Contacts of the strand formed by residues 90 - 93 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5C LEU* 5.2 0.4 - - + -
8C THR* 3.7 34.8 - - + -
9C ASN 2.9 10.2 + - - +
10C ILE* 4.6 3.1 - - + -
11C ILE* 3.0 31.0 + - - +
34C TYR* 3.7 2.2 - - - -
35C THR* 3.4 33.7 - - + -
37C LEU* 4.0 16.8 - - + -
80C MET* 3.6 52.5 - - + -
83C LYS* 4.5 3.1 - - + -
84C VAL* 4.0 15.5 - - + -
87C SER* 3.9 18.6 - - - -
89C GLY* 1.3 74.5 - - - -
91C LEU* 1.3 60.0 + - - +
92C ILE* 4.0 15.5 - - + -
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Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ILE* 3.5 25.1 - - + -
13C VAL* 4.4 7.2 - - + -
25C CYS* 3.7 42.6 - - + +
28C ILE* 3.6 42.0 - - + -
29C VAL* 4.3 12.3 - - + -
34C TYR* 3.9 22.4 - - + -
35C THR 2.9 11.6 + - - +
36C HIS* 4.1 5.2 - - + -
37C LEU* 3.0 27.2 + - - +
90C PHE* 1.3 70.5 - - - +
92C ILE* 1.3 63.4 + - - +
93C ASP 3.6 0.6 + - - -
116C LEU* 6.0 0.2 - - + -
190C LEU* 5.6 0.7 - - + -
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Residues in contact with ILE 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ILE* 4.0 19.7 - - + -
11C ILE 2.8 17.3 + - - +
12C PHE* 3.6 10.0 - - + -
13C VAL* 2.7 32.8 + - - +
37C LEU* 3.8 7.4 - - + +
39C THR* 5.6 0.7 - - + -
76C LEU* 3.8 35.9 - - + -
80C MET* 4.0 26.7 - - + -
90C PHE* 4.0 17.9 - - + -
91C LEU* 1.3 77.4 - - - +
93C ASP* 1.3 56.8 + - - +
95C TYR* 3.4 27.3 - - + +
105C PHE* 4.4 6.1 - - + -
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Residues in contact with ASP 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C VAL* 3.8 6.5 - - - -
21C LYS* 3.4 28.5 - - - +
22C GLY* 3.6 17.0 + - - -
25C CYS* 4.3 7.0 - - - -
36C HIS* 2.9 39.7 + - + +
37C LEU 2.9 11.4 + - - +
38C SER* 3.4 11.7 + - - -
39C THR* 3.3 24.6 + - - +
92C ILE* 1.3 71.2 - - - +
94C GLY* 1.3 64.1 + - - +
95C TYR 3.4 1.9 + - - -
621C ZN 4.1 3.7 - - - -
633C AP5 4.7 6.9 + - - -
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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