Contacts of the helix formed by residues 69 - 79 (chain C) in PDB entry 1O94
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 VAL 69 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C VAL* 6.2 0.2 - - + -
9C GLN* 3.6 32.1 - - + +
63C SER* 3.3 35.9 - - - +
64C VAL 4.9 0.9 - - - +
65C GLY* 3.9 19.7 - - - -
66C PRO* 3.0 17.4 + - + +
68C ARG* 1.3 86.9 - - - +
70C ASP* 1.3 65.2 + - - +
72C SER* 2.8 16.8 + - - -
73C LEU* 3.1 20.9 + - + +
86C ARG* 4.3 7.0 - - + -
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Residues in contact with ASP 70 (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 ASP* 3.0 21.3 + - - +
69C VAL* 1.3 75.6 - - - +
71C GLU* 1.3 61.7 + - - +
73C LEU* 3.3 2.4 + - - -
74C ARG* 3.0 33.2 + - + +
86C ARG* 2.9 36.5 + - - -
205C ILE* 3.3 34.4 - - + +
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Residues in contact with GLU 71 (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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9C GLN* 4.1 6.1 - - - +
68C ARG 3.1 13.4 + - - +
69C VAL 2.9 1.0 + - - -
70C ASP* 1.3 78.3 - - - +
72C SER* 1.3 61.0 + - - +
74C ARG* 3.5 8.3 - - - +
75C LYS* 3.3 25.9 + - - +
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Residues in contact with SER 72 (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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7C VAL* 5.7 1.8 - - - -
8C LYS 5.4 0.2 - - - -
9C GLN* 2.8 41.7 + - - +
34C ASP* 3.4 2.8 + - - -
35C LEU* 3.4 35.3 + - - +
69C VAL* 2.8 15.2 + - - -
71C GLU* 1.3 72.1 - - - +
73C LEU* 1.3 63.3 + - - -
75C LYS* 3.3 11.8 + - - +
76C CYS* 3.2 25.0 + - - -
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Residues in contact with LEU 73 (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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7C VAL* 3.8 25.8 - - + -
61C VAL* 3.9 20.9 - - + +
63C SER* 3.9 9.9 - - - +
69C VAL* 3.1 31.9 + - + +
70C ASP* 3.9 0.7 - - - +
72C SER* 1.3 76.0 - - - +
74C ARG* 1.3 56.8 + - - +
76C CYS* 3.2 8.1 + - - +
77C LEU* 3.0 29.9 + - - +
84C ALA* 3.9 7.5 - - + +
85C VAL 3.9 13.2 - - - +
86C ARG* 3.7 32.5 - - + -
205C ILE* 3.9 25.4 - - + -
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Residues in contact with ARG 74 (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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70C ASP* 3.0 27.0 + - + +
71C GLU* 3.5 9.2 - - - +
72C SER 3.2 0.2 - - - -
73C LEU* 1.3 73.1 - - - +
75C LYS* 1.3 60.5 + - - +
77C LEU* 3.1 18.9 + - - +
78C ALA* 2.8 28.5 + - - +
200C ALA* 3.1 28.9 + - + +
201C ALA* 3.8 22.8 + - - +
203C LYS 2.4 31.1 + - - -
204C PRO* 5.2 0.2 - - - +
205C ILE* 3.9 21.8 - - + +
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Residues in contact with LYS 75 (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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459A LYS* 4.7 15.4 + - - -
34C ASP* 2.9 36.9 + - - +
35C LEU* 4.8 9.6 - - + -
71C GLU* 3.3 14.9 + - - +
72C SER* 3.5 10.5 - - - +
74C ARG* 1.3 79.3 - - + +
76C CYS* 1.3 57.4 + - - +
78C ALA* 3.2 9.3 + - - +
79C LYS* 2.9 50.9 + - - +
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Residues in contact with CYS 76 (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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7C VAL* 4.1 24.7 - - - -
35C LEU* 3.9 28.3 - - - -
39C ASP* 5.9 0.2 - - - -
43C LEU* 3.6 22.3 - - + +
61C VAL* 3.8 18.2 - - + -
72C SER 3.2 15.4 + - - -
73C LEU* 3.2 11.3 + - - +
75C LYS* 1.3 75.8 - - - +
77C LEU* 1.3 65.3 + - - +
79C LYS* 3.1 9.9 + - - -
80C GLY 3.1 1.4 + - - -
81C ALA* 2.9 21.8 + - - +
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Residues in contact with LEU 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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73C LEU 3.0 18.2 + - - +
74C ARG* 3.1 26.4 + - - +
76C CYS* 1.3 73.9 - - - +
78C ALA* 1.3 63.4 + - - +
80C GLY* 3.1 14.7 + - - -
81C ALA* 3.5 25.3 + - + +
82C ASP 4.1 3.6 - - - +
83C ARG* 3.8 32.3 - - - +
84C ALA* 3.9 13.2 - - + +
200C ALA* 4.0 13.4 - - + +
203C LYS* 3.8 34.9 + - + -
204C PRO 4.4 7.4 - - - +
205C ILE* 4.4 2.9 - - + -
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Residues in contact with ALA 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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74C ARG 2.8 13.2 + - - +
75C LYS* 3.5 12.3 - - - +
77C LEU* 1.3 76.8 - - - +
79C LYS* 1.3 58.2 + - + +
80C GLY* 3.3 2.8 + - - -
192C ALA* 3.2 31.4 - - + +
196C GLY* 4.3 7.4 - - - +
197C ILE* 4.0 20.0 - - + -
200C ALA* 3.5 16.7 - - + +
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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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462A GLN* 4.9 4.4 + - - -
35C LEU* 4.3 15.3 - - + -
40C ASP* 3.1 29.9 + - + +
43C LEU* 3.8 17.7 - - + +
44C GLU* 5.0 0.3 - - - +
47C MET* 3.9 10.2 - - - +
75C LYS* 2.9 36.3 + - - +
76C CYS 3.1 6.8 + - - +
78C ALA* 1.3 76.3 - - + +
80C GLY* 1.3 54.8 + - - +
81C ALA 3.8 0.2 - - - -
189C PRO* 5.8 1.9 - - + +
190C ARG* 3.4 54.0 + - + +
191C TYR* 4.5 17.8 - - - +
192C ALA* 4.8 8.7 - - + +
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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