Contacts of the helix formed by residues 69 - 79 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7E VAL* 6.2 0.2 - - + -
9E GLN* 3.5 34.1 - - + +
63E SER* 3.4 34.8 - - - +
64E VAL 5.2 0.4 - - - +
65E GLY* 4.0 9.9 - - - -
66E PRO* 3.0 34.5 + - + +
67E ASP 3.0 0.4 + - - -
68E ARG* 1.3 81.4 - - - +
70E ASP* 1.3 65.6 + - - +
72E SER* 2.8 15.0 + - - -
73E LEU* 3.0 19.5 + - + +
86E ARG* 4.5 5.2 - - + -
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Residues in contact with ASP 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E ASP* 3.0 19.3 + - - +
69E VAL* 1.3 76.2 - - - +
71E GLU* 1.3 57.8 + - - +
73E LEU* 3.2 5.0 + - - +
74E ARG* 2.8 40.2 + - + +
86E ARG* 2.8 36.3 + - - -
205E ILE* 3.4 34.5 - - + +
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Residues in contact with GLU 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E GLN* 4.3 4.7 - - - +
68E ARG 3.2 13.1 + - - +
69E VAL 3.1 1.2 + - - -
70E ASP* 1.3 77.6 - - - +
72E SER* 1.3 62.4 + - - +
74E ARG* 3.4 8.0 + - - +
75E LYS* 3.2 27.5 + - - +
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Residues in contact with SER 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E VAL* 5.8 1.8 - - - -
9E GLN* 2.9 37.5 + - - +
34E ASP* 3.5 3.5 + - - -
35E LEU* 3.5 33.5 + - - +
69E VAL* 2.8 14.2 + - - -
71E GLU* 1.3 73.5 - - - +
73E LEU* 1.3 66.5 + - - +
75E LYS* 3.4 11.2 + - - +
76E CYS* 3.2 26.8 + - - -
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Residues in contact with LEU 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E VAL* 3.8 17.7 - - + -
61E VAL* 3.9 16.2 - - + +
62E VAL 4.3 0.4 - - - -
63E SER* 3.6 26.7 - - - +
69E VAL* 3.0 27.7 + - + +
70E ASP* 3.7 8.7 - - - +
72E SER* 1.3 78.9 - - - +
74E ARG* 1.3 56.6 + - - +
76E CYS* 3.2 7.2 + - - +
77E LEU* 3.0 31.6 + - - +
84E ALA* 4.1 11.9 - - + +
85E VAL 4.0 8.3 - - - +
86E ARG* 3.6 32.8 - - + -
205E ILE* 4.1 16.8 - - + -
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Residues in contact with ARG 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E ASP* 2.8 25.1 + - - +
71E GLU* 3.6 8.5 - - - +
72E SER 3.2 0.2 - - - -
73E LEU* 1.3 74.8 - - - +
75E LYS* 1.3 60.2 + - - +
77E LEU* 3.2 12.1 + - + +
78E ALA* 2.9 28.5 + - - +
200E ALA* 2.8 31.6 + - + +
201E ALA* 3.6 23.6 + - - +
203E LYS* 2.8 31.3 + - - +
205E ILE* 3.6 28.0 - - + +
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Residues in contact with LYS 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459B LYS* 4.5 19.0 + - - +
34E ASP* 3.1 35.9 + - - +
35E LEU* 4.7 15.5 - - + -
71E GLU* 3.2 14.4 + - - +
72E SER* 3.4 11.8 + - - +
74E ARG* 1.3 73.2 - - + +
76E CYS* 1.3 60.2 + - - +
78E ALA* 3.2 8.4 + - - +
79E LYS* 2.8 41.9 + - + +
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Residues in contact with CYS 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E VAL* 4.1 20.9 - - - -
35E LEU* 3.9 28.9 - - - -
39E ASP 6.1 0.2 - - - -
43E LEU* 3.7 23.0 - - + +
61E VAL* 3.7 22.7 - - + -
72E SER 3.2 15.6 + - - -
73E LEU 3.2 8.7 + - - +
75E LYS* 1.3 79.3 - - - +
77E LEU* 1.3 63.2 + - - +
79E LYS* 3.1 4.4 + - - +
80E GLY 3.0 17.7 + - - -
81E ALA* 3.1 10.1 + - - +
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Residues in contact with LEU 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E LEU 3.0 19.9 + - - +
74E ARG* 3.2 15.0 + - - +
76E CYS* 1.3 76.2 - - - +
78E ALA* 1.3 62.6 + - - +
80E GLY* 3.0 13.9 + - - -
81E ALA* 3.6 25.6 - - + +
82E ASP 4.2 2.9 - - - +
83E ARG* 3.7 33.2 - - - +
84E ALA* 3.8 15.5 - - + +
200E ALA* 4.0 16.7 - - + +
203E LYS* 3.9 36.4 + - + -
204E PRO 4.6 2.0 - - - +
205E ILE* 4.4 11.7 - - + -
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Residues in contact with ALA 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E ARG 2.9 16.5 + - - +
75E LYS* 3.2 12.1 + - - +
77E LEU* 1.3 73.9 - - - +
79E LYS* 1.3 57.2 + - - +
80E GLY* 3.2 3.2 + - - -
190E ARG* 5.7 0.3 - - - -
192E ALA* 3.6 33.3 - - + +
196E GLY* 4.1 14.9 - - - +
197E ILE* 4.1 12.6 - - + -
200E ALA* 3.7 15.6 - - + +
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Residues in contact with LYS 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E LEU* 4.6 8.1 - - + -
40E ASP* 3.0 39.6 + - - +
43E LEU* 3.8 19.3 - - + +
44E GLU* 5.1 0.5 - - - +
47E MET* 3.9 11.6 - - - +
75E LYS* 2.8 30.1 + - + +
76E CYS 3.1 6.3 + - - +
78E ALA* 1.3 76.4 - - - +
80E GLY* 1.3 56.5 + - - +
81E ALA 3.9 0.2 - - - -
189E PRO* 3.8 16.5 - - - +
190E ARG* 3.1 61.3 + - + +
191E TYR* 5.2 6.2 - - - +
192E ALA* 4.8 11.7 - - + +
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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