Contacts of the strand formed by residues 53 - 58 (chain C) in PDB entry 4ZHF
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 ALA 53 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LYS* 4.1 18.2 - - + -
31C TRP 3.3 10.3 - - - +
32C TYR* 4.1 12.1 - - + +
52C TYR* 1.3 77.6 - - - +
54C THR* 1.3 65.2 + - - +
55C ILE* 5.1 1.1 - - + -
67C THR 3.9 0.4 - - - +
68C SER* 3.1 4.2 - - - -
69C VAL* 2.8 36.5 + - + +
176C ILE* 4.0 24.8 - - + +
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Residues in contact with THR 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C GLY 3.8 1.2 - - - +
31C TRP* 2.8 39.0 + - - +
33C VAL* 4.3 1.5 - - - +
52C TYR* 3.8 6.2 - - - -
53C ALA* 1.3 74.2 + - - +
55C ILE* 1.3 64.2 + - - +
56C TYR* 3.6 16.2 - - + +
66C VAL* 3.5 30.5 - - + -
67C THR 3.3 3.1 - - - +
68C SER* 2.5 15.9 + - - +
81C ARG* 4.0 0.7 - - - +
138C TYR* 4.2 12.1 - - - +
204C SO4 2.5 28.5 + - - +
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Residues in contact with ILE 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C GLY* 3.4 15.9 - - - +
30C LYS* 4.1 34.1 - - + +
53C ALA 5.1 0.4 - - - -
54C THR* 1.3 80.0 - - - +
56C TYR* 1.3 67.7 + - - +
57C GLU* 4.3 20.6 - - + +
65C ASN 3.4 2.9 - - - +
66C VAL* 3.3 4.9 - - - -
67C THR* 2.6 49.3 + - + +
69C VAL* 4.2 22.9 - - + -
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Residues in contact with TYR 56 (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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27C PHE* 3.9 24.2 - + - +
28C GLN* 3.4 13.1 - - - +
29C GLY* 2.8 39.1 + - - +
31C TRP* 3.9 18.6 - + - -
54C THR* 3.6 20.4 - - + +
55C ILE* 1.3 74.8 - - - +
57C GLU* 1.3 64.0 + - - +
58C LEU 4.1 0.2 - - - -
64C TYR* 3.9 34.8 - + + -
65C ASN 3.7 2.7 - - - -
66C VAL* 4.1 10.1 - - + +
81C ARG* 5.6 0.3 + - - -
83C PHE* 3.8 34.8 - + - -
92C PHE* 6.1 1.8 - + - -
108C VAL* 5.4 1.4 - - + +
121C VAL* 4.9 3.1 - - - +
123C PHE* 4.2 5.5 - - - -
138C TYR* 2.7 37.7 + + - -
204C SO4 5.4 0.2 + - - -
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Residues in contact with GLU 57 (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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28C GLN* 4.0 4.9 - - - +
29C GLY* 6.3 0.4 - - - -
55C ILE* 4.3 16.8 - - + +
56C TYR* 1.3 75.1 - - - +
58C LEU* 1.3 64.6 + - - +
59C LYS* 3.5 2.2 + - + +
64C TYR* 3.2 5.8 - - - -
65C ASN* 2.8 56.2 + - + +
67C THR* 5.4 4.8 + - - -
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Residues in contact with LEU 58 (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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24C ASP* 3.7 37.5 - - + +
25C ASN* 3.9 27.4 - - + +
28C GLN* 3.0 29.0 + - + +
57C GLU* 1.3 71.8 - - - +
59C LYS* 1.3 67.0 + - - +
62C LYS* 3.7 42.6 - - + +
63C SER 3.8 2.5 - - - +
64C TYR* 3.7 20.2 - - + -
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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