Contacts of the helix formed by residues 224 - 238 (chain B) in PDB entry 4UTX
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 ASP 224 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153B ILE 5.6 1.2 + - - -
215B HIS* 6.0 4.0 - - + -
217B VAL* 5.7 2.2 - - - +
222B THR 3.9 0.4 + - - -
223B LEU* 1.4 70.8 - - - +
225B SER* 1.3 66.2 + - - +
226B ASP* 3.3 30.2 - - - +
227B ILE* 3.4 31.4 + - + +
228B LEU* 3.2 21.3 + - - +
1303B NA 2.8 22.6 - - - -
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Residues in contact with SER 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B LEU 3.7 4.8 + - - -
224B ASP* 1.3 72.4 + - - +
226B ASP* 1.3 62.5 + - - +
228B LEU* 3.2 11.9 + - - +
229B THR* 2.6 41.0 + - - +
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Residues in contact with ASP 226 (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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224B ASP* 3.3 9.2 - - - +
225B SER* 1.3 81.6 + - - +
227B ILE* 1.3 63.6 + - + +
229B THR* 2.7 19.7 + - - -
230B ALA* 3.2 10.2 + - - +
1303B NA 2.8 26.7 - - - -
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Residues in contact with ILE 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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151B TYR* 4.3 17.7 - - + -
152B GLU 4.0 19.5 - - - +
153B ILE* 4.5 21.3 - - + +
215B HIS* 6.2 1.8 - - - +
224B ASP* 3.4 32.6 + - + +
225B SER 3.2 0.6 - - - -
226B ASP* 1.3 77.4 - - + +
228B LEU* 1.3 65.6 + - + +
230B ALA* 2.9 18.0 + - - +
231B VAL* 3.0 28.9 + - + +
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Residues in contact with LEU 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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153B ILE* 5.8 3.4 - - + -
223B LEU* 3.8 42.8 - - + +
224B ASP 3.2 11.5 + - - +
225B SER* 3.2 13.7 + - - +
227B ILE* 1.3 80.3 - - + +
229B THR* 1.3 58.4 + - + +
231B VAL* 3.8 8.5 - - + +
232B GLU* 2.9 29.7 + - - +
255B MET* 5.1 7.2 - - - -
256B PHE* 4.4 24.7 - - + -
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Residues in contact with THR 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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225B SER* 2.6 22.6 + - - +
226B ASP* 2.7 17.0 + - - -
228B LEU* 1.3 76.5 - - + +
230B ALA* 1.3 60.0 + - - +
232B GLU* 3.6 16.8 - - - +
233B ARG* 3.1 33.9 + - - +
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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
----------------------------------------------------------
151B TYR* 3.7 29.8 - - + +
226B ASP 3.2 10.7 + - - +
227B ILE* 2.9 12.0 + - - +
229B THR* 1.3 76.0 - - - +
231B VAL* 1.3 61.0 + - - +
233B ARG* 2.9 13.9 + - - +
234B GLU* 2.8 32.8 + - - +
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Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ILE* 3.9 21.8 - - + -
151B TYR* 4.2 22.9 - - + -
153B ILE* 4.7 9.2 - - + -
227B ILE* 3.0 29.0 + - + +
228B LEU* 3.3 10.5 + - + +
230B ALA* 1.3 74.7 - - - +
232B GLU* 1.3 58.6 + - - +
234B GLU* 3.1 9.1 + - - +
235B LEU* 2.8 53.5 + - + +
256B PHE* 3.8 21.3 - - + -
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Residues in contact with GLU 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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228B LEU 2.9 16.4 + - - +
229B THR* 3.6 18.9 - - - +
231B VAL* 1.3 74.4 - - - +
233B ARG* 1.3 66.2 + - + +
235B LEU* 2.9 9.9 + - - +
236B GLU* 2.8 42.9 + - + +
259B GLN* 6.1 1.3 - - - +
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Residues in contact with ARG 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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229B THR* 3.1 20.2 + - - +
230B ALA* 2.9 14.2 + - - +
232B GLU* 1.3 77.8 - - + +
234B GLU* 1.3 63.6 + - + +
236B GLU* 3.1 35.2 - - - +
237B LYS* 3.2 30.6 + - - +
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Residues in contact with GLU 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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48B HIS* 5.7 1.0 + - - +
50B ALA* 5.3 0.5 - - - +
130B SER* 5.2 2.4 + - - -
132B VAL* 3.8 33.2 - - + +
134B ILE* 5.6 2.2 - - + -
149B HIS* 5.8 1.4 - - - +
151B TYR* 3.2 38.1 + - + +
230B ALA 2.8 18.8 + - - +
231B VAL* 3.4 9.6 - - + +
233B ARG* 1.3 79.4 - - + +
235B LEU* 1.3 65.1 + - + +
237B LYS* 3.2 27.1 + - - +
238B CYS* 3.3 15.8 + - - +
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Residues in contact with LEU 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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50B ALA* 3.9 26.2 - - + -
52B ILE* 5.1 5.6 - - + -
134B ILE* 4.0 10.5 - - + -
231B VAL* 2.8 34.0 + - + +
232B GLU* 3.8 5.8 - - - +
234B GLU* 1.3 71.4 - - - +
236B GLU* 1.3 64.2 - - - +
237B LYS 3.2 0.2 - - - -
238B CYS* 3.5 13.6 + - - -
241B CYS* 5.2 2.2 - - - -
256B PHE* 3.6 43.7 - - + +
259B GLN* 5.8 4.0 - - + -
260B VAL* 3.9 28.3 - - + +
263B ARG* 3.1 16.0 + - - -
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Residues in contact with GLU 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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232B GLU* 2.8 36.2 + - + +
233B ARG* 3.1 26.0 - - - +
235B LEU* 1.3 77.9 - - - +
237B LYS* 1.3 62.0 + - + +
263B ARG* 2.8 29.2 + - - +
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Residues in contact with LYS 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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48B HIS* 3.4 39.2 - - + +
233B ARG* 3.2 33.7 + - - +
234B GLU* 3.2 18.2 + - - +
235B LEU 3.2 0.4 - - - -
236B GLU* 1.3 85.5 - - + +
238B CYS* 1.3 61.6 + - - +
239B ASP* 3.6 2.1 + - - +
263B ARG* 4.6 0.2 - - - -
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Residues in contact with CYS 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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48B HIS* 3.1 22.4 - - + +
49B ILE 4.7 0.2 - - - -
50B ALA* 4.2 19.7 - - + -
132B VAL* 6.2 0.9 - - + -
234B GLU 3.3 13.0 + - - +
235B LEU* 3.5 15.1 + - - -
236B GLU 3.4 2.2 - - - -
237B LYS* 1.3 80.1 - - - +
239B ASP* 1.3 57.7 + - - +
240B LEU 3.6 22.9 - - - +
241B CYS* 4.4 1.8 - - - -
260B VAL* 4.2 23.6 - - - -
263B ARG* 3.2 19.4 + - - -
265B VAL* 3.9 5.2 - - - +
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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
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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