Contacts of the strand formed by residues 73 - 78 (chain B) in PDB entry 2VBJ
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 VAL 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B THR* 3.8 22.4 - - + -
47B GLN 3.6 10.1 - - - +
48B LYS* 4.4 0.9 - - - -
49B THR* 3.1 10.0 + - - -
70B SER* 2.8 44.6 + - - +
72B SER* 1.3 94.8 - - - +
74B SER* 1.3 53.8 + - - +
75B ASN* 4.2 8.7 - - - +
13E A 4.0 21.8 - - + -
14E A 4.0 26.0 - - + +
15E A 5.9 2.5 - - - +
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Residues in contact with SER 74 (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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46B THR* 3.4 1.4 - - - +
47B GLN 2.7 32.9 + - - -
49B THR* 2.9 26.6 + - - +
52B ARG* 3.9 20.5 + - - +
55B LEU* 3.7 16.6 - - - -
67B VAL* 4.3 2.5 - - - -
68B ARG 3.2 13.0 - - - -
69B ASP* 3.8 8.8 - - - -
70B SER 4.4 0.2 - - - +
73B VAL* 1.3 71.6 + - - +
75B ASN* 1.3 71.1 + - - +
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Residues in contact with ASN 75 (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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44B GLN* 3.0 31.2 - - + +
45B VAL 3.2 4.7 - - - +
46B THR* 2.4 40.8 + - - +
55B LEU* 4.0 4.7 - - - -
66B TYR 3.7 0.5 - - - +
67B VAL* 3.2 4.2 - - - -
68B ARG* 2.9 33.1 + - + +
70B SER* 4.5 9.9 + - - -
73B VAL* 4.2 8.3 - - - +
74B SER* 1.3 77.4 - - - +
76B TYR* 1.3 59.7 + - - +
77B ILE* 3.8 19.4 - - + +
15E A 5.1 1.7 + - - +
16E A 5.9 1.4 + - - -
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Residues in contact with TYR 76 (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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43B PHE* 3.6 38.4 - + - -
44B GLN* 3.2 7.6 - - - +
45B VAL* 2.8 37.1 + - + +
55B LEU* 3.9 22.4 - - + +
58B LEU* 4.0 14.6 - - + -
59B VAL* 3.6 41.3 - - + -
62B ILE* 3.3 26.2 - - + +
64B VAL 2.6 30.3 + - - -
66B TYR 3.4 13.7 - - - -
67B VAL* 4.4 3.1 - - + +
75B ASN* 1.3 72.3 - - - +
77B ILE* 1.3 66.2 + - - +
78B LEU* 3.6 15.0 - - + +
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Residues in contact with ILE 77 (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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42B THR* 3.9 23.8 - - + -
43B PHE 3.4 3.1 - - - +
44B GLN* 4.9 8.1 - - + +
65B GLY* 3.2 5.7 - - - -
66B TYR* 2.9 73.9 + - + +
68B ARG* 4.3 13.7 - - + -
75B ASN* 3.8 27.6 - - + +
76B TYR* 1.3 81.4 - - - +
78B LEU* 1.3 61.9 + - - +
79B SER* 3.9 11.4 - - - +
7C T 6.0 4.0 - - + -
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Residues in contact with LEU 78 (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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42B THR* 3.8 0.5 - - - -
43B PHE* 2.9 41.2 + - + +
62B ILE* 4.4 0.7 - - + -
64B VAL* 3.7 32.5 - - + -
65B GLY* 4.0 12.6 - - - +
66B TYR* 5.6 0.4 - - - -
76B TYR* 3.6 23.5 - - + +
77B ILE* 1.3 74.4 - - - +
79B SER* 1.3 64.6 + - - +
80B GLU* 4.4 8.5 - - + +
83B PRO* 4.1 9.4 - - + +
84B LEU* 3.9 31.0 - - + +
87B PHE* 4.0 31.0 - - + -
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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