Contacts of the strand formed by residues 81 - 90 (chain B) in PDB entry 3VF1
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 TYR 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B THR* 3.4 11.3 - - - +
10B GLY* 2.9 44.5 + - - -
11B ASP* 4.1 6.1 + - - -
12B LEU* 3.7 47.0 + - + +
42B PHE* 5.9 0.2 - - - -
79B ASP 3.6 4.0 + - - -
80B TRP* 1.3 73.1 - - - +
82B ILE* 1.3 58.5 + - - +
105B TYR* 3.8 49.0 + + - +
106B ARG* 3.6 14.1 - - - -
107B TRP* 3.6 44.6 - + + -
403B TYR* 5.6 0.5 + - - -
407B LYS* 4.7 9.9 + - - -
628B ASP* 4.4 7.3 + - - -
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Residues in contact with ILE 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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7B VAL* 3.9 16.6 - - + -
8B GLU 3.6 11.4 - - - +
9B THR* 4.5 0.2 - - - +
10B GLY* 4.1 0.9 - - - -
21B VAL* 5.2 1.1 - - + -
38B LEU* 6.4 0.2 - - + -
69B LEU* 4.0 21.5 - - + -
80B TRP* 3.8 37.5 - - + +
81B TYR* 1.3 75.3 - - - +
83B ALA* 1.3 56.1 + - - +
84B LYS* 3.7 22.0 - - - +
85B VAL* 4.0 8.3 - - + -
104B CYS* 3.5 12.7 - - + +
105B TYR* 2.8 33.8 + - - -
106B ARG 3.1 9.8 + - - +
108B VAL* 3.9 22.9 - - + -
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLU* 2.8 25.9 + - + +
9B THR 4.1 2.5 - - - +
10B GLY* 3.4 21.6 - - - +
82B ILE* 1.3 69.7 - - - +
84B LYS* 1.3 64.2 + - + +
104B CYS* 2.9 9.3 + - - -
105B TYR* 2.9 53.3 + - + +
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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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6B THR 4.1 0.3 - - - +
8B GLU* 3.0 62.5 + - + +
82B ILE* 3.6 4.3 - - - +
83B ALA* 1.3 85.0 - - + +
85B VAL* 1.3 67.1 + - - +
86B ILE* 4.6 12.0 - - + +
101B ILE* 4.1 20.8 - - + +
102B PHE 3.3 16.2 - - - +
103B PRO* 3.9 9.9 - - + -
104B CYS* 4.1 1.3 - - - +
105B TYR* 4.5 13.6 + - - +
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 3.8 24.0 - - + -
6B THR 3.4 9.9 - - - +
7B VAL* 4.5 12.3 - - + -
23B ILE* 4.3 4.7 - - + -
67B ILE* 3.9 29.8 - - + -
69B LEU* 4.8 10.1 - - + -
82B ILE* 4.0 17.3 - - + -
84B LYS* 1.3 80.8 - - - +
86B ILE* 1.3 65.5 + - - +
87B ILE* 4.0 13.5 - - + -
101B ILE* 3.6 1.4 - - - +
102B PHE* 2.8 41.3 + - + +
104B CYS* 5.6 2.0 - - + -
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Residues in contact with ILE 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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4B LYS 3.3 3.8 - - - +
6B THR* 2.7 56.0 + - + +
8B GLU* 3.8 25.6 - - + +
84B LYS* 4.6 12.3 - - + +
85B VAL* 1.3 77.4 - - - +
87B ILE* 1.3 65.2 + - - +
88B GLU* 4.9 2.2 - - + +
99B LYS* 4.4 23.8 - - + -
100B TYR 3.7 2.7 - - - +
101B ILE* 3.6 34.5 - - + -
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Residues in contact with ILE 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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3B TYR* 4.5 9.0 - - + -
4B LYS 3.5 3.4 - - - +
5B ILE* 4.1 17.5 - - + -
23B ILE* 4.1 7.0 - - + -
25B LEU* 3.4 39.5 - - + -
64B ILE* 3.5 24.6 - - + +
67B ILE* 3.7 20.2 - - + -
85B VAL* 4.0 11.9 - - + -
86B ILE* 1.3 76.3 - - - +
88B GLU* 1.3 68.1 + - - +
98B ASN 3.6 3.1 - - - +
99B LYS* 4.5 0.9 - - - -
100B TYR* 3.0 35.5 + - - +
102B PHE* 3.8 10.3 - - + -
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Residues in contact with GLU 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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2B LYS* 4.2 12.1 + - - +
3B TYR* 3.8 1.2 - - - -
4B LYS* 2.9 63.3 + - + +
86B ILE* 4.0 3.4 + - + -
87B ILE* 1.3 71.4 - - - +
89B LYS* 1.3 71.0 + - - +
97B SER* 3.6 21.3 + - - -
98B ASN 3.5 10.3 - - - +
99B LYS* 3.8 33.8 - - + +
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Residues in contact with LYS 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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1B MET* 4.0 10.3 - - + -
2B LYS* 3.8 12.6 - - - +
3B TYR* 3.6 40.4 - - + -
60B ASP* 4.4 1.8 + - - -
61B VAL* 4.9 0.4 - - - -
62B GLY* 2.8 37.7 + - - +
64B ILE* 4.0 19.1 - - + -
87B ILE* 5.1 0.9 - - + +
88B GLU* 1.3 76.3 - - - +
90B ILE* 1.3 94.7 + - - +
91B ASP* 3.8 8.9 - - - +
97B SER* 3.3 3.1 - - - -
98B ASN* 2.9 28.0 + - + -
100B TYR* 3.9 21.7 + - + +
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Residues in contact with ILE 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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1B MET* 3.3 23.7 - - + +
2B LYS* 3.7 30.5 - - + +
89B LYS* 1.3 98.7 + - - +
91B ASP* 1.3 63.2 + - - +
92B GLU* 3.3 4.2 + - - +
95B GLY* 4.6 8.7 - - - -
96B PHE* 3.1 25.8 - - - +
97B SER* 3.7 8.3 - - - +
98B ASN* 5.8 0.2 - - - +
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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