Contacts of the strand formed by residues 76 - 81 (chain L) in PDB entry 4JZJ
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 ASP 76 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23L CYS 3.6 2.5 - - - +
24L GLU* 3.4 22.7 - - - +
72L GLY* 3.3 5.2 - - - -
73L SER 3.2 26.5 + - - +
75L THR* 1.3 104.4 - - - +
77L PHE* 1.3 63.2 + - - +
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Residues in contact with PHE 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L ASN* 3.6 4.0 - - - +
23L CYS* 2.8 42.3 + - + +
25L SER* 4.5 3.1 - - - -
29L LEU* 3.9 27.4 - - + -
37L ASN* 3.6 27.4 - - + -
39L LEU* 3.5 31.6 - - + -
41L TRP* 4.4 2.5 - - + +
57L ALA* 3.8 18.6 - - + -
71L SER 3.5 10.3 - - - +
72L GLY* 4.3 0.9 - - - -
73L SER* 3.7 13.9 - - - -
74L GLY 3.3 36.6 - - - -
75L THR 3.8 4.9 - - - -
76L ASP* 1.3 85.4 - - - +
78L THR* 1.3 62.3 + - - +
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Residues in contact with THR 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L THR* 4.6 4.7 - - - -
21L ILE 3.3 10.6 + - - -
22L ASN* 3.2 21.8 + - - -
41L TRP* 3.9 7.2 + - - -
70L GLY* 3.2 5.8 - - - -
71L SER* 3.0 48.6 + - - +
72L GLY* 6.1 0.4 - - - -
77L PHE* 1.3 74.6 - - - +
79L LEU* 1.3 60.0 + - - +
80L THR* 3.8 21.5 - - - +
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Residues in contact with LEU 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L ALA 3.9 0.3 - - - +
20L THR* 3.3 3.8 - - - -
21L ILE* 2.9 53.4 + - + +
41L TRP* 3.6 47.0 - - + -
53L LEU* 4.9 3.1 - - + -
54L ILE* 4.2 16.6 - - + -
68L PHE* 4.7 12.3 - - + -
69L SER 3.7 12.6 - - - +
78L THR* 1.3 74.9 - - - +
80L THR* 1.3 66.7 + - - +
81L ILE* 5.1 6.3 - - + -
92L TYR* 3.6 34.1 - - + -
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Residues in contact with THR 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L ARG* 4.1 25.1 + - - +
19L ALA 3.4 3.6 - - - +
20L THR* 3.3 19.8 - - - +
67L ARG 3.4 2.5 - - - +
68L PHE* 3.6 1.0 - - - -
69L SER* 2.9 47.9 + - - +
78L THR* 3.8 13.5 - - - +
79L LEU* 1.3 77.2 - - - +
81L ILE* 1.3 76.6 + - - +
82L SER* 4.2 5.8 - - - +
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Residues in contact with ILE 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L GLU 4.3 0.3 - - - +
18L ARG* 3.2 4.3 - - - +
19L ALA* 2.7 40.9 + - + +
21L ILE* 5.5 3.1 - - + -
67L ARG* 3.1 22.4 - - + +
68L PHE* 3.5 32.1 - - + -
79L LEU* 5.1 7.4 - - + +
80L THR* 1.3 82.8 - - - +
82L SER* 1.3 64.7 + - - +
83L SER 4.1 10.3 - - - +
84L LEU* 4.3 9.0 - - + -
88L ASP* 3.7 19.1 - - + +
92L TYR* 3.9 10.1 - - + +
110L LEU* 3.8 28.0 - - + -
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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