Contacts of the strand formed by residues 79 - 86 (chain B) in PDB entry 3D87
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 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ASP 2.6 15.7 + - - +
8B VAL* 3.9 17.9 - - + +
9B TYR 2.6 33.8 + - - +
64B GLY* 3.2 31.6 - - - +
65B GLN* 3.5 25.4 + - + +
78B SER* 1.3 69.8 - - - +
80B LEU* 1.3 63.3 + - - +
81B LEU* 3.5 32.8 - - + -
193B VAL* 5.9 0.4 - - + -
195B LYS 4.5 4.0 - - - +
196B LEU* 4.0 15.3 - - + -
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Residues in contact with LEU 80 (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 ILE* 4.9 3.1 - - + -
9B TYR* 3.3 19.3 - - + -
11B VAL* 4.1 18.4 - - + -
24B VAL* 3.9 31.2 - - + -
26B LEU* 3.9 13.2 - - + -
55B ILE* 4.7 4.3 - - + -
57B VAL* 5.0 3.1 - - + -
62B ASP 5.5 0.4 - - - +
63B ALA* 2.8 34.9 - - + +
64B GLY* 2.8 17.5 + - - +
66B TYR* 3.9 18.6 - - + -
78B SER 3.2 14.6 - - - +
79B LEU* 1.3 82.0 - - - +
81B LEU* 1.3 66.9 + - - +
82B LEU* 5.2 0.2 - - + -
196B LEU* 3.7 5.4 - - - +
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 5.1 1.1 - - + -
8B VAL* 3.4 31.9 - - + -
9B TYR 2.6 12.0 + - - +
10B VAL* 4.2 9.6 - - + -
11B VAL* 2.8 24.7 + - - +
63B ALA* 4.6 0.2 - - - -
79B LEU* 3.5 17.5 - - + -
80B LEU* 1.3 76.7 - - - +
82B LEU* 1.3 66.6 + - - +
193B VAL* 4.1 27.1 - - + -
195B LYS 3.0 28.9 - - - +
196B LEU* 2.9 28.7 - - + +
198B TYR* 4.0 13.5 - - + -
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Residues in contact with LEU 82 (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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10B VAL* 4.4 0.7 - - - -
11B VAL* 3.6 8.7 - - + -
13B LEU* 3.9 21.8 - - + -
16B TYR* 5.1 2.0 - - + -
57B VAL* 3.7 21.8 - - + -
58B LYS 4.4 0.4 - - - +
59B GLU* 3.2 38.6 - - - +
60B PHE* 3.6 32.3 - - + +
63B ALA* 3.6 20.2 - - + -
80B LEU* 4.9 0.7 - - + -
81B LEU* 1.3 86.9 - - - +
83B HIS* 1.3 60.1 + - - +
84B LYS* 4.0 7.2 + - + +
196B LEU 3.0 5.7 + - - -
197B LYS* 3.8 1.2 - - - -
198B TYR* 2.8 29.9 + - - +
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Residues in contact with HIS 83 (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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10B VAL* 3.7 9.9 - - + -
11B VAL 2.8 11.4 + - - +
12B GLU* 3.1 25.9 + - - +
13B LEU* 2.9 28.8 + - - +
82B LEU* 1.3 73.0 - - - +
84B LYS* 1.3 58.7 + - - +
90B TRP* 2.9 62.7 - + + +
91B SER* 5.6 0.7 - - - -
198B TYR* 2.8 42.6 + + - -
199B GLU* 4.6 1.0 - - - -
200B GLN* 4.3 21.1 + - + -
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Residues in contact with LYS 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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13B LEU* 3.6 1.8 - - + -
16B TYR* 3.3 33.6 - - + -
60B PHE* 3.4 38.7 - - + -
82B LEU* 4.4 7.2 - - + +
83B HIS* 1.3 79.1 - - - +
85B LYS* 1.3 59.3 + - - +
86B GLU* 3.3 27.4 + - + +
90B TRP* 3.1 12.4 - - - -
91B SER* 3.3 48.9 + - - +
93B ASP* 3.0 20.8 + - - -
197B LYS* 3.8 16.0 - - + +
198B TYR 4.5 2.9 + - - +
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Residues in contact with LYS 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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13B LEU 3.0 7.1 + - - -
14B ASP* 3.6 11.7 + - + +
15B TRP* 3.6 29.6 + - + +
16B TYR* 3.5 21.1 + - - +
84B LYS* 1.3 69.3 - - - +
86B GLU* 1.3 62.1 + - - +
87B ASP 3.6 2.4 + - - -
88B GLY* 3.8 23.4 + - - -
89B ILE* 3.8 15.9 - - - +
90B TRP* 3.1 57.0 - - + +
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Residues in contact with GLU 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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16B TYR* 4.7 16.4 - - + -
84B LYS* 3.3 41.4 + - + +
85B LYS* 1.3 69.1 - - - +
87B ASP* 1.3 71.4 + - + +
88B GLY 3.1 1.1 - - - -
89B ILE* 2.7 36.8 + - - +
90B TRP 4.9 1.8 - - - +
91B SER* 3.9 12.1 - - - -
93B ASP* 3.7 15.1 - - - +
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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