Contacts of the strand formed by residues 231 - 238 (chain C) in PDB entry 3BQM
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 THR 231 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C BQM 4.5 11.6 - - - -
128C GLY 5.7 2.8 + - - -
129C ASN 2.8 14.5 + - - -
130C VAL* 3.4 14.1 - - - +
131C ASP 3.0 24.9 + - - +
229C ASP 3.8 1.1 + - - -
230C ALA* 1.3 70.7 - - - +
232C LYS* 1.3 64.4 + - - +
233C VAL* 4.6 1.6 - - + -
255C ILE* 3.6 31.2 - - + -
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Residues in contact with LYS 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ASP* 3.5 7.2 - - + +
220C PHE* 3.6 42.6 - - + -
227C ARG 5.9 1.6 - - - +
230C ALA* 3.6 11.2 + - + +
231C THR* 1.3 76.2 - - - +
233C VAL* 1.3 63.4 + - - +
253C ASP* 3.5 40.9 + - - +
254C ILE* 3.7 17.5 - - + +
255C ILE* 2.9 28.2 + - - +
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Residues in contact with VAL 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C BQM 4.2 26.7 - - + +
130C VAL* 3.6 22.2 - - + -
131C ASP 2.9 8.1 + - - +
132C LEU* 3.3 30.2 - - + -
133C VAL 2.9 26.0 + - - -
220C PHE* 3.6 4.9 - - - -
231C THR* 4.4 3.4 - - + +
232C LYS* 1.3 80.6 - - - +
234C LEU* 1.3 62.9 + - - +
235C ILE* 4.2 4.0 - - + -
254C ILE* 3.9 2.5 - - - -
255C ILE* 3.4 15.5 - - + +
257C TYR* 4.0 23.8 - - + -
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Residues in contact with LEU 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C VAL* 3.4 19.3 - - + +
135C LEU* 3.8 26.0 - - + -
212C ILE* 4.4 21.8 - - + +
215C VAL* 3.9 28.0 - - + -
220C PHE* 5.0 1.3 - - + -
233C VAL* 1.3 74.3 - - - +
235C ILE* 1.3 60.9 + - - +
236C ILE* 3.8 22.2 - - + -
254C ILE* 3.7 18.6 - - + +
255C ILE 2.7 12.4 + - - +
256C ARG* 3.6 19.5 - - + -
257C TYR* 2.8 34.0 + - - +
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Residues in contact with ILE 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C BQM 3.5 52.0 - - + -
132C LEU* 3.9 23.8 - - + -
133C VAL 2.8 8.7 + - - +
134C PHE* 3.5 12.8 - - + -
135C LEU 2.7 32.3 + - - +
233C VAL* 4.2 4.0 - - + -
234C LEU* 1.3 71.2 - - - +
236C ILE* 1.3 57.4 + - - +
237C ILE* 3.9 14.7 + - + +
257C TYR* 3.6 37.5 - - + +
259C ILE* 4.0 19.3 - - + -
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Residues in contact with ILE 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C LEU* 3.3 20.2 - - + +
173C PHE* 4.4 19.3 - - + -
208C THR* 4.5 7.2 - - + -
212C ILE* 3.7 26.2 - - + -
234C LEU* 3.8 26.2 - - + -
235C ILE* 1.3 71.0 - - - +
237C ILE* 1.3 63.4 + - - +
238C THR* 4.1 1.6 - - - -
256C ARG* 4.6 3.4 - - + -
257C TYR 2.8 21.9 + - - +
258C ILE* 3.4 21.2 - - + +
259C ILE* 2.7 33.4 + - - +
277C PHE* 4.1 21.3 - - + +
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Residues in contact with ILE 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C PHE* 4.8 3.6 - - + -
135C LEU 2.9 11.9 + - - +
136C PHE* 3.6 7.2 - - + -
137C ASP* 2.9 29.9 + - - +
150C ILE* 4.1 34.1 - - + -
153C PHE* 4.1 26.5 - - + -
154C MET* 4.3 14.8 - - + -
173C PHE* 4.2 0.9 - - - -
235C ILE* 4.0 17.5 - - + +
236C ILE* 1.3 79.0 - - - +
238C THR* 1.3 62.1 + - - +
259C ILE* 3.5 18.6 - - + +
261C ILE* 3.8 26.5 - - + -
295C LEU* 5.3 2.9 - - + -
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Residues in contact with THR 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ASP* 2.9 23.9 + - - -
150C ILE* 6.1 1.3 - - - -
173C PHE* 4.2 9.3 - - - -
206C THR* 3.8 7.8 - - - +
208C THR* 4.7 3.2 + - + +
236C ILE* 4.9 2.5 - - + -
237C ILE* 1.3 77.1 - - - +
239C ASP* 1.3 59.3 + - - +
240C GLY 3.1 23.4 + - - +
258C ILE* 4.2 15.3 - - + -
259C ILE 2.9 13.6 + - - +
260C GLY* 3.3 6.5 - - - -
261C ILE* 2.9 29.3 + - - +
265C PHE* 4.1 10.8 - - + -
274C LEU* 4.2 13.9 - - + -
292C PHE* 6.1 0.2 - - - -
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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