Contacts of the helix formed by residues 76 - 88 (chain C) in PDB entry 6V3O
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 ASP 76 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71C TYR* 3.6 9.8 - - - -
74C LYS 2.5 14.8 + - - +
75C GLY* 1.3 70.3 - - - -
77C THR* 1.3 66.9 + - - +
78C THR* 2.5 30.0 + - - +
79C LYS* 3.1 38.2 + - + +
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Residues in contact with THR 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C TYR* 4.1 3.2 + - - -
75C GLY 3.6 7.0 + - - -
76C ASP* 1.3 73.4 + - - +
78C THR* 1.3 61.9 + - - +
80C LEU* 3.0 42.4 + - + +
81C GLY 3.6 3.1 + - - -
839C GLY* 4.0 25.3 - - - +
842C GLY 6.0 0.7 - - - -
843C LEU* 5.0 8.6 - - + +
846C GLU* 4.9 12.6 - - - +
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Residues in contact with THR 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ASP* 2.5 34.7 + - - +
77C THR* 1.3 77.8 - - - +
79C LYS* 1.3 63.5 + - - +
81C GLY* 3.3 3.9 + - - +
82C GLU* 3.3 28.2 + - - +
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Residues in contact with LYS 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C VAL* 5.0 20.8 - - + +
70C ASP* 6.4 1.8 - - + -
71C TYR* 5.2 9.9 - - + +
76C ASP* 3.1 33.1 + - + +
78C THR* 1.3 80.7 - - - +
80C LEU* 1.3 63.0 + - - +
82C GLU* 3.3 26.7 + - - +
83C LEU* 3.0 22.3 + - - +
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Residues in contact with LEU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C SER* 5.6 1.1 - - - +
71C TYR* 3.6 48.2 - - + +
77C THR* 3.0 28.7 + - + +
79C LYS* 1.3 77.8 - - - +
81C GLY* 1.3 51.7 + - - +
83C LEU* 3.2 10.0 + - + +
84C GLY* 2.7 33.4 + - - -
839C GLY 4.6 2.5 - - - +
840C ILE* 4.3 12.6 - - + -
843C LEU* 3.9 15.7 - - + -
899C THR* 3.8 23.3 - - + -
903C VAL* 3.6 31.1 - - + +
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Residues in contact with GLY 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C THR 3.6 4.6 + - - -
78C THR* 3.3 6.6 + - - -
79C LYS 3.3 0.8 - - - -
80C LEU* 1.3 79.0 - - - +
82C GLU* 1.3 51.8 + - - +
84C GLY* 3.3 1.4 + - - -
85C ALA* 2.7 33.5 + - - +
843C LEU* 5.1 5.9 - - - +
907C TYR* 3.4 22.8 + - - -
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Residues in contact with GLU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C THR* 3.3 15.9 + - - +
79C LYS* 3.6 35.4 + - - +
80C LEU 3.3 0.2 - - - -
81C GLY* 1.3 73.2 - - - +
83C LEU* 1.3 66.1 + - - +
85C ALA* 2.9 19.0 + - - +
86C LYS* 3.1 19.6 + - - +
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Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C CYS* 3.5 23.6 - - + +
67C VAL* 3.5 26.7 - - + -
68C SER* 3.4 25.6 - - - +
79C LYS 3.0 14.0 + - - +
80C LEU* 3.3 10.5 - - + +
82C GLU* 1.3 71.3 - - - +
84C GLY* 1.3 57.5 + - - +
86C LYS* 2.7 29.8 + - + +
87C LEU* 3.1 39.4 - - + +
900C THR* 4.4 9.6 - - + +
903C VAL* 4.2 24.2 - - + -
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Residues in contact with GLY 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C LEU 2.7 15.4 + - - -
81C GLY 3.5 4.5 - - - -
83C LEU* 1.3 71.2 - - - +
85C ALA* 1.3 50.0 + - - +
86C LYS 3.1 0.3 + - - -
87C LEU* 3.3 5.7 + - - +
88C THR* 2.8 37.7 + - - +
903C VAL* 3.5 22.0 - - - +
907C TYR* 3.6 24.3 - - - -
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Residues in contact with ALA 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C GLY 2.7 16.4 + - - +
82C GLU* 2.9 16.3 + - - +
84C GLY* 1.3 71.7 - - - +
86C LYS* 1.3 80.0 + - - +
88C THR* 3.3 24.4 + - - +
907C TYR* 4.7 1.8 - - - -
920C THR* 5.0 0.7 + - - -
922C GLN* 4.4 2.3 + - - -
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Residues in contact with LYS 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C PHE* 4.0 26.2 - - + -
64C CYS* 5.8 0.7 - - - -
82C GLU* 3.5 14.6 - - - +
83C LEU* 2.7 19.6 + - + +
85C ALA* 1.3 101.2 + - - +
87C LEU* 1.3 65.6 + - + +
88C THR 3.1 2.5 + - - -
89C GLY* 3.4 10.6 + - - -
90C LEU* 4.1 10.0 + - - +
922C GLN* 3.4 28.5 + - - +
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C PHE* 3.8 22.7 - - + -
64C CYS* 4.0 9.2 - - - -
83C LEU* 3.1 56.8 + - + +
84C GLY* 3.9 7.9 - - - +
86C LYS* 1.3 74.0 - - + +
88C THR* 1.3 67.6 + - - +
89C GLY 3.1 0.7 + - - -
90C LEU* 3.5 23.1 + - + +
95C ALA* 5.5 0.7 - - - +
98C VAL* 4.3 5.4 - - + -
900C THR* 5.4 7.0 - - + +
903C VAL* 5.2 2.2 - - + -
904C PHE* 3.6 59.1 - - + -
907C TYR* 6.1 2.7 - - + -
911C ARG* 4.6 2.9 + - - -
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Residues in contact with THR 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C GLY 2.8 27.9 + - - +
85C ALA* 3.3 26.6 + - - +
87C LEU* 1.3 77.6 - - - +
89C GLY* 1.3 74.5 + - - +
90C LEU 3.6 2.4 + - - +
907C TYR* 4.6 17.4 - - + +
911C ARG* 3.1 31.7 + - - +
917C PHE* 5.9 0.2 - - + -
919C VAL* 3.5 44.2 - - + +
920C THR* 3.9 5.7 + - - -
922C GLN* 5.0 0.2 + - - -
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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