Contacts of the strand formed by residues 83 - 90 (chain B) in PDB entry 3BPL
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 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-2B ALA 3.5 21.0 - - - +
-1B ASP* 3.8 19.8 + - - +
0B PRO* 5.4 2.8 - - + +
79B TRP* 3.6 2.7 - - - -
80B ALA* 3.1 32.3 + - + +
81B GLY 3.3 2.4 - - - -
82B GLN* 1.3 79.2 - - - +
84B LEU* 1.3 75.7 + - - +
85B LEU* 3.1 23.2 + - + +
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Residues in contact with LEU 84 (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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77B ASP* 4.0 14.6 - - + +
78B LEU 3.4 17.3 - - - +
79B TRP* 3.4 38.4 - - + -
82B GLN 3.7 0.6 + - - -
83B GLN* 1.3 86.1 + - - +
85B LEU* 1.3 62.9 + - - +
86B TRP 3.4 27.4 - - - +
87B LYS* 4.4 21.5 - - + -
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Residues in contact with LEU 85 (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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-1B ASP* 3.7 3.4 - - - +
1B PHE* 3.4 38.4 - - + +
2B LYS 4.5 0.2 - - - +
3B VAL* 3.8 27.2 + - + +
23B MET* 4.6 5.4 - - + -
33B LEU* 3.9 13.0 - - + -
78B LEU* 2.8 20.4 + - + +
79B TRP 4.6 0.4 - - - -
80B ALA* 3.8 25.8 - - + +
83B GLN* 3.3 34.3 - - + +
84B LEU* 1.3 75.6 - - - +
86B TRP* 1.3 64.7 + - - +
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Residues in contact with TRP 86 (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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3B VAL* 4.3 18.2 - - + -
6B GLU* 2.9 38.3 + - + -
7B PRO* 3.4 43.7 - - + +
9B CYS* 5.8 0.9 - - - -
21B TRP* 6.5 0.2 - + - -
35B LEU* 5.4 5.6 - - + -
76B LEU* 3.8 37.2 - - + -
77B ASP* 3.6 0.2 - - - -
78B LEU* 3.0 42.6 + - + -
84B LEU* 3.4 10.2 - - - +
85B LEU* 1.3 82.7 - - - +
87B LYS* 1.3 74.1 + - - +
88B GLY* 3.6 24.0 - - - -
89B SER 5.1 2.0 - - - -
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Residues in contact with LYS 87 (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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6B GLU* 5.3 1.0 - - - +
75B THR* 3.1 27.3 - - + +
76B LEU 3.4 4.3 - - - +
77B ASP* 2.6 31.1 + - - +
84B LEU* 4.4 17.0 - - + -
86B TRP* 1.3 93.0 + - - +
88B GLY* 1.3 60.7 + - - +
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Residues in contact with GLY 88 (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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75B THR* 3.6 6.6 - - - +
76B LEU* 2.8 36.8 + - - +
86B TRP* 3.6 19.0 - - - -
87B LYS* 1.3 77.9 - - - +
89B SER* 1.3 64.0 + - - -
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Residues in contact with SER 89 (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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73B GLN* 3.7 26.1 + - - -
74B TYR 3.1 9.0 + - - -
75B THR* 5.2 2.1 - - - +
76B LEU* 5.0 2.3 - - - +
86B TRP* 5.5 1.9 - - - -
88B GLY* 1.3 76.1 + - - -
90B PHE* 1.3 64.0 + - - +
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Residues in contact with PHE 90 (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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9B CYS* 3.5 45.1 - - + -
10B VAL 4.1 9.2 - - - -
11B SER 4.3 0.2 - - - -
17B SER* 3.3 30.5 - - - -
63B LEU* 5.5 2.0 - - + -
65B MET* 4.4 4.5 - - + -
73B GLN* 4.4 2.2 - - - -
74B TYR* 2.8 45.2 + - + +
76B LEU* 4.0 22.9 - - + -
89B SER* 1.3 79.8 - - - +
91B LYS* 1.3 58.8 + - - +
92B PRO* 3.4 33.5 - - + +
95B HIS* 3.9 24.7 - + + -
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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