Contacts of the helix formed by residues 157 - 164 (chain B) in PDB entry 3BWB
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 ASP 157 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B VAL* 4.0 1.6 - - - +
127B ILE* 4.5 14.2 - - + +
156B GLY* 1.3 71.4 - - - -
158B GLY* 1.3 65.7 + - - +
159B LEU* 3.3 29.4 + - - +
160B ALA* 3.7 23.1 + - + +
161B PHE* 3.2 25.6 + - - +
163B ARG* 5.1 3.3 + - - -
181B ALA* 4.4 14.2 - - - +
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Residues in contact with GLY 158 (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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102B ILE* 4.7 17.9 - - - -
125B VAL* 3.9 16.5 - - - +
127B ILE* 5.8 0.8 - - - +
156B GLY 3.5 4.6 + - - -
157B ASP* 1.3 73.5 + - - +
159B LEU* 1.3 65.8 + - - +
161B PHE* 3.8 2.3 - - - +
162B VAL* 3.1 32.4 + - - +
192B PHE* 4.4 4.0 - - - -
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Residues in contact with LEU 159 (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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157B ASP* 3.3 18.1 + - - +
158B GLY* 1.3 74.7 - - - +
160B ALA* 1.3 65.4 + - - +
162B VAL* 3.3 7.8 - - - +
163B ARG* 3.2 30.3 + - - +
179B ASP* 4.7 15.3 - - - +
181B ALA* 6.2 2.5 - - + -
187B LEU* 6.3 1.6 - - + -
188B PHE* 3.9 37.2 - - + +
192B PHE* 3.3 41.5 - - + -
195B ASP* 4.5 1.0 - - - +
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Residues in contact with ALA 160 (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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157B ASP* 3.6 25.0 + - + +
158B GLY 3.4 0.2 - - - -
159B LEU* 1.3 78.0 - - - +
161B PHE* 1.3 62.9 + - - +
163B ARG* 3.4 32.5 - - - +
164B GLN* 3.2 35.1 + - - +
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Residues in contact with PHE 161 (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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100B LEU* 3.7 32.5 - - + -
102B ILE* 6.4 0.4 - - + -
123B ASP* 4.6 9.0 - - + -
125B VAL* 3.9 23.1 - - + -
154B ARG* 4.1 28.0 - - - -
157B ASP 3.2 15.3 + - - +
158B GLY* 3.8 8.5 - - - +
159B LEU 3.3 0.2 - - - -
160B ALA* 1.3 80.7 - - - +
162B VAL* 1.3 63.9 + - + +
164B GLN* 3.2 6.2 + - - +
165B THR* 2.8 43.5 + - - -
170B TYR* 3.7 16.4 - + - -
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Residues in contact with VAL 162 (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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100B LEU* 4.0 15.9 - - + -
102B ILE* 4.6 6.5 - - + -
158B GLY 3.1 19.2 + - - +
159B LEU* 3.3 8.5 - - - +
161B PHE* 1.3 78.5 - - + +
163B ARG* 1.3 64.1 + - - +
165B THR* 3.4 15.8 + - - +
192B PHE* 3.6 32.5 - - + -
195B ASP* 3.8 22.4 - - + +
196B VAL* 4.6 5.2 - - + -
198B ARG* 3.8 2.1 + - - -
199B ILE* 3.6 39.4 - - + +
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Residues in contact with ARG 163 (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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157B ASP* 5.1 3.0 + - - -
159B LEU* 3.2 11.7 + - - +
160B ALA* 3.4 34.5 - - - +
162B VAL* 1.3 81.1 - - - +
164B GLN* 1.3 82.6 + - + +
165B THR 3.3 0.7 - - - -
195B ASP* 3.5 26.5 - - - +
198B ARG* 3.7 12.7 + - - +
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Residues in contact with GLN 164 (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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160B ALA* 3.2 27.7 + - - +
161B PHE* 3.2 7.6 + - - +
163B ARG* 1.3 100.9 - - + +
165B THR* 1.3 59.7 + - - +
166B PRO* 3.9 5.4 - - - +
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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