.6 29.2 - - + -
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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