Contacts of the helix formed by residues 68 - 84 (chain C) in PDB entry 1Z83
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 PRO 68 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C LEU* 4.8 5.2 - - + -
60C ILE* 4.4 14.8 - - + -
66C LEU 4.5 1.1 - - - +
67C VAL* 1.3 92.7 - - + +
69C LEU* 1.3 66.4 + - - +
70C GLU* 3.3 3.6 - - + +
71C THR* 3.3 20.6 + - - +
72C VAL* 3.2 19.6 + - - +
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Residues in contact with LEU 69 (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 VAL 3.5 3.3 + - - -
68C PRO* 1.3 70.9 - - - +
70C GLU* 1.3 69.5 + - + +
72C VAL* 3.3 10.9 - - - +
73C LEU* 2.9 37.4 + - + +
95C TYR* 4.4 2.5 - - - +
98C GLU* 4.2 5.6 - - - +
100C GLN* 3.7 22.0 - - + +
101C GLN* 3.7 47.8 - - + +
104C GLU* 4.1 25.1 - - + -
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Residues in contact with GLU 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C PRO* 3.3 2.9 - - + +
69C LEU* 1.3 88.7 - - + +
71C THR* 1.3 58.8 + - - +
73C LEU* 4.6 0.9 - - - -
74C ASP* 2.9 31.8 + - - +
104C GLU* 5.0 0.9 - - - +
108C ARG* 2.8 39.1 + - - -
645C ZN 2.1 37.9 - - - -
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Residues in contact with THR 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 5.1 1.8 - - + -
57C LEU* 4.4 21.5 - - + +
67C VAL* 5.2 0.4 - - - -
68C PRO* 3.3 27.6 + - - +
69C LEU 3.2 0.2 - - - -
70C GLU* 1.3 80.8 - - - +
72C VAL* 1.3 61.8 + - - +
74C ASP* 4.2 3.5 - - - +
75C MET* 3.3 40.4 + - + +
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Residues in contact with VAL 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C THR* 3.6 32.8 - - + -
43C LEU* 4.4 11.2 - - + -
67C VAL* 3.9 11.0 - - + -
68C PRO 3.2 11.6 + - - +
69C LEU* 3.3 16.2 - - - +
71C THR* 1.3 81.0 - - - +
73C LEU* 1.3 62.1 + - - +
75C MET* 3.4 9.7 + - + +
76C LEU* 3.0 27.9 + - - +
95C TYR* 4.0 12.6 - - + -
101C GLN* 4.1 0.9 - - - +
633C AP5 3.8 31.4 - - + +
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Residues in contact with LEU 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LEU* 2.9 23.0 + - + +
70C GLU* 4.0 2.7 - - - +
72C VAL* 1.3 78.1 - - - +
74C ASP* 1.3 58.1 + - - +
76C LEU* 3.3 4.5 + - + -
77C ARG* 2.8 31.5 + - + +
95C TYR* 3.5 33.2 - - + +
104C GLU* 3.5 39.5 - - + +
105C PHE* 4.1 21.8 - - + -
108C ARG* 3.7 25.8 - - + +
109C ILE* 4.2 13.7 - - + -
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Residues in contact with ASP 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C GLU* 2.9 22.5 + - - +
71C THR* 4.2 4.4 - - - +
73C LEU* 1.3 76.6 - - - +
75C MET* 1.3 61.8 + - - +
77C ARG* 3.9 6.0 - - - +
78C ASP* 3.0 34.7 + - - +
108C ARG* 2.8 27.4 + - - -
645C ZN 1.9 32.2 - - - -
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Residues in contact with MET 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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42C LEU* 3.7 49.8 - - + +
43C LEU* 3.9 26.0 - - + -
46C GLU* 4.8 11.9 - - + +
57C LEU* 4.6 7.4 - - + -
71C THR* 3.3 27.8 + - + +
72C VAL* 3.5 11.0 - - + +
74C ASP* 1.3 77.3 - - - +
76C LEU* 1.3 62.5 + - - +
78C ASP* 3.5 8.5 + - - +
79C ALA* 3.2 22.2 + - - +
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Residues in contact with LEU 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 4.1 31.2 - - + +
39C THR* 4.1 12.8 - - + -
42C LEU* 3.9 9.8 - - + +
72C VAL 3.0 15.2 + - - +
73C LEU* 3.5 6.1 - - + +
75C MET* 1.3 77.4 - - - +
77C ARG* 1.3 66.8 + - - +
79C ALA* 3.1 5.9 + - - +
80C MET* 3.0 22.8 + - + +
92C ILE* 3.8 20.9 - - + -
95C TYR* 3.7 34.8 - - + -
