Contacts of the strand formed by residues 143 - 148 (chain B) in PDB entry 2BG9
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 143 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ASN* 3.7 18.3 - - + +
128B CYS* 2.9 16.7 - - - -
129B THR* 4.5 2.3 - - - +
142B CYS* 1.3 77.7 - - - +
144B MET* 1.3 57.0 + - - +
145B VAL* 3.2 26.5 - - + -
208B THR* 3.0 29.3 - - + +
210B TYR* 3.6 11.8 + - - -
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Residues in contact with MET 144 (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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50B MET* 3.6 22.0 - - + +
95B ASN* 3.2 12.8 - - - +
124B TYR* 5.4 8.1 - - - +
128B CYS* 3.1 21.1 - - - -
143B THR* 1.3 71.2 - - - +
145B VAL* 1.4 51.7 + - - +
146B PHE* 4.4 9.9 - - + -
176B ASN* 5.1 1.3 - - - +
191B LYS* 2.8 44.4 - - + +
207B VAL 2.6 20.3 - - - +
208B THR* 4.1 0.2 - - - -
209B PHE* 2.7 50.5 + - + +
211B LEU* 3.0 39.0 - - + -
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Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B VAL 3.4 0.9 - - - +
92B LEU* 2.6 33.0 - - - -
93B MET* 2.7 33.0 + - + +
94B ASN 4.0 6.7 - - - +
95B ASN* 3.3 6.3 + - - -
143B THR* 3.2 26.5 - - + +
144B MET* 1.4 68.9 - - - +
146B PHE* 1.3 57.0 + - - +
196B ASN* 3.5 4.9 - - - +
206B ASP* 2.9 33.9 - - + +
207B VAL 2.9 26.2 - - - +
208B THR* 3.3 11.2 - - - +
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Residues in contact with PHE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 4.1 26.9 - - + -
90B ILE* 3.8 14.8 - - + -
91B VAL 3.4 0.2 - - - -
92B LEU* 3.1 40.2 - - + -
95B ASN* 5.3 0.2 - - - -
124B TYR* 3.2 38.8 - + - -
144B MET* 4.3 13.5 - - + -
145B VAL* 1.3 75.1 - - - +
147B LYS* 1.3 68.2 + - - +
158B LEU* 5.8 2.1 - - - +
206B ASP* 3.1 13.7 - - - -
207B VAL* 3.1 14.8 + - + +
209B PHE* 3.9 31.9 - + + -
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Residues in contact with LYS 147 (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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86B TRP* 6.0 3.4 - - - -
88B PRO* 6.5 0.2 - - + -
90B ILE* 2.8 19.7 - - + +
91B VAL* 2.3 46.5 + - + +
93B MET* 6.0 1.6 - - + -
146B PHE* 1.3 78.3 - - - +
148B SER* 1.3 85.6 + - - +
151B TYR* 3.7 3.9 + - - -
152B ASP 3.8 0.4 - - - -
153B THR* 3.0 20.4 + - - +
156B VAL* 6.0 4.7 - - - -
158B LEU* 5.4 15.9 - - + -
204B TYR 2.8 20.4 + - - -
205B GLU* 2.3 67.4 + - - +
206B ASP* 3.4 14.6 - - + +
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Residues in contact with SER 148 (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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86B TRP* 5.3 1.9 - - - -
88B PRO* 4.0 9.9 - - - -
89B ASP* 2.9 41.3 - - - -
90B ILE* 3.4 2.7 - - - +
91B VAL* 4.0 3.8 - - - +
147B LYS* 1.3 103.3 - - - +
149B TYR* 1.3 59.3 + - - +
150B THR 3.6 1.1 + - - -
151B TYR* 3.3 24.2 + - - +
205B GLU* 3.2 20.6 - - - +
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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