Contacts of the strand formed by residues 51 - 56 (chain E) in PDB entry 3QSU
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 LYS 51 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47E ASN* 3.6 2.0 - - - -
48E SER 2.8 40.7 + - - +
49E GLN* 2.9 7.0 + - + +
50E GLY* 1.3 82.1 - - - +
52E GLN* 1.3 64.5 + - - +
53E HIS* 3.2 16.4 + - + +
64F THR* 4.7 12.8 - - + -
65F VAL* 4.8 24.7 - - + +
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Residues in contact with GLN 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E SER* 3.6 23.6 + - - +
46E LEU 3.6 4.9 - - - +
47E ASN* 3.7 12.6 - - - +
50E GLY 4.0 0.8 + - - -
51E LYS* 1.3 78.8 - - - +
53E HIS* 1.3 65.8 + - - +
54E LEU* 4.2 10.1 + - - +
11F ALA* 5.7 4.7 - - - +
15F PHE* 5.3 8.7 - - - -
63F TYR 4.1 0.5 - - - +
64F THR* 3.0 25.8 - - - +
65F VAL* 4.6 3.7 + - + +
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Residues in contact with HIS 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E MET* 4.0 21.0 - - + -
44E VAL 3.5 2.4 - - - +
45E SER* 3.5 0.9 - - - -
46E LEU* 2.7 42.4 + - + +
48E SER* 3.5 28.0 - - - -
51E LYS* 3.2 26.9 + - + -
52E GLN* 1.3 76.0 - - - +
54E LEU* 1.3 61.7 + - - +
55E ILE* 3.6 13.0 + - + +
78E ZN 2.2 36.2 - - - -
25F PHE* 5.8 1.6 - + - -
62F THR* 3.7 13.7 - - + -
63F TYR 3.6 4.5 - - - -
64F THR* 3.5 19.8 - - + +
7P A 5.3 1.3 - - - -
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Residues in contact with LEU 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E VAL* 4.0 18.6 - - + -
44E VAL 3.7 7.0 - - - +
45E SER* 4.3 11.0 - - - +
52E GLN* 4.2 9.9 + - - +
53E HIS* 1.3 71.5 - - - +
55E ILE* 1.3 58.5 + - - +
56E TYR* 4.2 0.9 + - - -
7F ILE* 3.7 28.5 - - + +
8F GLN* 4.2 17.3 - - + +
11F ALA* 4.1 25.1 - - + -
12F LEU* 4.8 1.8 - - + -
15F PHE* 5.5 2.7 - - + -
62F THR* 3.2 3.6 - - - -
63F TYR* 2.8 72.2 + - + +
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Residues in contact with ILE 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E VAL* 4.8 8.1 - - + -
26E PHE* 3.6 32.3 - - + -
32E MET* 4.7 0.9 - - - -
43E VAL* 3.3 5.2 - - - -
44E VAL* 2.7 46.8 + - + +
46E LEU* 3.9 37.0 - - + -
53E HIS* 4.0 6.7 - - + +
54E LEU* 1.3 75.8 - - - +
56E TYR* 1.3 76.5 + - - +
59E ALA* 4.7 0.2 - - + -
60E ILE* 3.5 24.5 - - + -
61F SER 3.5 5.8 - - - +
62F THR* 3.6 19.1 - - + +
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Residues in contact with TYR 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E TYR* 3.6 10.3 - + + -
43E VAL* 3.7 16.8 - - + -
55E ILE* 1.3 85.6 - - - +
57E LYS* 1.3 64.9 + - - +
58E HIS* 3.4 33.7 - + + +
59E ALA* 3.0 12.4 + - - +
60E ILE* 3.6 1.6 - - - +
79E ZN 4.6 4.3 - - - -
8F GLN* 2.5 40.8 + - + +
57F LYS* 3.4 20.6 - - + +
60F ILE* 3.5 36.1 - - + +
61F SER 3.1 9.9 + - - +
63F TYR* 3.1 43.8 + + - -
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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