Contacts of the helix formed by residues 8 - 16 (chain F) in PDB entry 1V8O
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 8 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F LEU 4.0 1.0 + - - -
7F VAL* 1.3 75.2 - - - +
9F ALA* 1.3 54.4 + - - +
10F SER* 2.8 23.4 + - - -
11F ALA* 2.9 10.0 + - - +
12F LEU* 2.7 35.3 + - - +
35F THR* 3.9 4.9 - - - -
95F TYR* 3.4 37.9 - - + -
106F LEU* 4.6 2.0 - - + -
107F VAL 3.3 6.4 + - - +
108F THR* 2.7 33.6 + - - -
110F ASP* 5.0 0.9 - - - +
113F LEU* 3.9 10.0 - - - +
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Residues in contact with ALA 9 (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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8F ASP* 1.3 75.3 + - - +
10F SER* 1.3 65.0 + - - +
12F LEU* 3.5 8.2 - - - +
13F TYR* 3.1 29.4 + - + -
35F THR* 3.9 8.1 - - + +
38F GLU* 3.8 37.0 + - + +
39F ALA* 4.2 12.6 - - - +
95F TYR* 4.2 1.6 + - - -
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Residues in contact with SER 10 (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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8F ASP* 2.8 25.4 + - - -
9F ALA* 1.3 74.7 - - - +
11F ALA* 1.3 59.8 + - - +
13F TYR* 3.6 6.7 + - - +
14F ALA* 3.3 20.1 + - - +
108F THR* 3.6 1.6 + - - -
109F GLN* 3.0 30.4 + - - +
110F ASP* 3.8 2.3 + - - +
49H LEU* 3.5 35.2 - - - +
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Residues in contact with ALA 11 (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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7F VAL* 3.3 17.3 - - + -
8F ASP* 2.9 7.9 + - - +
10F SER* 1.3 75.6 + - - +
12F LEU* 1.3 66.7 + - - +
13F TYR 3.0 1.9 + - - -
14F ALA* 3.1 2.8 + - - +
15F LEU* 2.8 26.9 + - - +
107F VAL* 3.0 35.7 - - + +
108F THR* 4.2 1.8 - - - -
109F GLN 4.8 1.3 - - - +
123F VAL* 3.8 20.0 - - + -
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Residues in contact with LEU 12 (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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7F VAL* 3.5 6.3 - - + +
8F ASP 2.7 18.8 + - - +
9F ALA* 3.5 10.5 - - - +
11F ALA* 1.3 72.6 - - - +
13F TYR* 1.3 62.1 + - + +
15F LEU* 3.5 4.0 + - - +
16F ALA* 2.8 27.8 + - + +
22F TRP* 6.4 0.2 - - + -
31F ILE* 4.0 20.0 - - + -
35F THR* 4.6 2.2 - - + -
39F ALA* 5.0 3.8 - - + -
61F LEU* 4.2 10.3 - - + -
64F VAL* 4.1 17.7 - - + -
65F MSE 3.9 35.4 - - + -
68F PHE* 3.8 35.7 - - + -
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Residues in contact with TYR 13 (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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9F ALA* 3.1 17.1 + - + +
10F SER* 3.7 10.1 - - - +
11F ALA 3.0 0.8 - - - -
12F LEU* 1.3 76.8 - - + +
14F ALA* 1.3 69.9 + - - +
16F ALA* 3.0 20.3 + - + +
17F ALA* 3.9 3.6 + - - +
39F ALA* 3.8 25.1 - - + -
42F ALA* 3.8 14.1 - - + -
43F LEU* 2.9 46.3 + - + +
46F GLU* 4.8 15.3 - - + -
61F LEU* 4.5 11.6 - - + +
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Residues in contact with ALA 14 (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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10F SER 3.3 7.5 + - - +
11F ALA 3.1 2.1 + - - +
13F TYR* 1.3 78.1 - - - +
15F LEU* 1.3 65.7 + - - +
17F ALA* 3.2 12.5 + - - +
18F HIS* 3.6 16.0 + - + -
109F GLN* 3.9 16.2 - - + +
123F VAL* 3.5 31.0 - - + -
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Residues in contact with LEU 15 (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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7F VAL* 3.5 40.4 - - + -
11F ALA* 2.8 22.4 + - + +
12F LEU* 3.6 5.4 - - - +
14F ALA* 1.3 72.9 - - - +
16F ALA* 1.3 52.0 + - - +
17F ALA 2.5 15.4 + - - -
18F HIS* 2.6 17.8 + - - -
22F TRP* 3.0 49.7 + - + +
29F LEU* 4.8 1.1 - - + -
68F PHE* 4.5 11.2 - - + -
123F VAL* 4.2 19.9 - - + +
126F LEU* 4.0 24.0 - - + -
127F LEU* 4.2 7.6 - - + -
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Residues in contact with ALA 16 (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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12F LEU* 2.8 23.9 + - + +
13F TYR* 3.0 13.3 + - + +
15F LEU* 1.3 68.7 - - - +
17F ALA* 1.3 56.7 + - - +
18F HIS 3.6 1.1 - - - -
19F TYR* 4.4 9.3 + - - +
22F TRP* 4.6 3.3 - - - -
61F LEU* 5.7 4.3 - - + -
64F VAL* 4.3 31.9 - - + +
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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