Contacts of the helix formed by residues 76 - 82 (chain F) in PDB entry 3E8C
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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F LEU 3.3 1.0 + - - -
75F ASP* 1.3 70.3 - - - +
77F GLN* 1.3 62.3 + - - +
79F VAL* 3.2 4.7 + - - +
80F VAL* 3.0 28.2 + - - +
111F LYS* 5.0 8.5 - - - +
112F ASP 2.8 29.0 + - - -
113F ASN 3.4 12.2 + - - -
114F SER 3.1 20.5 + - - +
115F ASN 3.9 5.2 - - - +
116F LEU* 3.7 29.2 - - + -
341F GLU* 4.3 11.7 + - - +
342F LYS* 2.9 26.4 + - + +
343F CYS* 4.0 11.0 + - + -
344F GLY* 5.2 1.0 - - - -
347F PHE* 3.5 38.6 - - + +
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Residues in contact with GLN 77 (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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75F ASP* 3.0 13.7 + - - +
76F LYS* 1.3 76.5 - - - +
78F LYS* 1.3 57.4 + - - +
80F VAL* 3.5 3.4 + - - +
81F LYS* 3.0 43.9 + - - +
114F SER 5.7 0.7 - - - +
342F LYS* 3.5 50.2 - - + +
343F CYS* 4.1 11.4 - - - -
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Residues in contact with LYS 78 (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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53F SER 3.7 19.8 + - - +
54F PHE* 3.5 19.3 - - + -
55F GLY* 5.3 4.4 - - - +
75F ASP* 3.1 34.1 + - + +
77F GLN* 1.3 74.4 - - + +
79F VAL* 1.3 60.1 + - - +
81F LYS* 3.8 24.7 - - + +
82F LEU* 3.0 36.2 + - + +
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Residues in contact with VAL 79 (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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54F PHE* 3.4 29.4 - - + -
74F LEU* 4.0 17.3 - - + -
75F ASP 2.9 19.3 + - - +
76F LYS* 3.5 9.2 - - - +
78F LYS* 1.3 78.5 - - - +
80F VAL* 1.3 59.4 + - - +
82F LEU 3.8 0.2 - - - -
83F LYS 3.2 3.1 + - - -
84F GLN* 2.8 46.9 + - + +
85F ILE 3.6 1.3 + - - +
88F THR* 3.4 22.2 - - - +
116F LEU* 4.9 1.1 - - + -
347F PHE* 3.5 24.2 - - + -
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Residues in contact with VAL 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F LYS 3.0 16.2 + - - +
77F GLN* 3.7 4.9 - - - +
79F VAL* 1.3 74.7 - - - +
81F LYS* 1.3 67.4 + - - +
83F LYS* 3.2 15.2 + - - +
85F ILE* 3.8 24.8 - - + +
343F CYS* 3.6 16.4 - - - -
346F GLU* 4.2 14.8 - - + +
347F PHE* 3.6 22.0 - - + -
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Residues in contact with LYS 81 (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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77F GLN* 3.0 29.7 + - - +
78F LYS* 3.7 32.7 - - + +
80F VAL* 1.3 78.7 - - - +
82F LEU* 1.3 65.6 + - + +
83F LYS* 3.3 11.4 + - - +
24L ASP* 5.6 0.9 - - - +
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Residues in contact with LEU 82 (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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53F SER* 3.5 36.8 - - - +
54F PHE* 3.6 21.5 - - + -
78F LYS* 3.0 20.9 + - + +
81F LYS* 1.3 81.5 - - + +
83F LYS* 1.3 64.6 + - - +
84F GLN* 2.9 34.6 + - + +
23L HIS* 4.6 25.6 - - + +
24L ASP* 5.3 4.3 - - - +
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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