Contacts of the strand formed by residues 231 - 238 (chain A) in PDB entry 1BRW
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 ARG 231 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A VAL* 3.8 15.2 - - - +
194A ASP* 3.0 17.7 + - - +
195A ALA* 3.2 11.8 - - + +
196A ILE 2.8 25.8 + - - +
226A LYS* 5.7 0.9 - - - +
229A GLY 3.9 3.3 + - - +
230A ARG* 1.3 68.5 - - - +
232A THR* 1.3 59.7 + - - +
282A LEU* 3.0 49.7 + - + +
284A GLU* 2.9 32.2 + - - +
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Residues in contact with THR 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A MET* 4.1 12.3 - - + +
196A ILE* 3.3 15.3 - - + +
198A LEU* 3.7 26.7 - - + -
222A VAL* 3.8 31.1 - - - +
225A GLY* 3.3 21.5 - - - -
226A LYS* 3.6 24.5 - - - +
230A ARG* 3.2 12.8 + - - +
231A ARG* 1.3 75.3 - - - +
233A MET* 1.3 66.5 + - - +
433A VAL 4.6 3.6 - - - +
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Residues in contact with MET 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ILE 3.0 9.7 + - - +
197A VAL* 4.0 17.0 - - - -
198A LEU* 2.8 27.9 + - - +
222A VAL* 4.1 4.5 - - - -
232A THR* 1.3 75.8 - - - +
234A ALA* 1.3 67.1 + - - +
235A VAL* 3.4 30.7 - - + -
275A LEU* 4.9 4.3 - - + -
278A HIS* 3.3 53.4 - - + +
282A LEU* 4.5 13.7 - - + -
431A THR* 3.9 6.3 - - + -
432A ILE 3.5 13.5 - - - +
433A VAL* 3.9 17.9 - - + +
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Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A LEU* 3.3 22.2 - - + +
200A VAL* 4.7 1.1 - - + -
218A ALA* 4.1 21.8 - - + -
222A VAL* 3.8 17.9 - - + -
233A MET* 1.3 80.8 - - - +
235A VAL* 1.3 64.7 + - - +
430A GLU 4.8 0.2 - - - -
431A THR* 3.4 7.1 - - - +
432A ILE* 2.8 39.8 + - + +
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Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A LEU 3.0 13.6 + - - +
199A ASP* 3.4 19.5 - - - +
200A VAL* 2.8 28.8 + - - +
233A MET* 3.4 26.2 - - + -
234A ALA* 1.3 73.7 - - - +
236A ILE* 1.3 63.8 + - - +
237A SER* 4.9 0.9 - - - +
271A LEU* 4.8 8.1 - - + -
274A THR* 4.8 16.6 - - + -
275A LEU* 3.8 21.5 - - + -
278A HIS* 5.1 0.2 - - - +
428A ILE* 4.6 10.3 - - + -
430A GLU 3.5 6.3 - - - +
431A THR* 3.9 13.9 - - - +
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Residues in contact with ILE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A VAL* 3.2 12.1 - - + +
202A THR* 4.0 8.7 - - + -
211A LEU* 3.9 25.8 - - + -
214A ALA* 3.9 17.9 - - + +
215A ARG* 3.6 35.2 - - + +
218A ALA* 4.3 13.2 - - + -
234A ALA 5.9 0.2 - - - -
235A VAL* 1.3 75.0 - - - +
237A SER* 1.3 57.9 + - - +
428A ILE* 3.5 3.3 - - - +
429A TYR* 2.7 39.0 + - + -
430A GLU* 3.0 39.5 + - + +
432A ILE* 4.9 4.3 - - + -
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Residues in contact with SER 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASP* 3.0 23.0 + - - -
200A VAL 3.0 7.7 + - - -
201A LYS* 3.4 22.9 + - - +
202A THR* 3.1 25.5 + - - +
235A VAL* 3.9 1.9 + - - -
236A ILE* 1.3 74.8 - - - +
238A ASP* 1.3 62.6 + - - +
271A LEU* 4.3 19.9 - - - +
427A LEU* 3.2 15.5 - - - -
428A ILE* 4.7 3.1 - - - -
429A TYR* 4.2 6.1 - - - -
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Residues in contact with ASP 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A LYS* 5.2 0.9 + - - -
202A THR 4.0 4.8 - - - +
237A SER* 1.3 75.2 + - - +
239A MET* 1.3 73.3 + - - +
240A SER* 3.0 31.6 + - - -
241A GLN* 3.8 19.2 - - - +
243A LEU* 5.4 6.1 - - - +
425A PRO* 3.5 20.3 - - - +
426A PRO 3.3 22.7 - - - +
427A LEU* 2.9 23.0 + - + +
429A TYR* 4.0 15.2 + - + -
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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