Contacts of the helix formed by residues 176 - 186 (chain B) in PDB entry 3BRW
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 LYS 176 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B TYR* 3.2 38.8 + - + +
175B PRO* 1.3 76.8 - - - +
177B ALA* 1.3 61.4 + - - +
178B SER 3.6 1.3 - - - -
179B ARG* 3.4 28.9 - - + +
180B LEU* 3.4 12.8 + - + +
118C TYR* 3.7 18.8 + - + +
125C GLU* 2.9 29.7 + - - -
148C THR* 5.2 12.1 + - - +
150C PHE* 3.8 22.0 - - + -
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Residues in contact with ALA 177 (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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101B ASN* 4.8 4.0 - - - +
172B VAL* 3.5 15.3 - - + +
174B TYR* 2.8 25.4 + - + +
175B PRO 3.0 1.6 - - - -
176B LYS* 1.3 74.7 - - - +
178B SER* 1.3 61.4 + - - +
180B LEU* 2.9 7.0 + - - +
181B ILE* 2.8 36.6 + - + +
401B LEU* 3.5 28.0 - - + +
100C PHE* 5.8 1.3 - - + -
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Residues in contact with SER 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TYR* 3.4 26.5 - - - -
95B LEU* 4.0 10.1 - - - +
99B HIS* 4.2 2.5 - - - -
101B ASN* 4.9 2.6 - - - +
175B PRO 4.3 7.1 + - - -
177B ALA* 1.3 77.4 - - - +
179B ARG* 1.3 75.1 + - - +
180B LEU 3.0 0.7 + - - -
181B ILE* 3.8 3.1 - - - +
182B VAL* 3.1 27.5 + - - +
98C GLU* 2.7 40.7 + - - -
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Residues in contact with ARG 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 4.6 5.6 - - + +
175B PRO 5.0 2.8 + - - -
176B LYS* 3.4 23.6 + - + +
178B SER* 1.3 86.0 + - - +
180B LEU* 1.3 56.8 + - + +
182B VAL* 3.4 19.8 - - - +
183B THR* 3.4 16.3 + - - +
98C GLU* 5.8 1.4 + - - -
118C TYR* 3.7 41.8 + - - -
119C ASP* 5.0 1.8 + - - +
120C VAL* 3.4 36.0 - - - +
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Residues in contact with LEU 180 (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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174B TYR* 4.5 19.7 - - + -
176B LYS* 3.4 8.5 + - + +
177B ALA* 2.9 11.5 + - - +
179B ARG* 1.3 76.9 - - - +
181B ILE* 1.3 65.0 + - - +
182B VAL 3.4 0.4 - - - -
183B THR* 3.5 14.0 + - - +
184B PHE* 3.4 14.2 + - - +
397B LEU* 3.4 27.8 - - + +
400B GLU* 3.9 34.5 - - + +
401B LEU* 5.2 2.5 - - + -
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Residues in contact with ILE 181 (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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90B TYR* 3.8 19.5 - - + +
101B ASN* 3.5 43.1 - - + +
113B VAL* 4.6 6.7 - - + -
115B SER* 4.7 0.2 - - - +
132B ARG* 3.2 37.5 - - - +
177B ALA* 2.8 24.4 + - + +
178B SER 3.2 4.0 + - - +
180B LEU* 1.3 77.6 - - - +
182B VAL* 1.3 60.5 + - - +
184B PHE* 3.3 5.1 + - - +
185B ASP* 2.9 26.2 + - - +
397B LEU* 4.2 8.7 - - + -
401B LEU* 4.4 20.4 - - + -
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Residues in contact with VAL 182 (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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90B TYR* 3.8 22.2 - - + -
91B ARG* 3.9 52.5 - - + +
95B LEU* 4.6 13.0 - - + -
178B SER 3.1 15.2 + - - +
179B ARG* 3.4 19.7 - - - +
181B ILE* 1.3 78.2 - - - +
183B THR* 1.3 66.3 + - + +
185B ASP* 3.1 6.7 + - + +
186B GLU* 3.0 34.0 + - + +
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Residues in contact with THR 183 (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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91B ARG* 5.7 3.6 - - - +
179B ARG 3.4 18.3 + - - +
180B LEU* 3.5 21.5 + - - +
181B ILE 3.3 0.2 - - - -
182B VAL* 1.3 80.5 - - + +
184B PHE* 1.3 65.8 + - - +
186B GLU* 3.8 5.6 + - - +
187B HIS* 3.7 17.2 + - - +
393B LEU* 6.0 0.2 - - - +
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Residues in contact with PHE 184 (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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132B ARG* 3.6 34.8 - - + -
133B THR 5.3 0.7 - - - -
180B LEU 3.4 11.2 + - - +
181B ILE 3.3 8.2 + - - +
182B VAL 3.2 0.4 - - - -
183B THR* 1.3 80.4 + - - +
185B ASP* 1.3 72.7 + - - +
186B GLU 3.1 0.7 + - - -
187B HIS* 2.8 41.1 + + - -
390B ARG* 3.8 34.5 - - + -
393B LEU* 4.1 23.1 - - + -
394B LEU* 3.6 49.6 - - + -
397B LEU* 3.7 18.4 - - + -
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Residues in contact with ASP 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B THR 4.1 10.2 - - - +
87B ALA* 3.5 34.4 - - - +
90B TYR* 3.4 18.1 - - + +
130B LEU* 4.0 7.8 - - - +
132B ARG* 2.8 41.8 + - - +
137B THR* 4.6 4.0 + - - -
181B ILE 2.9 9.8 + - - +
182B VAL* 3.1 13.0 + - + +
184B PHE* 1.3 90.5 - - - +
186B GLU* 1.3 57.4 + - + +
187B HIS* 3.5 4.1 + - - -
188B VAL* 4.6 2.4 + - - +
390B ARG* 4.5 12.7 + - - +
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Residues in contact with GLU 186 (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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87B ALA 3.3 19.3 - - - +
88B ARG* 4.2 9.7 - - + +
91B ARG* 2.8 56.7 + - - +
182B VAL* 3.0 20.2 + - + +
183B THR* 3.8 6.6 + - - +
184B PHE 3.1 0.2 - - - -
185B ASP* 1.3 75.8 - - + +
187B HIS* 1.3 59.9 + - - +
188B VAL 3.1 6.7 + - - -
189B ILE* 3.3 43.9 + - + +
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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