Contacts of the helix formed by residues 72 - 85 (chain C) in PDB entry 1ORZ
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 72 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66C VAL* 5.3 0.9 - - - +
70C LEU* 3.6 6.0 - - - -
71C GLY* 1.3 96.9 - - - +
73C GLY* 1.3 60.6 + - - +
74C LEU* 4.0 14.1 - - + +
75C THR* 2.6 47.5 + - + +
76C THR* 2.8 20.2 + - - +
78C LYS* 5.8 0.9 - - - +
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Residues in contact with GLY 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C LEU* 4.3 11.5 - - - +
72C LEU* 1.3 71.8 - - - +
74C LEU* 1.3 67.5 + - - +
76C THR* 2.6 25.7 + - - -
77C GLU* 3.1 8.1 + - - +
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Residues in contact with LEU 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C LEU* 4.5 14.6 - - + -
73C GLY* 1.3 84.6 - - - +
75C THR* 1.3 62.2 + - + +
77C GLU* 2.9 42.2 - - - +
78C LYS* 3.0 25.8 + - - +
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Residues in contact with THR 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C VAL* 2.6 52.5 + - + +
71C GLY 3.8 0.2 - - - -
72C LEU* 2.6 59.5 + - + -
74C LEU* 1.3 75.0 - - + +
76C THR* 1.3 63.6 + - - +
78C LYS* 2.9 22.2 + - - +
79C VAL* 2.9 18.9 + - - +
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Residues in contact with THR 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C SER* 2.9 27.4 - - - +
68C GLY 4.1 7.0 - - - +
69C LEU 4.6 6.1 - - - +
70C LEU* 4.8 4.3 - - + -
71C GLY 4.4 3.6 - - - +
72C LEU 2.8 22.6 + - - +
73C GLY* 2.6 23.9 + - - -
75C THR* 1.3 76.2 - - - +
77C GLU* 1.3 60.7 + - - +
79C VAL* 2.7 31.6 - - - +
80C SER* 2.9 8.0 + - - -
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Residues in contact with GLU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C GLY 3.1 4.2 + - - +
74C LEU* 2.9 41.1 + - - +
76C THR* 1.3 83.2 + - - +
78C LYS* 1.3 57.1 + - + +
80C SER* 2.9 9.9 + - - -
81C ASN* 2.7 53.6 + - - +
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Residues in contact with LYS 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C VAL* 4.5 7.6 - - + -
72C LEU* 5.8 1.0 - - - +
74C LEU* 3.0 25.7 + - - +
75C THR* 2.9 33.8 + - + +
77C GLU* 1.3 86.1 - - + +
79C VAL* 1.3 62.9 + - - +
81C ASN* 3.2 11.3 + - - +
82C TRP* 2.9 40.0 + - + +
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Residues in contact with VAL 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C LEU* 3.6 22.5 - - + +
66C VAL* 3.3 21.8 - - + -
67C SER* 3.2 50.9 - - - +
75C THR 2.9 2.6 + - - +
76C THR* 2.7 25.8 - - - +
78C LYS* 1.3 74.8 - - - +
80C SER* 1.3 72.1 + - - +
82C TRP* 3.1 9.9 + - + +
83C TYR* 3.0 26.8 + - + +
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Residues in contact with SER 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C THR 3.5 8.3 - - - -
77C GLU* 2.9 13.8 + - - -
79C VAL* 1.3 84.3 - - - +
81C ASN* 1.3 63.9 + - - +
83C TYR* 2.9 44.3 + - - -
84C HIS* 3.2 10.4 + - - +
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Residues in contact with ASN 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C GLU* 2.7 48.0 + - - +
78C LYS* 3.5 10.7 - - - +
80C SER* 1.3 79.4 + - - +
82C TRP* 1.3 64.8 + - + +
84C HIS* 3.1 19.8 + - - +
85C GLN* 3.4 17.9 + - - +
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Residues in contact with TRP 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C LEU* 5.2 16.2 - - + -
78C LYS* 2.9 41.5 + - + +
79C VAL* 3.7 9.4 - - + +
81C ASN* 1.3 81.3 - - + +
83C TYR* 1.3 64.7 + - - +
84C HIS 3.1 0.3 + - - -
85C GLN* 3.3 10.8 + - - +
90C ILE* 3.7 30.3 - - + -
92C GLU* 2.9 65.4 - - + +
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Residues in contact with TYR 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C LEU* 6.0 6.7 - - + -
79C VAL* 3.0 19.3 + - + +
80C SER* 2.9 44.0 + - - -
82C TRP* 1.3 77.2 - - - +
84C HIS* 1.3 79.7 + - + +
85C GLN 3.3 7.1 + - - +
86C LYS* 5.0 0.2 - - - -
92C GLU* 4.7 5.5 - - - +
93C TRP* 4.7 12.0 + - - +
96C LYS* 6.2 4.0 - - + -
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Residues in contact with HIS 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C SER* 3.2 10.9 + - - +
81C ASN* 3.1 13.9 + - - +
82C TRP 3.1 0.6 - - - -
83C TYR* 1.3 100.3 + - + +
85C GLN* 1.3 64.2 + - + +
86C LYS* 2.8 12.8 + - - +
93C TRP* 5.2 2.3 - - - -
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Residues in contact with GLN 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ASN* 3.4 15.7 + - - +
82C TRP* 3.3 9.9 + - - -
83C TYR 3.3 4.4 + - - +
84C HIS* 1.3 82.1 - - + +
86C LYS* 1.4 63.8 + - - +
87C PHE 4.4 2.9 - - - +
88C SER* 2.6 39.3 + - - -
90C ILE* 5.6 0.5 - - - +
92C GLU* 2.8 46.8 + - - +
93C TRP 3.4 9.5 + - - -
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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