Contacts of the helix formed by residues 76 - 85 (chain F) in PDB entry 6E07
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 76 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74F ARG 5.3 1.8 - - - +
75F LEU* 1.3 81.1 - - - +
77F VAL* 1.3 63.3 + - - +
78F ALA* 3.0 22.7 + - - +
79F ASP* 2.9 33.5 + - - +
80F ILE* 3.4 8.1 + - - +
107F TYR* 4.6 6.7 - - - -
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Residues in contact with VAL 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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76F THR* 1.3 71.3 - - - +
78F ALA* 1.3 60.8 + - - +
80F ILE* 3.1 12.2 + - + +
81F ARG* 2.9 29.2 + - + +
102F PHE* 4.1 38.8 - - + +
105F ASN* 3.6 12.3 - - + +
106F SER* 3.5 37.9 - - - -
107F TYR* 4.1 4.0 - - + +
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Residues in contact with ALA 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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76F THR* 3.0 10.4 + - - +
77F VAL* 1.3 78.6 - - - +
79F ASP* 1.3 62.1 + - - +
81F ARG* 3.5 10.6 + - - +
82F LYS* 3.1 24.6 + - - +
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Residues in contact with ASP 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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74F ARG 4.8 1.0 - - - +
75F LEU* 3.5 26.4 - - + +
76F THR* 2.9 39.5 + - - +
77F VAL 3.1 0.2 - - - -
78F ALA* 1.3 78.7 - - - +
80F ILE* 1.3 57.6 + - - +
82F LYS* 3.3 7.3 + - - +
83F GLN* 3.0 31.8 + - - +
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Residues in contact with ILE 80 (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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39F ALA 4.9 5.8 - - - +
49F TYR* 3.3 50.3 - - + +
75F LEU* 3.9 25.4 - - + -
76F THR 3.4 7.8 + - - +
77F VAL* 3.1 21.4 + - + +
79F ASP* 1.3 78.2 - - - +
81F ARG* 1.3 60.1 + - - +
83F GLN* 4.2 16.4 - - - +
84F SER* 2.9 37.1 + - - +
102F PHE* 4.2 13.2 - - + -
105F ASN* 4.1 8.3 - - - +
106F SER 6.0 0.4 - - - +
107F TYR* 4.0 20.9 - - + -
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Residues in contact with ARG 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 VAL* 2.9 16.9 + - - +
78F ALA* 3.5 10.5 - - - +
80F ILE* 1.3 76.7 - - - +
82F LYS* 1.3 59.3 + - - +
85F GLU* 2.8 65.6 + - - +
95F LYS* 5.9 2.2 - - - +
98F LEU* 3.7 23.0 - - - +
99F GLU* 3.0 29.9 + - - -
102F PHE* 3.5 55.9 - - + +
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Residues in contact with LYS 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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78F ALA 3.1 10.9 + - - +
79F ASP* 3.6 9.9 - - - +
81F ARG* 1.3 79.2 - - - +
83F GLN* 1.3 63.4 + - - +
85F GLU* 5.2 1.3 - - - -
86F PRO* 3.1 23.5 - - + +
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Residues in contact with GLN 83 (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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39F ALA 3.8 16.4 + - - -
40F SER* 3.9 18.3 + - - +
45F LYS* 3.4 60.6 - - + +
75F LEU* 4.3 13.0 - - - +
79F ASP* 3.0 16.9 + - - +
80F ILE* 3.8 11.9 + - - +
82F LYS* 1.3 80.1 - - - +
84F SER* 1.3 64.1 + - - +
86F PRO* 4.2 4.0 - - - +
87F PHE* 3.9 8.5 - - - -
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Residues in contact with SER 84 (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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45F LYS* 3.6 36.4 - - - +
49F TYR* 4.0 15.4 - - - -
80F ILE* 2.9 20.5 + - - -
81F ARG* 5.0 0.4 - - - -
83F GLN* 1.3 80.9 + - - +
85F GLU* 1.3 58.9 + - - +
86F PRO* 3.2 3.8 - - - -
87F PHE* 2.8 25.9 + - - +
88F PHE* 3.2 25.3 - - - -
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Residues in contact with GLU 85 (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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81F ARG* 2.8 60.3 + - + +
82F LYS* 5.2 1.5 - - - -
84F SER* 1.3 71.9 - - - +
86F PRO* 1.4 66.0 - - + +
88F PHE* 3.0 34.8 + - + +
89F LYS 4.2 1.9 + - - -
90F ALA* 4.9 7.2 + - + +
98F LEU* 3.2 29.4 - - + +
102F PHE* 5.0 2.0 - - + -
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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