Contacts of the strand formed by residues 90 - 93 (chain B) in PDB entry 1Z83
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 PHE 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B LEU* 5.4 0.2 - - + -
8B THR* 3.8 37.0 - - + -
9B ASN 2.8 11.9 + - - +
10B ILE* 4.6 2.7 - - - -
11B ILE* 2.9 33.1 + - - +
34B TYR* 3.8 3.7 - - - -
35B THR* 3.5 30.1 - - + -
37B LEU* 3.9 18.4 - - + -
80B MET* 3.6 52.9 - - + -
83B LYS* 4.1 4.9 - - + -
84B VAL* 4.1 12.8 - - + -
87B SER* 3.9 18.4 - - - -
89B GLY* 1.3 74.3 - - - -
91B LEU* 1.3 56.8 + - - +
92B ILE* 3.9 15.7 - - + -
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Residues in contact with LEU 91 (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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11B ILE* 3.5 36.3 - - + -
13B VAL* 4.5 6.1 - - + -
25B CYS* 3.8 37.9 - - + +
28B ILE* 3.7 42.2 - - + -
29B VAL* 4.1 13.9 - - + -
34B TYR* 4.0 13.5 - - + -
35B THR 2.8 11.1 + - - +
36B HIS* 3.6 5.9 - - + -
37B LEU* 2.9 29.6 + - - +
90B PHE* 1.3 70.4 - - - +
92B ILE* 1.3 62.4 + - - +
93B ASP 3.6 1.1 + - - -
116B LEU* 6.0 0.2 - - + -
190B LEU* 5.8 0.4 - - + -
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Residues in contact with ILE 92 (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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10B ILE* 4.0 25.8 - - + -
11B ILE 2.9 13.0 + - - +
12B PHE* 4.0 11.2 - - + -
13B VAL* 2.8 29.3 + - - +
37B LEU* 3.7 10.3 - - + +
39B THR* 5.7 0.4 - - + -
76B LEU* 3.9 26.2 - - + -
80B MET* 4.1 21.3 - - + -
90B PHE* 4.0 18.8 - - + -
91B LEU* 1.3 74.3 - - - +
93B ASP* 1.3 57.4 + - - +
95B TYR* 3.2 41.9 - - + +
105B PHE* 4.6 2.2 - - + -
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Residues in contact with ASP 93 (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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13B VAL* 3.8 6.7 - - - -
21B LYS* 3.4 29.2 - - - +
22B GLY* 3.7 17.0 + - - -
25B CYS* 4.2 7.6 - - - -
36B HIS* 2.8 40.2 + - + +
37B LEU 3.0 10.7 + - - +
38B SER* 3.5 11.2 + - - -
39B THR* 3.3 24.8 + - - +
92B ILE* 1.3 71.5 - - - +
94B GLY* 1.3 64.4 + - - +
95B TYR 3.4 1.0 + - - -
611B ZN 4.2 8.6 - - - -
632B AP5 4.6 2.9 + - - -
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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