Contacts of the helix formed by residues 226 - 242 (chain B) in PDB entry 1UXI
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 TYR 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 6.0 0.3 - - - -
15A SER* 4.6 1.9 + - - -
42A LYS* 3.4 28.8 - - + +
45A ASP* 2.6 12.1 + - - -
12B PHE* 3.4 63.1 - + + +
13B VAL* 3.9 4.3 - - - +
16B THR* 3.4 18.5 - - - +
220B LEU* 4.4 15.0 - - + -
224B SER 3.4 16.6 - - - -
225B ALA* 1.3 75.2 - - - +
227B TYR* 1.3 107.2 + + - +
229B PRO* 3.5 9.4 - - - +
230B ALA* 2.9 34.5 + - - +
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Residues in contact with TYR 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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15A SER* 3.0 40.6 + - - -
16A THR* 3.9 3.9 + - - -
19A HIS* 3.7 35.2 - + + -
42A LYS* 3.8 31.9 - - + -
45A ASP* 2.9 23.5 + - + +
46A LEU* 3.7 32.3 - - + -
49A ALA* 4.1 2.5 - - + -
16B THR* 4.0 12.3 - - + -
20B TRP* 3.0 11.9 + + + +
226B TYR* 1.3 109.7 - + - +
228B ALA* 1.3 57.1 + - - +
231B ALA* 2.9 25.3 + - - +
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Residues in contact with ALA 228 (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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45A ASP* 2.8 22.8 + - - +
48A GLU* 3.9 26.0 - - + +
49A ALA* 3.7 11.9 - - - +
52A ILE* 3.6 6.9 - - + +
147B LEU* 3.3 20.0 - - + -
151B ARG* 5.3 0.2 - - - +
227B TYR* 1.3 73.4 - - - +
229B PRO* 1.3 67.8 - - + +
231B ALA* 3.0 4.0 + - - +
232B ALA* 2.9 26.5 + - - +
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Residues in contact with PRO 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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45A ASP* 3.5 6.5 - - - +
13B VAL* 4.4 6.5 - - + -
118B VAL* 5.7 0.4 - - + +
143B GLN* 4.3 3.2 - - - +
147B LEU* 3.6 20.6 - - + -
225B ALA* 3.7 22.2 - - + -
226B TYR* 3.5 16.2 - - - +
228B ALA* 1.3 96.8 - - + +
230B ALA* 1.3 56.1 + - - +
232B ALA* 3.4 5.0 + - + +
233B THR* 3.0 31.9 + - - -
1310B NAD 3.4 37.0 - - + -
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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
----------------------------------------------------------
13B VAL* 3.8 6.7 - - + +
16B THR* 3.5 24.7 - - - -
17B THR* 3.5 22.8 + - - +
20B TRP* 3.5 12.6 - - + -
226B TYR 2.9 22.2 + - - +
229B PRO* 1.3 74.9 - - - +
231B ALA* 1.3 66.9 + - - +
233B THR* 3.4 2.5 + - - -
234B ALA* 3.0 25.3 + - - +
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Residues in contact with ALA 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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49A ALA* 3.9 15.0 - - + -
52A ILE* 3.3 24.8 - - + +
53A GLU* 4.3 8.3 - - + +
20B TRP* 3.3 27.1 - - + +
227B TYR 2.9 18.3 + - - +
228B ALA 3.4 5.2 - - - +
230B ALA* 1.3 78.5 - - - +
232B ALA* 1.3 55.7 - - - +
234B ALA* 3.5 3.0 + - - +
235B GLN* 3.0 22.2 + - - +
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Residues in contact with ALA 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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52A ILE* 3.5 13.4 - - + +
143B GLN* 3.1 34.1 - - - +
146B VAL* 3.6 18.8 - - + +
147B LEU* 3.8 6.1 - - + +
228B ALA 2.9 11.9 + - - +
229B PRO 3.5 4.7 - - - +
231B ALA* 1.3 74.9 - - - +
233B THR* 1.3 66.1 + - - +
235B GLN* 3.1 12.5 + - - +
236B MET* 3.2 17.5 + - - +
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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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13B VAL* 4.8 1.4 - - - +
17B THR* 4.0 16.3 + - + +
75B VAL* 3.7 37.5 - - + -
116B ILE* 4.4 7.6 - - + -
118B VAL* 3.6 24.6 - - + +
143B GLN* 3.6 14.0 - - - +
229B PRO 3.0 17.7 + - - -
230B ALA* 3.4 4.8 + - - -
232B ALA* 1.3 74.8 - - - +
234B ALA* 1.3 58.0 + - - +
236B MET* 3.2 7.4 + - - +
237B VAL* 3.0 26.6 + - + +
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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
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53A GLU* 5.1 0.2 - - - +
17B THR* 4.4 5.6 - - + +
20B TRP* 3.8 20.2 - - + -
21B LEU* 3.5 28.4 - - + +
24B LYS* 4.4 10.4 - - - -
230B ALA 3.0 18.3 + - - +
231B ALA 3.7 4.9 - - - +
