Contacts of the helix formed by residues 76 - 82 (chain B) in PDB entry 3E8E
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 76 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B LEU 3.3 1.4 + - - -
75B ASP* 1.3 69.9 - - - +
77B GLN* 1.3 57.8 + - - +
79B VAL* 3.3 5.4 + - - +
80B VAL* 3.1 33.1 + - - +
111B LYS* 5.4 5.8 - - + +
112B ASP 2.9 25.4 + - - -
113B ASN* 3.1 19.8 + - - +
114B SER 3.0 22.2 + - - +
115B ASN 3.8 1.8 - - - +
116B LEU* 3.6 32.3 - - + -
341B GLU* 4.3 7.7 - - - +
342B LYS* 2.7 29.8 + - + +
343B CYS* 4.1 9.8 + - - -
344B GLY* 4.9 2.0 - - - +
347B PHE* 3.6 31.9 - - + +
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Residues in contact with GLN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASP* 3.0 12.6 + - - +
76B LYS* 1.3 77.4 - - - +
78B LYS* 1.3 59.1 + - + +
80B VAL* 3.6 3.3 + - - +
81B LYS* 3.1 31.7 + - - +
114B SER 4.7 0.4 + - - +
342B LYS* 3.2 50.2 - - + +
343B CYS* 4.1 12.8 - - - -
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Residues in contact with LYS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B SER 3.7 19.1 + - - +
54B PHE* 3.7 19.1 - - + -
75B ASP* 3.1 37.2 + - + +
77B GLN* 1.3 76.3 - - + +
79B VAL* 1.3 60.8 + - - +
81B LYS* 3.8 23.1 - - + +
82B LEU* 3.0 36.8 + - + +
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B PHE* 3.8 26.0 - - + -
74B LEU* 4.0 20.0 - - + -
75B ASP 2.9 21.6 + - - +
76B LYS* 3.3 9.2 + - - +
78B LYS* 1.3 77.8 - - - +
80B VAL* 1.3 55.6 + - - +
82B LEU 3.6 0.3 - - - -
83B LYS 3.0 7.8 + - - -
84B GLN* 2.9 61.1 + - + +
85B ILE* 3.6 3.4 - - - +
88B THR* 3.7 9.2 - - + -
116B LEU* 4.9 2.0 - - + -
347B PHE* 3.6 20.0 - - + -
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LYS 3.1 17.2 + - - +
77B GLN* 3.9 4.9 - - - +
79B VAL* 1.3 76.2 - - - +
81B LYS* 1.3 62.7 + - - +
83B LYS* 3.2 16.6 + - - +
85B ILE* 4.0 25.4 - - + +
343B CYS* 3.8 18.8 - - + -
346B GLU* 4.4 13.7 - - + +
347B PHE* 3.6 22.2 - - + -
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Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLN* 3.1 20.9 + - - +
78B LYS* 3.8 25.2 - - - +
80B VAL* 1.3 78.7 - - - +
82B LEU* 1.3 69.9 - - + +
83B LYS* 3.2 12.7 + - - +
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B SER* 3.5 40.2 - - - +
54B PHE* 3.7 15.5 - - + -
78B LYS* 3.0 24.3 + - + +
81B LYS* 1.3 87.2 - - + +
83B LYS* 1.3 72.1 + - - +
84B GLN* 3.1 27.8 + - + +
23C HIS* 5.7 7.9 - - + +
24C ASP* 4.1 6.9 + - - +
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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