Contacts of the helix formed by residues 180 - 188 (chain B) in PDB entry 2BV1
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 SER 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B PHE* 3.7 29.4 - - - -
176B ARG 3.2 3.2 + - - -
177B PHE* 2.5 25.1 + - - -
178B LEU 3.4 0.4 - - - -
179B LYS* 1.3 80.0 - - - +
181B ASP* 1.3 64.2 + - - +
182B ILE* 3.4 10.6 - - - +
183B TYR* 3.3 13.5 + - - +
184B LEU* 3.0 27.1 + - - +
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Residues in contact with ASP 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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84A ASN* 3.8 12.1 + - - +
179B LYS 3.9 1.4 + - - +
180B SER* 1.3 72.9 - - - +
182B ILE* 1.3 58.2 + - - +
184B LEU* 4.8 3.4 - - - +
185B ASN* 2.8 56.3 + - - +
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Residues in contact with ILE 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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81A THR* 4.9 6.3 + - + +
84A ASN* 3.6 27.5 - - + +
85A VAL* 4.1 20.4 - - + -
88A SER* 3.9 21.8 - - - +
85B VAL* 4.1 17.0 - - + +
88B SER* 4.0 21.3 - - - -
89B PHE* 4.2 15.3 - - + +
177B PHE* 4.2 13.9 - - + -
180B SER* 3.4 15.2 - - - +
181B ASP* 1.3 80.7 - - - +
183B TYR* 1.3 66.0 + - - +
185B ASN* 4.6 0.7 - - - +
186B LEU* 3.4 20.8 + - + +
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Residues in contact with TYR 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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66B VAL* 2.6 46.9 + - + +
67B MET* 3.6 6.1 + - - -
69B TRP* 3.7 19.1 - + + -
70B SER* 2.9 28.8 + - - -
85B VAL* 5.1 0.2 - - - -
177B PHE* 3.2 46.9 - + + +
178B LEU* 3.3 36.3 - - + -
180B SER* 3.3 2.5 + - - +
182B ILE* 1.3 82.4 - - - +
184B LEU* 1.3 68.8 - - + +
186B LEU* 3.1 22.0 + - - +
187B LEU* 3.2 26.1 + - + +
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Residues in contact with LEU 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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178B LEU 3.4 18.6 - - - +
179B LYS* 3.5 30.3 - - - +
180B SER 3.0 16.2 + - - +
181B ASP* 4.4 3.4 - - - +
183B TYR* 1.3 85.3 - - + +
185B ASN* 1.3 60.7 + - - +
187B LEU* 3.2 13.4 + - + +
188B ASN* 2.8 44.6 + - - +
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Residues in contact with ASN 185 (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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80A GLN* 3.5 44.4 + - + +
81A THR* 4.5 8.1 + - - +
84A ASN* 2.7 35.1 + - - +
181B ASP* 2.8 39.5 + - - +
182B ILE 4.6 0.7 - - - +
184B LEU* 1.3 73.7 - - - +
186B LEU* 1.3 61.9 + - - +
187B LEU 3.5 0.2 + - - -
188B ASN* 3.5 20.1 + - - +
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Residues in contact with LEU 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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60A VAL* 3.1 38.6 - - + +
61A LEU* 4.2 25.4 - - + -
81A THR* 3.7 31.1 + - + +
61B LEU* 4.0 12.6 - - + -
66B VAL* 4.1 13.2 - - + -
69B TRP* 3.9 28.3 - - + -
85B VAL* 4.1 22.0 - - + -
182B ILE* 3.4 10.8 + - + +
183B TYR* 3.1 10.9 + - - +
185B ASN* 1.3 78.1 - - - +
187B LEU* 1.3 63.1 + - - +
188B ASN 4.6 1.0 - - - -
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Residues in contact with LEU 187 (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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60A VAL* 4.1 11.3 - - - +
63B ALA* 3.9 13.7 - - + +
66B VAL* 3.7 20.8 - - + +
67B MET* 3.4 36.8 - - + +
70B SER* 5.5 0.7 - - - +
183B TYR* 3.2 32.4 + - + +
184B LEU* 3.4 20.0 - - + +
186B LEU* 1.3 81.7 - - - +
188B ASN* 1.3 68.7 + - - +
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Residues in contact with ASN 188 (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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60A VAL* 5.8 1.3 - - - -
80A GLN* 6.0 0.9 - - - +
184B LEU* 2.8 38.0 + - - +
185B ASN* 3.9 16.4 - - - +
186B LEU 3.4 2.4 - - - -
187B LEU* 1.3 89.8 - - - +
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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