233B THR* 1.3 74.2 - - - +
235B GLN* 1.3 61.2 + - - +
237B VAL* 3.7 3.4 - - - +
238B GLU* 3.0 29.3 + - - +
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Residues in contact with GLN 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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51A PRO 5.2 0.2 - - - +
52A ILE* 3.5 32.5 - - + +
24B LYS* 5.3 3.3 - - - +
146B VAL* 3.2 28.7 - - - +
153B ARG* 5.5 4.8 + - - +
231B ALA 3.0 14.0 + - - +
232B ALA 3.1 7.3 + - - +
234B ALA* 1.3 77.3 - - - +
236B MET* 1.3 59.0 + - - +
238B GLU* 3.6 12.7 + - - +
239B ALA* 3.0 25.5 + - - +
246B ARG* 3.4 36.4 + - - +
248B MET* 3.8 16.3 - - + +
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Residues in contact with MET 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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116B ILE* 4.0 19.3 - - + -
141B ILE* 3.4 36.1 - - + -
142B GLY 3.9 13.0 - - - +
143B GLN* 3.5 34.8 - - - -
144B ALA 5.1 0.2 - - - -
146B VAL* 4.2 12.3 - - + -
232B ALA 3.2 10.7 + - - +
233B THR* 3.5 6.7 - - - +
234B ALA 3.2 0.2 - - - -
235B GLN* 1.3 76.5 - - - +
237B VAL* 1.3 65.2 + - - +
239B ALA* 3.1 2.6 + - - +
240B VAL* 3.0 27.5 + - - +
248B MET* 3.8 21.3 - - - -
250B VAL* 3.8 16.8 - - + -
271B LEU* 3.8 10.4 - - + +
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Residues in contact with VAL 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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5B ILE* 3.9 21.8 - - + -
21B LEU* 4.2 16.4 - - + -
26B LEU* 4.9 0.4 - - + -
73B VAL* 4.1 8.3 - - + -
75B VAL* 3.7 28.7 - - + -
116B ILE* 3.8 13.9 - - + -
233B THR* 3.0 23.1 + - + +
234B ALA* 3.4 7.6 + - - +
236B MET* 1.3 73.6 - - - +
238B GLU* 1.3 59.4 + - - +
240B VAL* 3.2 5.7 + - - +
241B LEU* 2.9 49.7 + - + +
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Residues in contact with GLU 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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24B LYS* 4.2 23.1 + - + +
26B LEU* 3.8 32.0 - - + +
234B ALA 3.0 17.9 + - - +
235B GLN* 3.7 13.6 - - - +
237B VAL* 1.3 74.9 - - - +
239B ALA* 1.3 66.4 + - - +
241B LEU* 4.5 1.8 - - - +
242B LYS* 2.9 32.1 + - + +
244B LYS* 3.5 32.2 - - - +
246B ARG* 4.4 9.9 + - - -
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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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235B GLN 3.0 16.2 + - - +
236B MET 3.1 8.9 + - - +
238B GLU* 1.3 75.3 - - - +
240B VAL* 1.3 57.6 + - - +
243B ASP* 3.0 9.4 + - - -
244B LYS* 3.0 35.8 + - - -
246B ARG* 3.7 23.6 - - + -
248B MET* 4.8 0.9 - - + -
271B LEU* 3.7 26.0 - - + +
272B GLY* 3.7 5.6 - - - -
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Residues in contact with VAL 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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72B ASP 5.2 0.9 - - - +
73B VAL* 4.0 18.2 - - + -
114B VAL* 4.0 35.7 - - + -
116B ILE* 4.8 6.7 - - + -
141B ILE* 5.4 0.2 - - + -
236B MET 3.0 14.4 + - - +
237B VAL 3.5 6.7 - - - +
239B ALA* 1.3 73.4 - - - +
241B LEU* 1.3 69.3 + - + +
243B ASP 3.0 11.1 + - - -
271B LEU* 4.1 19.1 - - + -
272B GLY 3.7 20.4 - - - +
273B ALA* 3.4 24.2 - - - +
275B GLY* 4.7 0.7 - - - -
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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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3B LYS* 4.0 40.1 + - + +
5B ILE* 3.4 35.7 - - + -
26B LEU* 3.9 26.5 - - + +
72B ASP* 3.8 21.8 - - + -
73B VAL* 3.7 23.1 - - + -
237B VAL* 2.9 28.0 + - + +
238B GLU* 4.2 3.1 - - - +
240B VAL* 1.3 74.7 - - + +
242B LYS* 1.3 63.8 + - + +
243B ASP* 3.3 0.9 + - - +
273B ALA* 6.0 0.2 - - - +
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Residues in contact with LYS 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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24B LYS 5.4 3.2 + - - -
25B GLU 6.0 0.7 - - - -
26B LEU* 3.8 28.5 - - + +
238B GLU* 2.9 26.2 + - + +
241B LEU* 1.3 74.2 - - + +
243B ASP* 1.3 73.3 + - - +
244B LYS* 3.0 37.7 + - + +
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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