Contacts of the strand formed by residues 132 - 137 (chain A) in PDB entry 2B3O
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 132 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU* 3.4 15.7 - - + +
127A LYS* 4.4 13.3 - - + +
129A GLU* 2.8 25.6 + - - +
130A PRO 4.4 0.2 + - - -
131A TRP* 1.3 76.9 - - - +
133A PHE* 1.3 58.9 - - - +
149A VAL* 4.1 1.1 - - - -
150A LEU* 3.1 25.3 + - - +
211A GLN* 2.9 45.4 + - - +
212A PRO 4.0 0.9 - - - -
213A TYR* 4.0 26.7 - - + +
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Residues in contact with PHE 133 (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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110A TRP* 3.5 32.8 - + + -
124A LEU* 5.1 0.2 - - - -
131A TRP 3.7 0.2 + - - -
132A THR* 1.3 74.4 - - - +
134A LEU* 1.3 68.1 + - - +
135A VAL* 5.1 0.9 - - + -
147A LEU* 4.3 5.8 - - + -
148A SER 3.5 5.6 - - - -
149A VAL* 3.6 7.6 - - + -
191A VAL* 3.7 13.7 - - + -
195A LYS* 3.9 23.6 - - + -
209A LEU* 3.4 60.3 - - + -
210A ARG 4.1 0.7 - - - -
211A GLN 2.8 24.9 + - - -
212A PRO* 3.3 32.6 - - + +
213A TYR* 3.0 27.4 + - - +
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A TRP 3.8 8.7 - - - +
112A HIS* 4.2 13.9 - - + -
115A MET* 3.6 29.2 - - + -
120A ALA* 4.6 3.1 - - + +
123A LEU* 5.4 0.2 - - + -
124A LEU* 3.2 29.2 - - + -
133A PHE* 1.3 85.2 - - - +
135A VAL* 1.3 82.3 + - - +
136A ARG* 4.2 15.3 - - + -
147A LEU* 3.7 1.0 - - - +
148A SER* 2.8 48.5 + - - +
213A TYR* 4.1 17.7 - - + -
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Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A TRP* 3.2 38.0 + - + -
111A TYR* 4.6 9.2 - - + -
112A HIS* 2.9 30.2 + - - +
113A GLY* 3.3 1.0 + - - -
133A PHE* 5.1 2.5 - - + -
134A LEU* 1.3 81.9 - - - +
136A ARG* 1.3 67.2 + - - +
145A PHE* 3.8 23.8 - - + -
146A VAL 3.3 12.6 - - - +
147A LEU* 4.1 18.8 - - + -
169A VAL* 5.8 2.2 - - + -
187A LEU* 4.6 11.4 - - + -
191A VAL* 4.2 12.6 - - + -
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Residues in contact with ARG 136 (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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113A GLY* 3.4 12.3 - - - +
115A MET* 3.3 25.3 + - + +
116A SER* 4.3 3.2 - - - +
117A GLY* 3.4 34.9 - - - +
120A ALA* 4.3 4.3 - - - -
134A LEU* 4.2 12.8 - - + -
135A VAL* 1.3 78.3 - - - +
137A GLU* 1.3 70.0 + - - +
138A SER* 5.2 1.6 - - - +
139A LEU* 5.3 5.7 - - - +
145A PHE* 2.9 11.8 - - - +
146A VAL* 2.8 69.1 + - + +
148A SER* 3.1 21.4 + - - -
166A HIS* 3.8 13.5 + - - +
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Residues in contact with GLU 137 (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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111A TYR* 5.1 2.9 - - - +
113A GLY* 2.5 32.3 + - - +
114A HIS* 3.2 42.7 + - - +
115A MET 4.1 1.6 - - - +
136A ARG* 1.3 87.4 + - - +
138A SER* 1.3 61.3 + - - +
139A LEU* 3.5 27.9 + - + +
144A ASP 4.5 0.2 - - - -
145A PHE* 4.1 12.8 - - + -
246A GLU* 5.4 8.1 - - - +
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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