Contacts of the helix formed by residues 68 - 75 (chain I) in PDB entry 1DWK
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 68 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66I ASP 4.0 1.4 + - - -
67I LEU* 1.3 79.3 - - - +
69I GLU* 1.3 65.6 + - - +
70I ASP* 3.4 9.7 + - - +
71I SER* 2.8 33.9 + - - -
72I ILE* 3.1 22.0 + - - +
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Residues in contact with GLU 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I ARG* 5.9 2.1 - - - +
67I LEU 5.3 0.3 - - - +
68I ASP* 1.3 74.7 - - - +
70I ASP* 1.3 69.1 + - - +
72I ILE* 3.5 25.4 + - - +
73I LEU* 3.1 23.0 + - - +
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Residues in contact with ASP 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H LEU* 4.3 14.0 - - + +
24H LYS* 3.6 34.3 + - - -
68I ASP* 3.4 10.6 + - - +
69I GLU* 1.3 79.0 - - - +
71I SER* 1.3 57.1 - - - +
73I LEU* 3.3 10.2 + - - +
74I LEU* 2.9 36.8 + - + +
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Residues in contact with SER 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I LEU* 3.5 28.4 - - - +
67I LEU* 3.9 19.8 - - - +
68I ASP* 2.8 29.5 + - - -
70I ASP* 1.3 73.9 - - - +
72I ILE* 1.3 65.1 + - - +
74I LEU* 3.1 12.5 + - - +
75I LEU* 3.1 28.0 + - - +
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Residues in contact with ILE 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I ALA* 3.8 10.8 - - - +
59I ARG* 4.0 29.4 - - + +
62I GLY* 3.9 29.2 - - - -
67I LEU* 3.6 24.9 - - + +
68I ASP 3.1 11.6 + - - +
69I GLU* 3.8 28.9 - - - +
71I SER* 1.3 77.7 - - - +
73I LEU* 1.3 59.0 + - - +
75I LEU* 3.4 16.6 + - - +
76I GLN* 2.9 29.3 + - - +
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Residues in contact with LEU 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H LEU* 5.0 9.2 - - + -
23H ALA* 4.2 19.7 - - + +
24H LYS* 4.1 40.4 - - + +
3I GLN* 6.3 1.3 - - + -
69I GLU 3.1 14.0 + - - +
70I ASP* 3.5 11.7 - - - +
71I SER 3.3 0.2 - - - -
72I ILE* 1.3 72.1 - - - +
74I LEU* 1.3 67.2 + - + +
76I GLN* 3.1 34.3 + - + +
77I MSE 3.4 12.7 - - + +
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Residues in contact with LEU 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H LEU* 4.7 16.4 - - + -
5I GLN* 4.3 6.7 - - - +
10I ILE* 3.9 31.9 - - + +
11I ARG* 3.1 22.8 + - - -
14I LEU* 3.8 28.7 - - + -
70I ASP* 2.9 20.7 + - + +
71I SER* 3.1 11.8 + - - +
73I LEU* 1.3 78.0 - - - +
75I LEU* 1.3 60.0 + - - +
77I MSE 3.0 37.7 + - + +
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Residues in contact with LEU 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I ARG* 3.9 12.2 + - - +
14I LEU* 3.9 17.7 - - + -
18I ILE* 4.0 12.6 - - + -
46I ALA 3.8 23.6 - - - +
47I LEU* 4.2 8.3 - - + +
52I ALA* 3.5 5.7 - - - -
53I LEU* 2.9 32.5 + - + +
58I ALA* 4.4 11.0 - - + +
61I VAL* 3.9 23.6 - - + -
67I LEU* 3.8 27.6 - - + -
71I SER 3.1 16.1 + - - +
72I ILE* 3.8 11.9 - - - +
73I LEU 3.2 0.8 - - - -
74I LEU* 1.3 74.4 - - - +
76I GLN* 1.3 59.8 + - - +
77I MSE 3.3 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