Contacts of the helix formed by residues 67 - 74 (chain A) in PDB entry 1DUS
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 GLY 67 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PHE* 4.2 0.7 - - - -
61A ASP* 4.5 0.9 - - - -
64A CYS 2.9 13.4 + - - -
65A GLY 3.1 2.0 + - - -
66A TYR* 1.3 80.5 - - - +
68A VAL* 1.3 67.1 + - - +
69A ILE 3.3 2.8 + - - -
70A GLY 3.4 1.8 + - - -
71A ILE* 3.0 33.2 + - - +
82A MSE 3.7 20.9 - - - +
93A ALA* 4.1 4.5 - - - -
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 3.5 29.2 - - + -
28A PHE* 3.7 19.7 - - + -
40A VAL* 4.2 12.8 - - + -
41A ASP 6.1 0.2 - - - +
44A THR* 3.8 25.1 - - + -
48A VAL* 4.3 4.7 - - + -
64A CYS 4.2 3.2 + - - -
66A TYR* 3.1 38.1 - - + +
67A GLY* 1.3 75.4 - - - +
69A ILE* 1.3 59.9 + - - +
71A ILE* 3.9 0.7 - - - +
72A ALA* 2.9 29.3 + - - +
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Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A THR* 3.8 17.5 - - + -
47A LEU* 4.0 23.1 - - + -
48A VAL* 3.8 25.8 - - + -
59A ILE* 5.9 0.4 - - + -
61A ASP* 3.5 26.8 + - + +
62A LEU 5.8 0.2 - - - +
63A GLY 5.8 2.2 - - - +
64A CYS 5.4 0.6 + - - -
67A GLY 3.4 0.8 - - - -
68A VAL* 1.3 74.2 - - - +
70A GLY* 1.3 64.2 + - - +
72A ALA* 3.4 0.7 + - - +
73A LEU* 3.1 39.6 + - + +
127A ILE* 3.7 28.9 - - + -
128A THR* 4.6 1.6 - - - -
129A ASN* 4.4 15.9 - - + +
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Residues in contact with GLY 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ILE* 5.1 2.0 - - - -
61A ASP* 3.0 17.5 + - - -
67A GLY 3.4 1.2 + - - -
69A ILE* 1.3 75.5 - - - +
71A ILE* 1.3 58.4 + - - +
73A LEU* 3.3 2.2 + - - -
74A ALA* 2.8 33.5 + - - +
80A THR* 3.8 21.0 - - - +
82A MSE 3.7 19.3 - - - -
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Residues in contact with ILE 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LYS* 5.5 0.5 - - - +
26A LEU* 4.4 9.7 - - + +
28A PHE* 3.9 18.6 - - + -
67A GLY* 3.0 25.9 + - - +
68A VAL 4.0 1.6 - - - +
70A GLY* 1.3 77.5 - - - +
72A ALA* 1.3 62.9 + - - +
73A LEU 3.3 0.9 + - - -
74A ALA* 3.6 4.6 + - - +
75A ASP* 4.4 5.2 - - - +
82A MSE 4.2 12.8 - - + -
93A ALA 4.1 6.3 - - - +
96A ASN* 3.4 42.0 - - + -
97A ILE* 3.9 5.8 - - + +
100A ASN* 3.7 22.2 - - + +
102A LEU* 3.5 35.0 - - + +
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 4.2 8.3 - - + +
22A ARG* 3.8 5.5 - - - -
24A LYS* 2.8 29.4 + - - +
26A LEU* 3.9 23.3 - - + -
48A VAL* 3.5 29.8 - - + -
68A VAL 2.9 18.3 + - - +
69A ILE 3.8 1.8 - - - +
71A ILE* 1.3 76.9 - - - +
73A LEU* 1.3 57.9 + - - +
76A GLU* 3.8 2.6 - - - +
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ARG* 3.4 42.6 - - - +
24A LYS* 4.4 1.3 - - - +
48A VAL* 4.6 2.7 - - + +
51A VAL* 3.7 17.9 - - + -
53A VAL* 4.4 11.9 - - + -
59A ILE* 4.0 17.3 - - + -
69A ILE* 3.1 28.1 + - + +
70A GLY 4.2 0.2 - - - +
72A ALA* 1.3 82.0 - - + +
74A ALA* 1.3 56.9 + - - +
75A ASP* 3.3 3.1 - - - -
76A GLU* 2.9 28.1 + - - +
77A VAL* 3.6 11.1 + - + +
80A THR* 4.9 0.4 - - - -
127A ILE* 3.4 32.8 - - + -
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLY 2.8 18.5 + - - +
71A ILE 3.6 9.1 + - - +
73A LEU* 1.3 75.4 - - - +
75A ASP* 1.3 59.6 + - - +
76A GLU 3.2 1.1 + - - -
77A VAL* 3.7 17.5 + - - +
78A LYS 5.8 0.2 - - - -
79A SER* 6.1 0.2 - - - -
80A THR* 3.7 12.6 + - - +
102A LEU* 4.0 8.7 - - + -
105A TYR* 3.9 12.5 - - + +
107A ILE* 3.3 37.9 - - + +
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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