Contacts of the strand formed by residues 122 - 128 (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 LEU 122 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B PRO* 5.2 1.1 - - + -
113B VAL* 4.9 5.6 - - + -
116B ALA* 3.6 39.0 - - + +
118B PRO 4.1 6.7 - - - +
119B ARG* 2.9 19.9 + - - +
120B ALA 4.5 0.7 - - - +
121B SER* 1.3 78.9 - - - +
123B THR* 1.3 62.6 + - - +
124B LEU* 4.2 14.6 - - + -
137B SER* 3.8 1.4 + - - -
138B PHE* 3.0 31.9 + - + +
147B GLY 4.3 3.4 - - - +
148B ALA* 3.8 25.1 - - + +
169B ALA* 4.9 2.2 - - + -
170B GLU 3.1 24.9 - - - +
171B LEU* 4.0 16.6 - - + -
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Residues in contact with THR 123 (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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121B SER 4.0 1.2 + - - -
122B LEU* 1.3 76.1 + - - +
124B LEU* 1.3 65.4 + - - +
125B THR* 4.3 0.7 - - - +
135B ARG* 3.7 46.1 + - + +
136B ARG 3.4 13.2 - - - +
137B SER* 3.8 15.7 + - - +
168B ARG 3.8 1.0 - - - +
169B ALA* 3.6 1.6 - - - -
170B GLU* 2.9 47.6 + - - +
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Residues in contact with LEU 124 (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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111B CYS* 4.2 9.6 - - - +
113B VAL* 4.0 28.9 - - + -
122B LEU* 4.2 13.2 - - + -
123B THR* 1.3 78.6 - - - +
125B THR* 1.3 63.4 + - - +
136B ARG 2.8 33.2 + - - -
138B PHE* 3.9 17.0 - - + -
148B ALA* 3.9 27.6 - - + +
149B VAL 4.0 1.8 - - - -
150B LEU* 3.3 45.3 - - + +
168B ARG 3.3 7.4 - - - +
169B ALA* 4.3 7.0 - - + -
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Residues in contact with THR 125 (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* 4.3 1.4 + - - +
124B LEU* 1.3 77.4 + - - +
126B LEU* 1.3 68.5 + - - +
127B LEU* 4.2 6.3 - - + +
132B GLU* 3.7 41.7 - - + +
134B ILE 3.2 12.8 - - - +
135B ARG* 2.9 28.8 + - + +
150B LEU* 4.4 0.7 - - - -
167B CYS* 3.1 8.2 - - - +
168B ARG* 2.9 45.6 + - - +
170B GLU* 4.2 2.9 + - - -
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Residues in contact with LEU 126 (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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94B LEU* 3.9 16.2 - - + -
109B LEU* 3.9 32.8 - - + +
111B CYS* 3.8 16.8 - - + +
125B THR* 1.3 74.0 - - - +
127B LEU* 1.3 55.0 + - - +
132B GLU* 3.7 2.9 - - - -
133B LEU* 2.7 35.7 + - + +
134B ILE* 2.8 19.9 + - + +
150B LEU* 4.0 22.9 - - + +
152B ALA* 3.7 29.8 - - + -
166B SER 3.7 2.2 - - - +
167B CYS* 3.6 23.1 - - + -
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Residues in contact with LEU 127 (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* 5.1 0.5 - - - +
125B THR* 4.2 10.3 - - + +
126B LEU* 1.3 77.9 - - - +
128B ARG* 1.3 58.8 + - - +
129B GLY 3.6 13.0 - - - +
130B ALA* 3.8 20.2 - - - +
131B GLN 3.2 5.6 - - - +
132B GLU* 3.5 27.8 - - + -
133B LEU* 4.3 3.1 - - - -
165B PHE* 3.2 11.2 - - - +
166B SER* 2.8 53.0 + - - +
167B CYS 4.3 0.4 - - - -
168B ARG* 3.9 44.0 - - + +
184B SER* 5.5 1.8 - - - +
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Residues in contact with ARG 128 (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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127B LEU* 1.3 71.7 - - - +
129B GLY* 1.3 65.5 + - - +
130B ALA 3.4 0.2 + - - -
131B GLN* 2.9 59.9 + - - +
133B LEU* 3.8 30.7 - - + +
154B VAL* 4.6 10.9 - - - +
155B LEU 5.3 1.0 + - - -
157B ARG* 3.2 34.3 - - - +
160B ASP* 3.5 26.3 + - - -
163B ALA* 4.1 15.5 - - + -
164B ASN 3.5 3.6 - - - +
165B PHE* 3.5 32.1 - - + -
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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