Contacts of the helix formed by residues 230 - 239 (chain B) in PDB entry 1UJN
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 230 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B ASN 3.1 1.6 + - - -
229B LEU* 1.3 78.1 - - - +
231B HIS* 1.3 59.0 + - - +
232B THR 3.4 3.3 - - - +
233B LEU 4.1 2.2 + - - -
234B GLY* 3.2 21.3 + - - -
251B VAL* 4.2 7.6 - - - +
254B GLY* 3.4 34.7 - - - -
255B LEU* 4.1 7.0 - - - -
258B ALA* 4.7 3.6 - - - +
312B VAL* 5.0 2.2 + - - +
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Residues in contact with HIS 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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125B ASP* 5.3 0.8 + - - -
173B GLU* 3.8 3.9 + - - -
176B LYS* 3.3 39.6 + - + -
227B LEU 3.8 2.4 + - - -
228B ASN* 2.9 29.7 + - + +
229B LEU 3.0 18.1 + - - -
230B GLY* 1.3 76.5 - - - +
232B THR* 1.3 59.9 + - - +
234B GLY* 3.6 4.7 - - - +
235B HIS* 2.8 32.1 + - + +
247B HIS* 3.4 37.9 + + - -
251B VAL* 3.8 16.8 - - + +
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Residues in contact with THR 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 ASN* 4.2 6.7 + - - +
230B GLY* 3.4 1.4 - - - +
231B HIS* 1.3 77.8 - - - +
233B LEU* 1.3 61.8 + - - +
235B HIS* 4.0 2.8 - - - +
236B ALA* 3.2 21.1 + - - +
297B TYR 4.9 3.6 - - - +
298B LEU* 4.2 5.0 - - + +
309B LEU* 3.4 35.3 - - + +
310B HIS 4.5 12.0 + - - -
311B TRP* 3.5 37.9 - - + -
312B VAL* 5.3 2.3 + - - +
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Residues in contact with LEU 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 GLY* 4.1 2.4 + - - -
232B THR* 1.3 77.7 - - - +
234B GLY* 1.3 60.9 + - - +
236B ALA* 3.1 4.6 + - + +
237B LEU* 2.8 35.5 + - + +
253B TYR 4.0 7.9 - - - +
254B GLY* 4.1 8.7 - - - +
257B TYR* 3.3 53.8 - - + -
294B LEU* 3.6 28.7 - - + -
298B LEU* 4.6 18.2 - - + -
311B TRP* 4.2 3.3 - - + -
334B PHE* 5.1 3.8 - - + -
337B TRP* 4.0 26.0 - - + -
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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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230B GLY 3.2 18.1 + - - -
231B HIS* 3.8 2.5 - - - -
232B THR 3.2 0.4 - - - -
233B LEU* 1.3 78.5 - - - +
235B HIS* 1.3 60.8 + - - +
237B LEU* 3.2 4.0 + - - +
238B GLU* 3.1 20.1 + - - +
250B ALA* 3.4 42.2 + - - +
251B VAL* 4.6 1.8 - - - -
254B GLY* 4.4 0.4 - - - -
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Residues in contact with HIS 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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231B HIS* 2.8 24.5 + - + +
232B THR* 4.0 2.9 - - - +
234B GLY* 1.3 71.5 - - - +
236B ALA* 1.3 55.7 + - - +
238B GLU* 3.0 16.2 + - + +
239B ALA* 2.6 53.9 + - + +
297B TYR* 5.2 5.1 - + + -
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Residues in contact with ALA 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 THR 3.2 12.9 + - - +
233B LEU* 3.1 14.9 + - + +
235B HIS* 1.3 81.4 - - - +
237B LEU* 1.3 57.7 + - - +
239B ALA* 3.7 0.9 - - - +
240B GLN* 2.8 32.2 + - - +
294B LEU* 3.6 15.4 - - + +
297B TYR* 3.8 31.9 - - + -
298B LEU* 4.0 12.1 - - + -
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Residues in contact with LEU 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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233B LEU* 2.8 25.2 + - + +
234B GLY 3.2 6.9 + - - +
236B ALA* 1.3 75.0 - - - +
238B GLU* 1.3 63.7 + - - +
240B GLN* 3.5 19.1 + - - +
245B LEU* 4.2 20.9 - - + +
250B ALA* 4.4 7.9 - - + +
253B TYR* 3.6 35.9 - - + -
286B LEU* 4.6 7.2 - - + -
289B LEU* 4.0 17.3 - - + -
294B LEU* 3.7 30.7 - - + -
337B TRP* 4.1 16.4 - - + -
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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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234B GLY 3.1 13.1 + - - +
235B HIS* 3.0 17.4 + - + +
237B LEU* 1.3 75.3 - - - +
239B ALA* 1.3 58.0 + - - +
240B GLN 2.9 14.4 + - - -
244B ALA 4.5 12.3 + - - +
245B LEU* 3.1 24.6 - - + +
247B HIS* 3.0 52.1 + - - +
250B ALA* 3.5 12.7 - - + +
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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 HIS* 2.6 43.8 + - + +
236B ALA 3.7 0.4 - - - -
238B GLU* 1.3 71.1 - - - +
240B GLN* 1.3 56.9 + - - +
297B TYR* 3.0 39.0 + - + -
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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