Contacts of the helix formed by residues 233 - 247 (chain B) in PDB entry 1UMZ
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 233 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231B ASP 3.8 0.4 + - - -
232B LEU* 1.3 76.5 - - - +
234B ALA* 1.3 66.4 + - - +
235B PHE* 3.1 11.3 + - - +
236B GLN* 2.8 47.3 + - - +
237B TYR* 3.0 21.5 + - - -
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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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233B ASP* 1.3 74.5 - - - +
235B PHE* 1.3 60.9 + - - +
237B TYR* 3.3 11.7 + - - +
238B ARG* 3.0 51.3 + - - +
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Residues in contact with PHE 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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233B ASP* 3.1 9.7 + - - +
234B ALA* 1.3 76.7 - - - +
236B GLN* 1.3 68.4 + - + +
238B ARG* 3.1 40.9 + - + +
239B ARG* 3.1 49.5 + - + +
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Residues in contact with GLN 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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142B LEU* 5.2 6.9 - - - +
145B ASP 5.5 4.0 - - - +
147B PRO* 3.7 24.6 - - + +
228B GLU 5.9 0.2 + - - -
231B ASP 4.5 2.0 + - - -
232B LEU* 3.3 29.2 - - + +
233B ASP* 2.8 57.2 + - - +
235B PHE* 1.3 76.2 - - + +
237B TYR* 1.3 58.4 + - - +
239B ARG* 3.2 8.8 + - - +
240B LEU* 2.9 28.2 + - - +
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Residues in contact with TYR 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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150B VAL* 4.6 4.8 - - + +
152B LYS* 2.4 34.6 + - - -
231B ASP* 2.6 17.7 + - - -
232B LEU* 3.4 38.7 - - + +
233B ASP 3.0 22.3 + - - -
234B ALA* 3.6 11.7 - - - +
235B PHE 3.2 0.4 - - - -
236B GLN* 1.3 78.3 - - - +
238B ARG* 1.3 56.9 + - - +
240B LEU* 3.4 18.2 + - + +
241B SER* 3.0 27.4 + - - -
270B ARG* 3.3 58.5 - - + +
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Residues in contact with ARG 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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234B ALA* 3.0 40.2 + - - +
235B PHE* 3.1 33.3 + - + +
237B TYR* 1.3 72.1 - - - +
239B ARG* 1.3 67.7 + - + +
241B SER* 3.3 8.7 + - - -
242B TRP* 3.2 30.7 + - + +
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Residues in contact with ARG 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ASP* 2.9 45.7 + - - +
146B VAL* 3.8 26.9 - - + +
147B PRO* 4.1 13.2 - - + -
235B PHE* 3.1 45.3 + - + +
236B GLN* 3.2 8.5 + - - +
238B ARG* 1.3 78.3 - - + +
240B LEU* 1.3 61.4 + - - +
242B TRP* 3.2 22.8 + - + +
243B VAL* 3.2 16.6 + - - +
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Residues in contact with LEU 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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147B PRO* 3.5 17.4 + - + +
148B ILE* 3.4 36.3 - - - +
149B ARG* 3.6 6.5 - - - +
150B VAL* 4.3 10.3 - - + +
232B LEU* 4.5 4.3 - - + -
236B GLN 2.9 17.6 + - - +
237B TYR* 3.6 27.6 - - + +
238B ARG 3.3 0.2 - - - -
239B ARG* 1.3 75.4 - - - +
241B SER* 1.3 59.2 + - - +
243B VAL* 3.2 5.5 + - + +
244B ARG* 2.9 42.0 + - + +
269B ASP 4.0 20.2 - - - +
270B ARG* 4.4 8.1 - - + +
271B ASP* 5.7 0.4 - - - +
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Residues in contact with SER 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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237B TYR 3.0 14.1 + - - -
238B ARG* 3.5 12.1 - - - -
239B ARG 3.2 0.4 - - - -
240B LEU* 1.3 76.4 - - - +
242B TRP* 1.3 59.6 + - - +
244B ARG* 3.2 6.6 + - - +
245B GLN* 2.9 44.3 + - - +
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Residues in contact with TRP 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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238B ARG* 3.2 32.9 + - + +
239B ARG* 3.2 14.2 + - + +
241B SER* 1.3 76.3 - - - +
243B VAL* 1.3 58.5 + - + +
245B GLN* 4.5 2.9 - - - +
246B LYS* 2.9 70.1 + - + +
247B TYR* 3.8 10.4 - + + -
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Residues in contact with VAL 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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117B ILE* 4.0 27.1 - - + -
120B TRP* 4.1 15.7 - - + -
146B VAL* 3.7 24.7 - - + -
147B PRO 4.0 7.4 - - - +
148B ILE* 4.1 19.3 - - + +
239B ARG 3.2 12.3 + - - +
240B LEU* 3.2 9.9 + - - +
242B TRP* 1.3 76.7 - - + +
244B ARG* 1.3 71.7 + - - +
247B TYR* 3.1 27.5 + - + -
248B THR* 2.9 13.7 + - - -
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Residues in contact with ARG 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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115B GLN* 3.4 22.0 + - - +
117B ILE* 3.9 13.3 - - - +
148B ILE 2.9 27.6 + - - -
149B ARG* 4.3 1.2 - - - +
240B LEU* 2.9 30.6 + - + +
241B SER* 3.2 9.2 + - - +
243B VAL* 1.3 79.8 - - - +
245B GLN* 1.3 73.8 + - - +
248B THR* 2.9 49.3 + - - +
251B ASN* 4.4 7.1 - - - +
270B ARG 3.8 18.6 - - - +
271B ASP* 3.1 38.6 + - - +
272B ILE 5.7 2.9 - - - -
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Residues in contact with GLN 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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241B SER* 2.9 30.8 + - - +
242B TRP* 4.4 2.0 - - - +
244B ARG* 1.3 91.2 + - - +
246B LYS* 1.3 72.2 + - + +
248B THR 5.2 0.7 - - - -
272B ILE 4.7 14.5 + - - -
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Residues in contact with LYS 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 TRP* 2.9 47.5 + - + +
245B GLN* 1.3 87.9 - - + +
247B TYR* 1.3 80.5 + - + +
248B THR 3.7 0.9 - - - -
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Residues in contact with TYR 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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117B ILE* 3.1 8.3 - - + -
118B TYR* 2.9 61.3 + - + +
119B LEU 3.9 5.2 - - - -
120B TRP* 3.4 47.0 - + + +
242B TRP* 3.8 16.4 - + + -
243B VAL* 3.1 20.4 + - + +
246B LYS* 1.3 97.9 - - + +
248B THR* 1.3 62.6 + - - +
249B ILE* 3.6 4.6 + - - +
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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