105C PHE* 3.8 27.4 - - + -
109C ILE* 5.2 0.4 - - + -
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Residues in contact with ARG 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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1C MET* 5.3 3.2 - - - +
2C GLU* 5.1 13.7 - - - +
5C LEU* 4.2 19.1 - - + +
73C LEU* 2.8 24.0 + - + +
74C ASP* 3.9 6.5 - - - +
76C LEU* 1.3 74.0 - - - +
78C ASP* 1.3 69.8 + - - +
80C MET* 3.2 5.2 + - + +
81C VAL* 2.9 45.1 + - + +
108C ARG* 3.4 36.9 + - - +
109C ILE* 3.6 33.5 - - + +
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Residues in contact with ASP 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ASP* 3.0 26.2 + - - +
75C MET* 3.6 8.6 - - - +
76C LEU 3.3 0.2 - - - -
77C ARG* 1.3 82.8 + - - +
79C ALA* 1.3 58.5 + - - +
81C VAL* 3.4 8.4 + - - +
82C ALA* 3.0 28.4 + - - +
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Residues in contact with ALA 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 4.0 28.2 - - + +
42C LEU* 4.2 18.6 - - + -
75C MET 3.2 9.1 + - - +
76C LEU 3.1 9.5 + - - +
78C ASP* 1.3 81.2 - - - +
80C MET* 1.3 60.2 + - - +
82C ALA* 3.4 14.2 + - - +
83C LYS* 3.5 18.8 + - + +
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Residues in contact with MET 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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5C LEU* 4.1 14.6 - - + -
8C THR* 5.0 0.9 - - + -
10C ILE* 4.0 17.0 - - + -
37C LEU* 3.6 16.8 - - + -
76C LEU* 3.0 18.3 + - + +
77C ARG* 3.6 8.1 - - + +
79C ALA* 1.3 74.1 - - - +
81C VAL* 1.3 64.8 + - - +
83C LYS 3.2 1.2 + - - -
84C VAL* 3.0 27.8 + - - +
90C PHE* 3.6 40.2 - - + -
92C ILE* 4.0 10.3 - - + -
105C PHE* 4.0 13.2 - - + -
109C ILE* 3.8 42.4 - - + -
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Residues in contact with VAL 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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1C MET* 3.9 45.2 - - + +
5C LEU* 4.0 12.8 - - + -
77C ARG* 2.9 41.3 + - - +
78C ASP* 3.7 8.5 - - - +
80C MET* 1.3 76.2 - - - +
82C ALA* 1.3 62.2 + - - +
83C LYS 3.4 0.3 + - - -
84C VAL* 3.8 13.6 + - - +
85C ASN* 5.0 1.2 + - - +
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Residues in contact with ALA 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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78C ASP 3.0 16.0 + - - +
79C ALA* 3.6 9.6 - - - +
80C MET 3.2 0.2 - - - -
81C VAL* 1.3 78.5 - - - +
83C LYS* 1.3 65.1 + - + +
85C ASN* 5.4 1.4 + - - +
86C THR* 5.4 0.2 + - - -
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Residues in contact with LYS 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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35C THR* 3.7 33.9 - - + +
37C LEU* 4.9 8.7 - - + -
79C ALA 3.5 13.1 + - - +
80C MET 3.2 4.1 + - - +
82C ALA* 1.3 82.6 - - + +
84C VAL* 1.3 60.9 + - - +
85C ASN* 3.4 2.7 - - - -
86C THR* 3.2 14.8 + - - +
87C SER* 2.9 26.9 + - - -
90C PHE* 4.3 4.0 - - + -
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Residues in contact with VAL 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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1C MET* 3.3 40.4 - - + -
4C LYS* 4.2 26.6 - - + +
5C LEU* 4.2 14.1 - - + -
8C THR* 4.4 9.5 + - + -
80C MET 3.0 13.5 + - - +
81C VAL 3.8 5.2 - - - +
82C ALA 3.7 0.6 - - - -
83C LYS* 1.3 77.9 - - - +
85C ASN* 1.3 70.5 + - - +
86C THR 3.1 1.2 + - - -
87C SER* 3.4 13.6 + - - +
90C PHE* 4.0 21.8 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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