Contacts of the helix formed by residues 226 - 243 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 3.6 63.2 - + + +
13A VAL* 4.0 5.5 - - + +
16A THR* 3.3 20.4 - - - -
220A LEU* 4.3 15.0 - - + -
224A SER 3.3 16.6 - - - -
225A ALA* 1.3 74.1 - - - +
227A TYR* 1.3 97.5 + + - -
229A PRO* 3.4 9.4 - - - -
230A ALA* 2.8 34.3 + - - +
15B SER* 4.7 2.3 + - - -
42B LYS* 3.6 27.5 - - + +
45B ASP* 2.7 13.9 + - - -
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Residues in contact with TYR 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 3.9 13.0 - - + -
20A TRP* 3.2 10.8 + - + +
226A TYR* 1.3 103.2 + + - +
228A ALA* 1.3 56.9 + - - +
231A ALA* 2.9 26.2 + - - +
15B SER* 3.2 37.1 + - - -
16B THR* 4.1 4.0 + - + -
19B HIS* 3.7 39.0 - + + -
42B LYS* 4.0 29.6 - - + -
45B ASP* 2.8 32.1 + - + +
46B LEU* 3.8 30.1 - - + -
49B ALA* 4.0 3.6 - - + -
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Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU* 3.4 18.8 - - + -
151A ARG* 5.6 0.2 - - - +
227A TYR* 1.3 70.7 - - - +
229A PRO* 1.3 71.4 - - + +
231A ALA* 3.1 1.9 + - - +
232A ALA* 2.7 31.9 + - - +
45B ASP* 2.9 23.0 + - - +
48B GLU* 4.0 14.8 - - + +
49B ALA* 3.6 23.1 - - - +
52B ILE* 3.8 3.6 - - + +
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Residues in contact with PRO 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 4.4 7.4 - - + -
118A VAL* 5.6 0.4 - - + -
143A GLN* 4.2 2.3 - - - +
147A LEU* 3.8 19.5 - - + -
225A ALA* 3.6 21.5 - - + +
226A TYR* 3.4 16.8 - - - +
228A ALA* 1.3 95.8 - - + +
230A ALA* 1.3 56.2 + - - +
232A ALA* 3.2 4.7 + - + +
233A THR* 2.8 35.0 + - - -
1310A NAD 3.4 37.0 - - + -
45B ASP* 3.6 6.5 - - - +
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Residues in contact with ALA 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 3.9 4.8 - - - +
16A THR* 3.4 14.8 - - + -
17A THR* 3.4 29.7 + - - +
20A TRP* 3.4 20.0 - - + -
226A TYR 2.8 23.3 + - - +
227A TYR 3.7 0.2 - - - +
229A PRO* 1.3 72.4 - - - +
231A ALA* 1.3 58.9 + - - +
233A THR* 3.2 2.5 + - - -
234A ALA* 2.8 31.4 + - - +
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Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TRP* 3.4 21.3 - - + +
227A TYR 2.9 18.3 + - - +
228A ALA 3.4 4.5 - - - +
230A ALA* 1.3 76.3 - - - +
232A ALA* 1.3 63.6 + - - +
234A ALA* 3.2 3.4 + - - +
235A GLN 2.9 19.6 + - - -
49B ALA* 3.8 18.4 - - + -
52B ILE* 3.6 24.3 - - + +
53B GLU* 4.1 10.6 - - + +
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Residues in contact with ALA 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A GLN* 3.3 30.5 - - - +
146A VAL* 3.7 24.5 - - + +
147A LEU* 3.7 9.2 - - + +
228A ALA 2.7 16.1 + - - +
229A PRO 3.4 8.3 - - - +
231A ALA* 1.3 73.1 - - - +
233A THR* 1.3 63.1 + - - +
235A GLN* 3.2 5.2 + - - +
236A MET* 3.2 23.0 + - - +
52B ILE* 3.7 5.5 - - + +
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Residues in contact with THR 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 4.7 1.2 - - - +
17A THR* 4.1 13.8 + - + +
75A VAL* 3.8 40.4 - - + -
116A ILE* 4.3 10.5 - - + -
118A VAL* 3.7 23.5 - - + +
143A GLN* 3.8 13.3 + - - +
229A PRO 2.8 19.2 + - - -
230A ALA* 3.2 7.2 + - - -
232A ALA* 1.3 73.6 - - - +
234A ALA* 1.3 59.2 + - - +
236A MET* 3.0 7.3 + - - +
237A VAL* 2.9 29.1 + - - +
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Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A THR* 4.5 3.7 - - + +
20A TRP* 3.9 21.1 - - + -
21A LEU* 3.4 30.1 - - + +
24A LYS* 4.2 10.8 - - - -
230A ALA 2.8 20.4 + - - +
231A ALA* 3.4 5.4 - - - +
233A THR* 1.3 73.7 - - - +
235A GLN* 1.3 57.7 + - - +
237A VAL* 3.0 5.1 + - - +
238A GLU* 2.8 31.5 + - - +
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Residues in contact with GLN 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LYS* 5.1 3.9 - - - +
