Contacts of the strand formed by residues 79 - 83 (chain E) in PDB entry 1UGI
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 ASN 79 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E VAL* 4.4 10.4 - - - +
56E MET* 4.7 1.1 - - - +
71E VAL* 3.7 24.0 - - + +
72E ILE 3.5 2.2 - - - -
73E GLN* 2.9 41.7 + - - +
78E GLU* 1.3 73.7 - - - +
80E LYS* 1.3 58.6 + - - +
81E ILE* 4.2 9.4 - - + +
1000E IMD 3.1 35.8 + - + +
78F GLU* 2.9 37.3 + - - +
79F ASN 4.2 2.3 + - - +
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Residues in contact with LYS 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E GLU* 5.9 0.9 - - - +
71E VAL* 3.5 2.6 - - - -
72E ILE* 2.8 51.6 + - + +
79E ASN* 1.3 71.7 - - - +
81E ILE* 1.3 64.5 + - - +
82E LYS* 4.1 22.4 - - + +
31F GLU 3.5 15.8 + - - -
32F VAL* 2.9 21.0 + - - +
33F ILE 4.7 1.8 - - - -
34F GLY* 4.8 1.4 - - - +
79F ASN* 3.7 15.7 - - + +
81F ILE* 3.5 27.8 - - + -
25H LEU* 5.6 5.0 - - + +
28H GLU* 4.3 8.9 + - - -
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Residues in contact with ILE 81 (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 VAL* 4.2 6.1 - - + +
33E ILE* 3.9 46.9 - - + +
69E ALA* 4.7 1.8 - - + -
70E LEU 3.4 7.6 - - - +
71E VAL* 4.5 11.7 - - + -
79E ASN* 4.8 7.9 - - + +
80E LYS* 1.3 77.5 - - - +
82E LYS* 1.3 60.7 + - - +
83E MET* 3.7 28.9 - - - -
78F GLU* 6.1 0.9 - - - +
79F ASN 2.9 13.0 + - - +
80F LYS* 3.4 12.4 - - + -
81F ILE* 2.8 35.3 + - - +
1014F IMD 4.0 22.4 - - - +
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Residues in contact with LYS 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E GLU* 2.6 37.5 + - - +
69E ALA* 3.2 0.9 - - - -
70E LEU* 2.8 50.9 + - + -
72E ILE* 4.1 12.1 - - + -
80E LYS* 4.1 22.2 - - - +
81E ILE* 1.3 76.8 - - - +
83E MET* 1.3 64.5 + - - +
84E LEU* 3.5 2.6 + - + +
1001E IMD 3.5 31.4 + - + +
33F ILE 4.2 8.5 - - - -
34F GLY* 4.0 20.4 + - - -
81F ILE* 3.6 11.2 - - + -
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Residues in contact with MET 83 (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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33E ILE* 4.0 9.0 - - + -
35E ASN* 4.0 15.5 - - - +
68E TRP* 3.8 44.4 - - + +
69E ALA* 3.9 7.4 - - + -
81E ILE* 3.7 22.0 - - - -
82E LYS* 1.3 71.3 - - - +
84E LEU* 1.3 63.2 + - - +
1001E IMD 2.9 19.8 + - - -
80F LYS* 4.1 17.5 - - + -
81F ILE 2.8 19.6 + - - +
82F LYS* 4.2 27.9 - - + +
83F MET* 4.8 2.3 + - - +
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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