Contacts of the helix formed by residues 67 - 77 (chain A) in PDB entry 2OZB
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 LEU 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LYS* 4.0 37.2 - - + +
63A LEU* 3.4 36.6 - - + +
64A GLU* 3.3 30.6 + - + +
66A ILE* 1.3 77.4 - - - +
68A HIS* 1.3 56.9 + - - +
69A LEU 3.3 0.4 - - - -
70A PRO* 3.1 21.7 - - + +
71A LEU* 4.0 8.7 - - - +
82A PHE* 4.1 17.7 - - + -
308B PHE* 3.4 36.0 - - + -
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Residues in contact with HIS 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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39A ALA* 4.9 2.9 - - + -
43A THR* 3.0 29.9 + - + +
64A GLU 4.5 0.2 + - - -
65A ILE 3.8 4.3 - - - -
66A ILE* 3.0 6.7 - - - -
67A LEU* 1.3 77.3 - - - +
69A LEU* 1.3 79.9 + - + +
71A LEU* 3.2 11.0 + - + +
72A LEU* 2.8 30.8 + - + +
242B SER* 3.6 32.3 - - - +
243B LYS* 3.9 20.6 - - + -
304B ARG* 3.3 44.7 + - + -
308B PHE* 3.8 13.2 - - + -
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Residues in contact with LEU 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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39A ALA* 4.5 4.3 - - - -
42A ALA* 4.2 11.2 - - + -
43A THR* 3.6 20.9 - - - +
46A LEU* 3.9 22.2 - - + -
54A ILE* 4.5 8.5 - - + -
56A MET* 3.8 17.9 - - + -
66A ILE* 3.0 21.0 + - + +
68A HIS* 1.3 103.0 - - + +
70A PRO* 1.4 58.8 - - + +
72A LEU* 3.1 5.1 + - + +
73A CYS* 2.8 34.9 + - - -
101A ALA* 3.6 30.3 - - + -
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Residues in contact with PRO 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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11A TYR 5.3 0.7 - - - +
56A MET* 4.2 10.7 - - + -
66A ILE 3.3 9.9 - - - +
67A LEU* 3.1 26.7 - - + +
69A LEU* 1.4 89.9 - - + +
71A LEU* 1.3 57.3 + - + +
73A CYS* 3.3 5.8 + - + +
74A GLU* 2.8 35.9 + - + +
80A TYR* 3.7 41.6 - - + +
82A PHE* 4.5 8.7 - - + -
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Residues in contact with LEU 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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67A LEU 4.0 6.3 - - - +
68A HIS* 3.2 10.7 + - - +
69A LEU 3.2 0.2 - - - -
70A PRO* 1.3 82.3 - - + +
72A LEU* 1.3 62.1 + - - +
74A GLU* 3.3 12.6 + - + +
75A ASP* 3.2 25.4 + - - +
239B THR* 5.7 8.7 - - + -
243B LYS* 5.1 11.9 - - - +
308B PHE* 3.9 31.0 - - + -
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Residues in contact with LEU 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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43A THR* 3.7 29.8 - - + -
46A LEU* 3.9 25.4 - - + -
47A ASN* 3.5 23.8 - - - +
68A HIS* 2.8 21.9 + - + +
69A LEU* 3.1 8.0 + - + +
71A LEU* 1.3 71.5 - - - +
73A CYS* 1.3 60.4 + - - +
75A ASP* 2.9 34.6 - - + +
76A LYS* 3.2 27.7 + - - +
243B LYS* 4.1 29.6 - - + +
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Residues in contact with CYS 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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46A LEU* 3.8 15.2 - - - +
54A ILE* 3.7 30.7 - - - -
69A LEU 2.8 28.9 + - - +
70A PRO 3.5 4.9 - - - +
72A LEU* 1.3 69.8 - - - +
74A GLU* 1.3 64.1 + - - +
76A LYS 3.1 0.8 + - - +
77A ASN* 3.0 5.4 + - - -
78A VAL* 2.9 53.7 + - - +
80A TYR* 3.6 22.7 - - + -
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Residues in contact with GLU 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 PRO 2.8 25.4 + - - +
71A LEU* 3.6 13.2 - - + +
72A LEU 3.3 0.2 - - - -
73A CYS* 1.3 73.2 - - - +
75A ASP* 1.3 63.6 + - - +
76A LYS 3.2 0.5 + - - -
77A ASN* 3.4 9.5 + - - +
80A TYR* 3.5 26.1 + - + +
127A LEU* 4.9 5.5 - - - +
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Residues in contact with ASP 75 (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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71A LEU 3.2 12.0 + - - +
72A LEU* 2.9 23.3 - - + +
74A GLU* 1.3 79.7 - - - +
76A LYS* 1.3 68.9 + - + +
77A ASN 3.4 0.9 + - - -
243B LYS* 4.1 17.7 + - - -
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Residues in contact with LYS 76 (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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46A LEU* 3.6 34.5 - - + +
47A ASN* 4.4 15.4 + - - +
49A GLY* 5.9 4.7 - - - -
72A LEU* 3.3 28.3 - - + +
73A CYS* 3.1 3.9 + - - +
75A ASP* 1.3 85.4 - - + +
77A ASN* 1.3 70.3 + - - +
78A VAL* 3.3 22.0 - - + +
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Residues in contact with ASN 77 (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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73A CYS 3.0 5.3 + - - -
74A GLU* 3.4 7.1 + - - +
75A ASP 3.4 4.0 + - - +
76A LYS* 1.3 79.0 - - - +
78A VAL* 1.3 59.5 - - - +
79A PRO* 4.1 5.1 - - - +
124A GLU* 4.7 3.3 - - - +
503A CA 3.0 24.9 - - - -
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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