Contacts of the strand formed by residues 77 - 82 (chain E) in PDB entry 2VWE
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 THR 77 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21E SER* 4.4 5.2 - - - -
22E CYS 3.5 29.2 - - - +
23E LYS* 3.4 17.1 - - + +
29E PHE* 3.8 5.1 - - - -
71E VAL* 3.7 1.0 - - - -
72E ASP* 2.9 30.4 + - - +
75E SER* 3.1 27.5 + - - -
76E SER* 1.3 74.3 - - - +
78E ALA* 1.3 62.6 - - - +
79E TYR* 3.7 34.5 + - + +
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Residues in contact with ALA 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E LEU 3.8 0.2 - - - +
21E SER* 3.7 1.4 - - - -
22E CYS* 2.8 42.1 + - + +
29E PHE* 3.9 9.5 - - + -
34E ILE* 3.7 31.4 - - + -
36E TRP* 3.5 9.0 - - + +
51E ILE* 4.9 1.8 - - + -
70E THR 3.6 4.9 - - - +
71E VAL* 4.1 15.5 - - + -
77E THR* 1.3 73.1 - - - +
79E TYR* 1.3 61.3 + - - +
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Residues in contact with TYR 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E LYS* 3.8 38.8 - - + -
20E LEU 3.2 16.4 - - - +
21E SER* 3.5 19.5 - - - -
36E TRP* 3.9 3.6 + - - -
51E ILE* 5.5 0.2 - - - +
69E LEU* 3.4 8.1 - - - +
70E THR* 2.6 55.3 + - - +
71E VAL 5.0 0.7 - - - -
72E ASP* 4.0 21.9 + - + -
75E SER* 4.6 7.4 + - - -
77E THR* 3.7 39.5 + - + +
78E ALA* 1.3 74.7 - - - +
80E MET* 1.3 60.1 + - - +
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Residues in contact with MET 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E VAL 3.1 5.2 - - - +
19E LYS* 3.3 2.6 - - - -
20E LEU* 2.8 50.8 + - + +
36E TRP* 3.6 58.9 - - + -
48E ILE* 3.6 35.9 - - + -
49E GLY 5.3 0.2 - - - +
59E TYR* 6.4 0.2 - - + -
67E ALA* 4.7 6.5 - - - -
68E THR 3.7 3.1 - - - -
69E LEU* 3.7 16.4 - - + -
79E TYR* 1.3 73.1 - - - +
81E GLN* 1.3 59.4 + - - +
82E LEU* 3.6 26.7 - - + -
90E TYR* 4.6 1.6 - - - -
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Residues in contact with GLN 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E SER* 4.2 11.4 - - - -
18E VAL 3.0 34.5 + - - +
19E LYS* 3.6 24.0 + - + +
67E ALA* 3.6 1.2 + - - -
68E THR* 2.7 55.5 + - + +
70E THR* 5.6 3.4 - - + +
79E TYR 4.2 0.2 - - - -
80E MET* 1.3 70.4 - - - +
82E LEU* 1.3 77.8 + - + +
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Residues in contact with LEU 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E SER* 3.2 28.3 - - - -
18E VAL* 3.0 15.0 + - + +
20E LEU* 4.4 9.9 - - + -
48E ILE* 5.2 2.2 - - + -
63E PHE* 6.1 1.3 - - + -
66E MET* 3.8 14.1 - - + +
67E ALA* 4.0 17.5 - - - +
80E MET* 3.6 30.7 + - + -
81E GLN* 1.3 71.0 - - - +
82E SER* 1.3 60.4 + - - +
90E TYR* 3.5 46.4 - - + +
109E VAL* 5.8 2.0 - - + -
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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