Contacts of the helix formed by residues 232 - 248 (chain B) in PDB entry 3KEU
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 GLY 232 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B TYR 3.6 14.1 - - - -
19B VAL* 4.0 2.9 - - - -
23B ALA* 3.6 4.0 - - - +
231B VAL* 1.3 71.0 - - - +
233B THR* 1.3 54.7 + - - -
235B ASP* 3.1 9.7 + - - +
236B LEU* 2.9 27.5 + - - +
291B LEU* 4.0 5.4 - - - -
500B PLP 2.7 37.7 + - - -
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Residues in contact with THR 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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230B PHE* 3.8 19.9 + - + -
231B VAL 3.4 0.4 - - - -
232B GLY* 1.3 73.2 - - - +
234B GLY* 1.3 59.0 + - - +
236B LEU* 4.2 3.1 - - - -
237B PHE* 2.9 27.2 + - - +
263B LEU* 3.5 20.6 - - + +
267B LEU* 3.7 21.8 - - + -
291B LEU* 3.6 29.2 - - + -
409B ATP 2.5 42.2 + - + +
500B PLP 4.0 0.3 + - - -
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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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113B ASP* 3.8 9.4 - - - +
148B THR* 5.2 0.5 + - - -
186B THR* 5.7 1.9 - - - +
233B THR* 1.3 74.7 + - - +
235B ASP* 1.3 59.9 + - - -
237B PHE* 3.4 4.9 + - - +
238B ALA* 3.2 18.2 + - - +
409B ATP 3.5 42.8 + - - -
500B PLP 2.4 20.6 + - - -
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Residues in contact with ASP 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLN* 3.8 15.0 + - - +
20B GLY* 2.8 39.4 + - - +
23B ALA* 4.0 7.0 - - + -
24B ALA* 4.5 3.7 - - - +
81B LEU* 5.8 0.3 - - - +
83B GLY* 5.1 0.9 - - - -
84B TYR 4.8 4.7 + - - -
113B ASP* 4.3 6.4 - - - +
232B GLY* 3.3 7.5 - - - +
234B GLY* 1.3 74.0 - - - +
236B LEU* 1.3 62.0 + - - +
238B ALA* 3.4 5.2 + - - +
239B ALA* 3.1 22.9 + - - +
405B MG 2.6 24.3 - - - -
500B PLP 2.6 34.8 + - - +
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Residues in contact with LEU 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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23B ALA* 3.5 26.4 - - + +
27B PRO* 3.7 18.8 - - + -
232B GLY 2.9 15.7 + - - +
233B THR* 3.8 6.7 - - - +
234B GLY 3.3 0.2 - - - -
235B ASP* 1.3 74.8 - - - +
237B PHE* 1.3 60.6 + - - +
239B ALA* 3.3 3.9 + - + +
240B MET* 3.0 53.4 + - + +
262B THR* 5.0 4.5 - - + -
263B LEU* 3.9 23.3 - - + -
266B VAL* 4.2 22.0 - - + -
291B LEU* 4.4 7.9 - - + -
293B MET* 4.1 19.1 - - + -
300B ILE* 5.7 0.7 - - + -
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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
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148B THR* 4.6 1.6 - - + -
184B VAL* 3.8 26.2 - - + -
186B THR* 3.5 29.8 - - + -
201B VAL* 4.3 11.4 - - + -
233B THR 2.9 18.3 + - - +
234B GLY* 3.5 9.9 - - - +
236B LEU* 1.3 73.3 - - - +
238B ALA* 1.3 70.6 + - - +
240B MET 3.3 0.2 + - - -
241B LEU* 2.8 35.5 + - + +
256B CYS* 5.4 4.3 - - - -
259B THR* 3.5 20.5 - - + +
260B VAL* 3.8 25.1 - - + -
263B LEU* 3.3 28.7 - - + +
409B ATP 4.2 19.7 - - - -
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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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81B LEU* 4.3 17.7 - - + -
111B VAL* 4.2 7.4 - - + +
113B ASP* 4.3 11.0 - - + -
148B THR* 3.8 35.2 + - + +
234B GLY 3.2 10.3 + - - +
235B ASP* 3.4 7.4 + - - +
237B PHE* 1.3 79.4 - - - +
239B ALA* 1.3 63.3 + - - +
241B LEU* 3.2 3.2 + - - +
242B LEU* 3.0 23.6 + - - +
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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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24B ALA* 3.7 31.4 - - + -
28B LEU* 3.4 21.0 - - + +
81B LEU* 4.4 12.7 - - + +
235B ASP 3.1 16.7 + - - +
236B LEU* 3.5 7.0 - - + +
237B PHE 3.2 0.2 - - - -
238B ALA* 1.3 78.2 - - - +
240B MET* 1.3 66.3 + - + +
242B LEU* 3.3 6.2 - - - +
243B ALA 3.1 19.4 + - - -
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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
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27B PRO* 3.6 30.5 - - + -
28B LEU* 3.9 12.6 - - + +
31B LEU* 3.9 28.7 - - + -
236B LEU* 3.0 32.9 + - + +
239B ALA* 1.3 84.9 - - + +
241B LEU* 1.3 60.2 + - - +
242B LEU 3.2 0.4 - - - -
243B ALA* 3.6 0.8 - - - +
244B TRP* 2.8 46.7 + - + -
