Contacts of the strand formed by residues 131 - 137 (chain B) in PDB entry 3BN3
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 GLN 131 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127B LEU* 3.2 4.7 - - - -
128B ARG* 2.9 71.9 + - - +
130B ALA* 1.3 77.7 - - - +
132B GLU* 1.3 70.4 + - - +
133B LEU* 3.4 14.1 + - - +
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Residues in contact with GLU 132 (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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125B THR* 3.7 12.9 - - + +
126B LEU 3.7 4.5 - - - -
127B LEU* 3.5 18.4 - - + -
130B ALA 3.7 3.7 + - - +
131B GLN* 1.3 80.9 + - - +
133B LEU* 1.3 63.3 + - - +
134B ILE 5.0 1.8 - - - +
135B ARG* 3.7 27.0 + - + +
168B ARG* 3.0 29.6 + - - -
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Residues in contact with LEU 133 (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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109B LEU* 4.3 12.3 - - + -
126B LEU* 2.7 17.1 + - + +
127B LEU 4.4 0.9 - - - -
128B ARG* 3.8 54.1 - - + +
131B GLN* 3.7 27.4 - - - +
132B GLU* 1.3 75.2 - - - +
134B ILE* 1.3 76.6 + - + +
154B VAL* 4.5 13.7 - - + -
165B PHE* 3.9 19.3 - - + -
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Residues in contact with ILE 134 (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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124B LEU 4.0 0.3 - - - +
125B THR* 3.2 6.5 - - - +
126B LEU* 2.8 38.5 + - + -
132B GLU* 5.2 0.7 - - - -
133B LEU* 1.3 91.7 - - + +
135B ARG* 1.3 69.7 + - - +
136B ARG* 5.0 1.6 - - + -
150B LEU* 4.1 26.4 - - + +
152B ALA* 4.1 21.8 - - + -
154B VAL* 6.4 1.1 - - + -
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Residues in contact with ARG 135 (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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123B THR* 3.7 19.6 + - + +
124B LEU 3.5 2.9 - - - -
125B THR* 2.9 30.2 + - + +
132B GLU* 3.7 18.7 + - + +
134B ILE* 1.3 80.0 - - - +
136B ARG* 1.3 63.7 + - - +
137B SER 4.2 1.0 + - - +
168B ARG* 3.4 12.5 - - - +
170B GLU* 3.1 34.4 + - - -
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Residues in contact with ARG 136 (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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123B THR* 3.4 5.3 - - - -
124B LEU 2.8 34.9 + - - +
134B ILE* 5.0 1.8 - - + -
135B ARG* 1.3 74.7 - - - +
137B SER* 1.3 70.8 + - - +
138B PHE* 3.5 31.3 - - + -
141B GLU* 4.4 5.5 + - - -
149B VAL 3.7 18.6 + - - -
150B LEU* 3.9 30.1 - - + +
151B THR 5.7 0.6 - - - +
204B GOL 3.6 19.0 + - - -
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Residues in contact with SER 137 (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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120B ALA 4.9 1.7 + - - -
122B LEU 3.8 6.4 + - - -
123B THR* 3.8 16.6 + - - +
135B ARG* 4.2 1.6 + - - +
136B ARG* 1.3 84.7 + - - +
138B PHE* 1.3 62.0 + - - +
139B ALA* 3.3 24.3 + - - +
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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