Contacts of the helix formed by residues 231 - 238 (chain B) in PDB entry 1LWU
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 HIS 231 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230B MET* 1.3 82.6 + - + +
232B CYS* 1.3 65.6 + - - +
233B GLU* 2.9 35.9 - - + +
234B ASP* 3.5 11.8 - - + +
235B ILE* 3.4 19.8 + - - +
248B ILE* 3.7 9.1 - - - +
250B PRO* 5.7 0.2 - - - -
269B GLY 3.2 8.2 + - - -
271B THR* 3.1 13.3 + - - -
322B LEU* 4.2 14.1 - - + +
328B GLN* 2.9 31.5 + - - -
474B LEU* 2.8 31.9 + - + -
475B ARG* 3.1 12.0 - - - -
476B PRO* 3.4 10.3 - - + +
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Residues in contact with CYS 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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231B HIS* 1.3 75.3 - - - +
233B GLU* 1.3 54.7 - - - +
234B ASP 3.0 1.3 - - - -
235B ILE* 2.7 8.5 + - - +
236B TYR* 2.7 34.8 + - - +
248B ILE* 4.8 0.4 - - - -
259B VAL* 4.0 6.3 - - - -
261B CYS* 2.0 56.1 - - - -
263B MET* 3.7 14.8 - - + +
269B GLY* 3.7 8.8 - - - +
270B TRP 3.9 0.4 - - - -
271B THR* 3.2 37.2 + - - +
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Residues in contact with GLU 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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231B HIS* 2.9 23.6 - - + -
232B CYS* 1.3 76.6 - - - +
234B ASP* 1.3 63.5 + - - +
236B TYR* 3.0 13.7 + - - +
237B ARG* 2.9 57.2 + - - +
268B GLY 4.6 1.3 - - - +
269B GLY* 3.2 15.8 + - - +
475B ARG* 3.3 29.1 + - - +
476B PRO* 3.7 19.9 - - + +
477B LYS 4.4 11.6 - - - +
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Residues in contact with ASP 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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229B GLY* 3.3 9.2 - - - -
230B MET* 3.2 37.2 + - + +
231B HIS* 3.5 20.2 + - + +
233B GLU* 1.3 81.0 - - - +
235B ILE* 1.3 62.3 + - - +
237B ARG* 3.2 21.0 + - - +
238B ASN* 3.1 33.7 + - - +
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Residues in contact with ILE 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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227B VAL* 4.4 5.2 - - + -
228B SER* 3.6 22.7 - - - -
229B GLY 3.6 0.4 - - - +
231B HIS 3.6 9.9 - - - +
232B CYS* 2.7 12.7 + - - +
234B ASP* 1.3 75.3 - - - +
236B TYR* 1.3 65.0 + - - +
238B ASN* 2.8 18.0 + - - +
239B GLY 3.2 0.3 + - - -
240B GLY* 3.0 27.5 + - - +
246B TYR* 3.3 61.5 - - + -
247B TYR 3.9 6.5 - - - +
248B ILE* 3.8 18.8 - - + -
261B CYS* 4.0 7.0 - - - -
263B MET* 4.6 4.7 - - - -
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Residues in contact with TYR 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 CYS 2.7 14.7 + - - +
233B GLU* 3.0 19.9 + - - +
235B ILE* 1.3 72.4 - - - +
237B ARG* 1.3 60.3 + - + +
238B ASN 2.8 6.6 + - - -
239B GLY 2.9 13.2 + - - -
240B GLY 3.3 14.3 + - - +
241B ARG* 2.9 70.9 + - + -
263B MET* 3.9 34.2 + - + -
267B GLY 4.1 16.6 + - - -
269B GLY* 4.2 12.6 - - - -
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Residues in contact with ARG 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 GLU* 2.9 43.5 + - - +
234B ASP* 3.2 25.8 + - - +
236B TYR* 1.3 78.7 - - + +
238B ASN* 1.3 66.5 + - - +
239B GLY 3.4 0.2 - - - -
241B ARG* 5.0 4.3 - - - +
477B LYS 6.2 1.6 - - - -
209C VAL* 3.7 14.7 - - - +
212C ARG* 5.9 0.5 + - - -
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Residues in contact with ASN 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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227B VAL* 3.3 26.1 - - + +
228B SER 3.1 18.8 - - - +
234B ASP* 3.1 21.7 + - - +
235B ILE 2.8 11.1 + - - +
237B ARG* 1.3 90.5 + - - +
239B GLY* 1.3 56.3 + - - +
240B GLY 3.4 0.4 - - - -
209C VAL* 4.1 7.1 - - - +
210C SER* 4.3 6.9 + - - -
212C ARG* 5.3 4.6 - - - +
213C GLU* 3.6 46.2 + - + +
214C GLY 4.6 1.4 - - - +
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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