259B THR* 3.4 21.9 + - + +
262B THR* 4.3 19.5 - - + -
263B LEU* 6.2 0.7 - - + -
300B ILE* 4.3 8.7 - - - +
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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
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146B ILE* 3.8 19.3 - - + -
148B THR* 3.6 26.7 - - + -
182B THR* 4.9 0.9 - - + -
184B VAL* 3.7 23.8 - - + -
237B PHE* 2.8 29.0 + - + +
238B ALA* 3.5 6.3 - - - +
240B MET* 1.3 76.2 - - - +
242B LEU* 1.3 57.7 + - - +
244B TRP* 5.1 0.2 - - - -
245B THR* 2.9 55.4 + - + +
252B LEU* 4.9 0.9 - - + -
255B ALA* 4.8 3.1 - - + -
256B CYS* 4.3 23.3 - - - -
259B THR* 3.4 15.2 + - - +
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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
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7B VAL* 4.1 24.0 - - + -
28B LEU* 4.4 8.7 - - + -
33B PHE* 3.9 27.1 - - + -
79B TYR* 3.6 34.3 + - + -
81B LEU* 4.2 16.6 - - + -
111B VAL* 3.8 31.1 - - + +
146B ILE* 5.2 0.9 - - - -
238B ALA 3.0 12.7 + - - +
239B ALA 3.3 8.7 - - - +
241B LEU* 1.3 76.8 - - - +
243B ALA* 1.3 64.7 + - - +
245B THR* 3.4 6.6 + - - -
246B HIS* 3.1 24.8 + - - +
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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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28B LEU* 3.6 24.9 - - + -
31B LEU* 3.6 24.9 - - + -
33B PHE* 3.7 20.7 - - + -
239B ALA 3.1 3.8 + - - +
240B MET* 3.2 10.3 + - - +
242B LEU* 1.3 81.3 - - - +
244B TRP* 1.3 61.4 + - + +
246B HIS* 3.3 18.9 - - - +
247B LYS* 3.3 10.4 + - - +
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Residues in contact with TRP 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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31B LEU* 4.1 18.8 - - + +
240B MET* 2.8 41.9 + - + +
241B LEU 4.5 0.2 - - - +
243B ALA* 1.3 72.1 - - + +
245B THR* 1.3 62.1 + - - +
246B HIS 3.1 1.1 - - - -
247B LYS* 3.7 29.8 - - + -
248B HIS* 3.0 31.8 + - + +
255B ALA* 3.5 25.3 - - + +
258B LYS* 3.5 47.6 - - + +
259B THR* 3.7 14.8 - - - +
262B THR* 4.1 12.9 + - - -
300B ILE 3.6 20.6 + - - -
301B GLU 3.9 15.7 - - - -
302B ASP* 5.2 0.2 - - - -
303B PRO* 3.7 14.4 - - + -
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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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79B TYR* 5.1 3.2 + - - -
146B ILE* 3.6 23.8 - - + +
182B THR* 5.2 1.3 - - + -
205B GLN* 4.4 17.9 - - - +
241B LEU* 2.9 41.9 + - + +
242B LEU 3.4 4.9 + - - -
244B TRP* 1.3 74.5 - - - +
246B HIS* 1.3 62.2 + - - +
247B LYS 3.2 0.2 - - - -
248B HIS 3.8 5.4 - - - +
249B PRO* 3.0 32.9 - - - +
252B LEU* 4.6 7.0 - - + -
255B ALA* 3.7 20.0 - - + -
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Residues in contact with HIS 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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5B CYS* 3.8 10.8 - - - +
33B PHE* 3.6 25.1 - + + -
79B TYR* 3.0 30.5 + - + +
242B LEU 3.1 20.2 + - - +
243B ALA 3.3 6.1 - - - +
245B THR* 1.3 80.9 + - - +
247B LYS* 1.3 64.7 + - + +
249B PRO* 3.8 9.6 - - - +
530B SO4 3.3 35.3 + - - -
534B SO4 3.5 21.1 + - - -
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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
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243B ALA 3.3 12.2 + - - +
244B TRP* 3.5 22.0 + - + +
246B HIS* 1.3 85.6 - - + +
248B HIS* 1.3 90.6 + - + +
249B PRO* 3.3 9.3 - - - +
258B LYS* 5.4 1.3 - - - +
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Residues in contact with HIS 248 (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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205B GLN* 5.2 0.3 + - - -
244B TRP* 3.0 25.5 + + + +
245B THR* 3.3 8.5 - - - +
247B LYS* 1.3 103.9 + - + +
249B PRO* 1.3 67.1 - - - +
250B ASN 3.1 4.1 + - - -
251B ASN* 3.1 36.3 + - + +
254B VAL* 3.4 25.0 - - + +
255B ALA* 4.4 2.8 - - - +
258B LYS* 2.6 35.6 + - + -
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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
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Atomic class I II III IV V VI VII VIII
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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