146A VAL* 3.2 33.9 - - - +
153A ARG* 5.6 3.9 + - - +
231A ALA 2.9 12.6 + - - +
232A ALA 3.6 6.7 - - - +
234A ALA* 1.3 74.8 - - - +
236A MET* 1.3 57.9 + - - +
238A GLU* 3.4 13.2 + - - +
239A ALA* 2.9 28.6 + - - +
246A ARG* 3.4 39.7 + - - +
248A MET* 4.7 10.5 - - + +
51B PRO 5.4 0.2 - - - +
52B ILE* 3.6 31.9 - - + +
53B GLU* 5.9 0.7 - - - +
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Residues in contact with MET 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ILE* 3.9 15.3 - - + -
141A ILE* 3.8 28.0 - - + -
142A GLY 3.8 13.7 - - - +
143A GLN* 3.4 38.4 - - - -
146A VAL* 4.4 8.3 - - + -
232A ALA 3.2 7.7 + - - +
233A THR* 3.0 9.0 + - - +
235A GLN* 1.3 74.5 - - - +
237A VAL* 1.3 65.8 + - - +
239A ALA* 3.1 10.6 + - - +
240A VAL* 3.1 19.2 + - - +
248A MET* 3.9 19.7 - - - -
249A PRO 5.5 0.2 - - - +
250A VAL* 3.4 29.4 - - + -
271A LEU* 4.0 10.0 - - + +
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Residues in contact with VAL 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 3.9 16.2 - - + -
17A THR* 5.3 0.4 - - + -
21A LEU* 4.2 21.1 - - + -
26A LEU* 4.8 0.7 - - + -
73A VAL* 4.3 7.9 - - + -
75A VAL* 3.7 29.2 - - + -
116A ILE* 4.1 12.1 - - + -
233A THR* 2.9 22.8 + - + +
234A ALA* 3.0 8.3 + - - +
236A MET* 1.3 74.4 - - - +
238A GLU* 1.3 59.3 + - - +
240A VAL* 3.2 5.8 + - - +
241A LEU* 2.9 51.1 + - + +
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Residues in contact with GLU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LYS* 4.1 24.7 + - + +
26A LEU* 3.9 24.1 - - + +
234A ALA 2.8 15.6 + - - +
235A GLN* 3.5 12.0 - - - +
237A VAL* 1.3 78.2 - - - +
239A ALA* 1.3 57.1 + - - +
241A LEU 4.5 0.4 - - - +
242A LYS* 2.8 52.4 + - + +
244A LYS* 3.8 33.1 + - + +
246A ARG* 4.3 10.9 + - - -
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Residues in contact with ALA 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A GLN 2.9 14.6 + - - +
236A MET 3.5 8.7 - - - +
238A GLU* 1.3 75.9 - - - +
240A VAL* 1.3 57.1 + - - +
243A ASP* 2.9 23.6 + - - -
244A LYS* 3.0 21.2 + - - -
246A ARG* 3.8 11.9 - - + -
248A MET* 3.7 27.1 - - + -
271A LEU* 3.9 14.4 - - + +
272A GLY* 3.8 4.5 - - - -
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ASP 5.2 0.7 - - - +
73A VAL* 4.0 15.7 - - + -
114A VAL* 3.8 38.4 - - + -
116A ILE* 4.7 6.7 - - + -
141A ILE* 5.1 0.2 - - + -
236A MET 3.1 15.8 + - - +
237A VAL 3.6 5.2 - - - +
238A GLU 3.1 0.2 - - - -
239A ALA* 1.3 75.4 - - - +
241A LEU* 1.3 68.1 + - + +
243A ASP* 3.1 9.9 + - - -
271A LEU* 4.0 19.1 - - + -
272A GLY 3.4 20.6 - - - +
273A ALA* 3.5 20.3 - - - +
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Residues in contact with LEU 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LYS* 3.8 45.6 + - + +
5A ILE* 3.4 30.3 - - + -
26A LEU* 3.9 32.5 - - + +
72A ASP* 3.9 21.3 - - + -
73A VAL* 4.0 11.0 - - + -
237A VAL* 2.9 34.0 + - + +
238A GLU 4.1 1.8 - - - +
240A VAL* 1.3 78.7 - - + +
242A LYS* 1.3 60.2 + - - +
243A ASP* 3.7 0.9 + - - +
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Residues in contact with LYS 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LYS 5.5 2.8 + - - -
26A LEU* 3.9 28.0 - - + +
238A GLU* 2.8 28.9 + - + +
241A LEU* 1.3 73.7 - - - +
243A ASP* 1.3 72.3 + - - +
244A LYS* 3.3 35.1 + - + +
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Residues in contact with ASP 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ALA 2.9 11.9 + - - -
240A VAL 3.1 7.3 + - - +
241A LEU 5.0 1.1 - - - +
242A LYS* 1.3 81.1 - - - +
244A LYS* 1.3 61.9 + - - +
245A LYS* 2.8 39.3 + - - +
272A GLY* 3.5 1.2 - - - -
273A ALA* 2.7 43.2 + - + +
277A GLU* 3.5 0.5 - - - +
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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