Contacts of the strand formed by residues 51 - 55 (chain F) in PDB entry 2ZSU
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 51 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F PHE* 4.5 0.2 - - - -
8F GLU* 3.4 23.3 - - + +
47F ALA* 3.3 4.4 - - - -
48F ILE* 2.8 44.1 + - - +
49F ASP* 3.7 11.2 - - + +
50F GLY* 1.3 83.1 - - - +
52F VAL* 1.3 65.9 + - - +
53F GLN* 3.4 1.4 + - - -
163F THR 5.6 1.4 + - - -
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Residues in contact with VAL 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F PHE* 3.5 29.4 - - + -
8F GLU* 2.7 22.6 + - + +
16F VAL* 5.1 1.8 - - + -
18F PHE* 4.3 11.9 - - + -
45F LEU* 4.6 9.9 - - + -
46F LEU 4.0 4.0 - - - +
47F ALA* 4.7 1.6 - - - +
51F THR* 1.3 73.9 + - - +
53F GLN* 1.3 62.0 + - - +
54F LEU* 3.6 24.5 - - - +
55F VAL* 4.8 2.5 - - + -
228F GLY* 3.4 36.1 - - - +
229F TYR* 3.2 18.0 - - + -
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Residues in contact with GLN 53 (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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46F LEU* 2.8 38.5 + - + +
48F ILE* 3.8 19.6 - - + +
51F THR* 3.4 3.5 + - - -
52F VAL* 1.3 74.4 - - - +
54F LEU* 1.3 66.3 + - + +
62F TYR* 5.1 3.6 - - - -
63F HIS* 5.5 0.8 + - - -
87F ASP* 3.6 21.3 + - - +
112F VAL* 6.3 1.1 - - + -
161F ASP* 4.2 17.6 + - - -
162F SER 4.9 4.9 + - - +
163F THR* 3.6 32.4 - - + +
229F TYR* 2.6 33.0 + - - -
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Residues in contact with LEU 54 (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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44F LYS 4.3 3.4 - - - +
45F LEU* 3.5 4.5 - - - +
46F LEU* 3.0 43.2 + - + +
52F VAL* 3.6 7.5 - - - -
53F GLN* 1.3 84.0 - - + +
55F VAL* 1.3 80.3 + - - +
56F THR* 3.7 7.0 - - - +
59F GLU* 4.0 17.5 - - + +
62F TYR* 6.2 1.1 - - + -
63F HIS* 4.3 8.1 - - + -
87F ASP* 3.6 41.5 - - + +
120F ILE* 4.2 19.3 - - + -
122F ILE* 4.0 10.8 - - + -
227F ILE 5.7 2.2 - - - -
229F TYR* 4.9 2.2 - - - -
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Residues in contact with VAL 55 (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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18F PHE* 3.9 26.7 - - + -
39F THR* 5.1 0.4 - - + -
42F PHE* 3.4 22.9 - - + +
44F LYS 3.4 4.9 - - - -
45F LEU* 4.0 20.6 - - + -
52F VAL* 4.8 3.6 - - + -
54F LEU* 1.3 79.5 - - - +
56F THR* 1.3 66.4 + - - +
57F GLU 3.9 17.0 - - - +
58F GLY* 4.2 2.5 - - - -
59F GLU* 3.0 24.2 + - - +
227F ILE* 4.1 30.7 - - + +
228F GLY* 4.7 0.7 - - - -
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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