Contacts of the strand formed by residues 77 - 85 (chain E) in PDB entry 6X0A
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 TRP 77 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2E PRO* 3.3 24.5 - - + +
4E ILE* 3.4 24.5 - - + +
73E LEU* 4.3 0.9 - - - +
74E ALA* 3.1 37.0 + - + +
75E GLU* 2.9 47.9 + - + -
76E GLY* 1.3 82.9 - - - +
78E ILE* 1.3 65.6 + - - +
79E GLU* 2.7 44.3 + - + +
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Residues in contact with ILE 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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2E PRO* 3.0 10.1 + - + +
3E ILE* 3.7 13.8 - - + +
4E ILE* 3.0 31.2 + - - +
42E LEU* 3.2 54.1 - - + +
43E ALA* 3.9 6.5 - - - +
46E PRO* 4.5 8.3 - - + -
71E TYR* 3.9 19.5 - - + -
72E ARG 3.8 11.0 - - - +
73E LEU* 3.8 14.4 - - + -
77E TRP* 1.3 76.9 - - - +
79E GLU* 1.3 67.4 + - - +
80E ILE* 4.5 6.3 - - + -
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Residues in contact with GLU 79 (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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4E ILE* 3.6 13.3 - - + +
71E TYR* 3.3 4.2 - - - -
72E ARG* 2.7 90.4 + - + +
74E ALA* 3.8 11.7 - - + +
77E TRP* 2.7 45.3 + - + +
78E ILE* 1.3 71.0 - - - +
80E ILE* 1.3 62.7 + - - +
81E VAL* 3.4 6.8 + - + +
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Residues in contact with ILE 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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3E ILE* 3.9 10.1 - - + -
4E ILE 2.9 18.4 + - - +
5E ARG* 4.2 8.7 - - + -
6E SER* 3.2 25.1 + - - -
9E ALA* 3.7 4.7 - - + +
13E LEU* 6.3 0.4 - - + -
39E ILE* 3.7 37.0 - - + -
42E LEU* 3.9 23.8 - - + -
69E ILE* 4.1 18.4 - - + -
70E LEU 4.0 4.3 - - - +
71E TYR* 4.0 9.9 - - + -
78E ILE* 4.5 4.5 - - + -
79E GLU* 1.3 68.3 - - - +
81E VAL* 1.3 61.3 + - - +
83E ILE* 3.9 26.7 - - + -
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Residues in contact with VAL 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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6E SER* 2.7 30.1 + - - +
9E ALA* 3.5 2.7 - - - +
70E LEU* 2.9 16.9 + - + +
71E TYR* 4.5 1.8 - - - -
72E ARG* 4.3 22.7 - - + +
79E GLU* 3.4 17.2 + - + +
80E ILE* 1.3 73.2 - - - +
82E ARG* 1.3 82.4 + - + +
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Residues in contact with ARG 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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8E ALA* 3.6 23.6 - - - +
9E ALA* 4.4 0.7 - - - -
12E ASP* 2.4 42.6 + - - -
69E ILE* 3.7 1.0 - - - +
70E LEU* 2.8 43.9 + - + +
80E ILE 3.7 1.0 - - - -
81E VAL* 1.3 103.6 - - + +
83E ILE* 1.3 73.8 + - - +
84E VAL* 3.6 28.4 - - + +
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Residues in contact with ILE 83 (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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9E ALA* 4.0 25.4 - - + +
12E ASP* 3.3 28.4 + - + +
13E LEU* 3.9 24.9 - - + -
16E ILE* 3.7 27.0 - - + +
35E ILE* 4.8 9.6 - - + -
39E ILE* 5.4 1.3 - - + -
64E ILE* 5.7 0.7 - - + -
67E TYR* 4.6 10.1 - - + -
68E LEU 3.1 15.0 - - - +
69E ILE* 4.4 19.7 - - + -
80E ILE* 3.9 20.2 - - + -
82E ARG* 1.3 82.5 - - - +
84E VAL* 1.3 58.4 + - - +
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Residues in contact with VAL 84 (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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12E ASP* 4.1 1.6 - - - +
67E TYR* 3.5 5.6 - - - -
68E LEU* 2.7 39.0 + - + +
70E LEU* 4.8 13.1 - - + +
82E ARG* 3.6 45.7 - - + +
83E ILE* 1.3 78.4 - - - +
85E HIS* 1.3 80.7 + - + +
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Residues in contact with HIS 85 (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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66E ASN* 3.6 29.0 - - + +
67E TYR* 3.2 50.6 - + + +
68E LEU* 5.2 0.9 - - - +
84E VAL* 1.3 89.1 - - + +
86E GLY* 1.3 90.0 + - - +
87E ALA 5.4 0.4 - - - -
88E ARG* 3.6 54.0 + - + +
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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