Contacts of the strand formed by residues 32 - 36 (chain F) in PDB entry 1ZMC
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 32 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9F VAL* 3.3 11.4 - - + +
11F VAL* 4.5 2.7 - - + -
22F ALA* 3.6 36.6 - - + +
25F ALA* 3.6 11.2 - - + +
26F ALA* 3.5 18.5 + - - +
30F PHE* 3.0 19.9 + - - +
31F LYS* 1.3 77.0 + - - +
33F VAL* 1.3 77.8 + - - +
111F LYS 4.1 6.1 + - - +
112F VAL* 3.7 6.9 - - + -
113F VAL* 3.0 25.5 + - - +
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Residues in contact with VAL 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F ILE* 4.1 20.4 - - + -
6F ASP 5.0 1.8 - - - +
7F ALA* 3.7 20.0 - - + -
9F VAL 2.8 7.0 + - - +
10F THR* 3.3 24.8 - - + +
11F VAL* 2.7 35.4 + - - +
31F LYS* 5.8 3.1 - - + +
32F THR* 1.3 81.6 - - - +
34F CYS* 1.3 62.9 + - - +
35F ILE* 4.1 4.3 - - + -
112F VAL* 4.7 0.2 - - - -
113F VAL* 3.3 18.2 - - + +
115F VAL* 3.8 22.2 - - + -
139F ILE* 4.1 8.1 - - + -
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Residues in contact with CYS 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F VAL* 3.2 9.6 - - + -
13F GLY 3.3 27.4 - - - -
14F SER* 3.7 21.1 - - - -
18F GLY 4.5 3.8 - - - -
22F ALA* 4.2 5.2 - - + -
33F VAL* 1.3 75.4 - - - +
35F ILE* 1.3 63.9 + - - +
36F GLU* 5.1 1.1 - - - -
41F LEU* 5.3 0.4 - - - -
107F PHE* 3.8 30.7 - - + -
112F VAL* 4.1 8.3 - - + +
113F VAL 2.9 7.4 + - - +
114F HIS* 3.5 5.9 - - - -
115F VAL 2.9 24.4 + - - +
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Residues in contact with ILE 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F THR* 3.7 11.9 - - + -
11F VAL 2.7 11.2 + - - +
12F ILE* 4.4 9.4 - - + -
13F GLY* 2.7 32.6 + - - -
33F VAL* 4.1 4.0 - - + -
34F CYS* 1.3 76.2 - - - +
36F GLU* 1.3 58.8 + - - +
115F VAL* 3.2 16.4 - - + +
117F GLY 3.4 23.1 - - - +
119F GLY* 4.0 14.8 - - - +
127F VAL* 3.4 26.9 - - + -
129F ALA* 4.1 13.7 - - + -
139F ILE* 3.4 33.2 - - + -
480F FAD 3.7 5.5 + - + -
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Residues in contact with GLU 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F SER* 2.8 48.8 + - - +
34F CYS* 4.0 0.8 + - - -
35F ILE* 1.3 74.0 - - - +
37F LYS* 1.3 62.1 + - - +
38F ASN* 2.9 24.3 + - - +
40F THR 3.6 20.2 - - - +
41F LEU* 3.7 16.2 - - + -
114F HIS* 4.1 7.6 - - + +
115F VAL 3.0 7.3 + - - -
116F ASN* 3.2 13.0 - - - +
117F GLY 3.1 19.7 + - - -
480F FAD 2.7 42.4 + - - -
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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