Contacts of the helix formed by residues 72 - 86 (chain C) in PDB entry 1WZN
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 HIS 72 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C TYR* 3.4 51.5 - + + +
5C TYR* 3.6 20.2 - - + +
6C THR* 3.4 20.6 - - + +
70C ASP* 2.9 14.1 + - - +
71C LEU* 1.3 98.3 - - + +
73C GLU* 1.3 64.5 + - - +
74C GLU* 3.5 10.5 - - - +
75C MET* 3.1 11.7 + - + -
76C LEU* 3.2 18.1 + - - +
1003C SAH 2.9 22.0 + - - +
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Residues in contact with GLU 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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71C LEU 3.9 2.6 + - - -
72C HIS* 1.3 72.4 - - - +
74C GLU* 1.3 63.1 + - - +
76C LEU* 3.2 7.2 + - - +
77C ARG* 2.8 33.3 + - + +
80C ARG* 2.5 36.3 + - - -
94C GLN* 3.8 26.7 - - + +
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Residues in contact with GLU 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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5C TYR 3.5 12.1 - - - +
6C THR* 3.5 34.6 - - - +
9C ALA* 3.5 21.9 - - + +
10C GLU* 4.6 2.4 - - - +
72C HIS* 3.5 12.8 - - - +
73C GLU* 1.3 86.8 + - + +
75C MET* 1.3 59.3 + - - +
77C ARG* 3.6 17.2 - - - +
78C VAL* 3.6 8.3 - - - +
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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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4C LEU 4.4 1.6 - - - +
5C TYR* 3.4 50.5 - - + +
9C ALA* 3.9 15.5 - - - -
12C TYR* 3.7 21.3 - - + -
51C GLY* 3.5 29.7 - - - +
52C THR* 3.7 24.1 - - + +
70C ASP* 3.9 8.5 - - - +
72C HIS* 3.1 10.3 + - + +
74C GLU* 1.3 76.0 - - - +
76C LEU* 1.3 66.2 + - - +
78C VAL* 3.0 15.2 + - - +
79C ALA 3.1 9.0 + - - -
1003C SAH 3.5 20.6 - - - +
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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
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50C CYS* 3.7 19.5 - - - -
51C GLY 4.4 1.3 - - - +
70C ASP* 3.6 26.7 - - + +
72C HIS 3.2 11.8 + - - +
73C GLU* 3.2 15.0 + - - +
75C MET* 1.3 76.8 - - - +
77C ARG* 1.3 57.9 + - - +
79C ALA* 3.0 5.3 + - - +
80C ARG* 2.8 56.6 + - - +
92C PHE* 4.1 15.3 - - + -
93C LEU 3.4 26.9 - - - +
94C GLN* 3.6 23.1 - - + -
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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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10C GLU* 4.2 7.2 + - - +
73C GLU* 2.8 19.5 + - + +
74C GLU* 3.6 11.0 - - - +
76C LEU* 1.3 76.9 - - - +
78C VAL* 1.3 60.4 + - - +
80C ARG* 4.1 10.5 - - - +
81C ARG* 3.2 38.0 + - - +
1006C SO4 2.9 39.2 + - - +
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Residues in contact with VAL 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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9C ALA 4.0 16.8 - - - +
10C GLU* 3.6 33.2 - - - +
13C ASP* 3.8 15.7 - - - +
52C THR* 3.8 25.1 - - + -
74C GLU 3.6 12.1 - - - +
75C MET 3.0 7.5 + - - +
77C ARG* 1.3 74.8 - - - +
79C ALA* 1.3 65.6 + - - +
81C ARG* 3.3 16.2 + - - +
82C LYS* 3.0 29.0 + - + +
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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
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51C GLY 3.9 7.6 - - - +
52C THR 3.4 31.2 + - - +
53C GLY 3.9 0.4 - - - +
57C LEU* 4.4 2.5 - - - +
75C MET 3.1 4.6 + - - -
76C LEU* 3.0 9.1 + - - +
78C VAL* 1.3 77.6 - - - +
80C ARG* 1.3 56.9 + - - +
82C LYS* 3.1 5.5 + - - +
83C ALA* 2.8 29.1 + - - +
92C PHE* 3.5 33.6 - - + -
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Residues in contact with ARG 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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73C GLU* 2.5 33.5 + - - -
76C LEU* 2.8 42.8 + - - +
77C ARG* 4.1 7.1 - - - +
79C ALA* 1.3 71.9 - - - +
81C ARG* 1.3 57.9 + - - +
83C ALA* 3.2 7.4 + - - +
84C LYS* 2.8 32.4 + - - +
92C PHE* 2.8 50.3 + - + +
93C LEU* 4.5 2.0 - - - +
94C GLN* 4.9 1.2 - - - +
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Residues in contact with ARG 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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10C GLU* 2.7 43.8 + - - -
77C ARG* 3.2 31.0 + - - +
78C VAL* 3.5 21.3 - - - +
79C ALA 3.2 0.2 - - - -
80C ARG* 1.3 79.4 - - - +
82C LYS* 1.3 60.3 + - - +
84C LYS* 3.5 6.5 - - - +
85C GLU* 3.0 53.6 + - + +
1006C SO4 2.7 45.4 + - - +
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Residues in contact with LYS 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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13C ASP* 2.8 30.4 + - - +
20C ILE* 5.3 1.2 - - - +
52C THR* 2.8 36.8 + - - -
54C ILE* 3.9 13.3 - - - +
57C LEU* 3.5 23.7 - - + +
78C VAL* 3.0 25.1 + - + +
79C ALA* 3.7 1.8 - - - +
81C ARG* 1.3 76.2 - - + +
83C ALA* 1.3 67.1 + - - +
85C GLU* 3.3 12.6 + - - +
86C ARG* 3.0 36.4 + - - +
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Residues in contact with ALA 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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57C LEU* 4.4 6.4 - - + +
79C ALA 2.8 16.6 + - - +
80C ARG* 3.2 6.5 + - - +
82C LYS* 1.3 75.9 - - - +
84C LYS* 1.3 58.9 + - - +
86C ARG* 3.4 0.6 + - - -
87C ASN* 2.9 8.7 + - - -
88C LEU* 2.8 50.9 + - - +
90C ILE* 4.4 10.8 - - + +
92C PHE* 4.0 19.3 - - + -
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Residues in contact with LYS 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 ARG 2.8 17.3 + - - +
81C ARG* 3.5 7.6 - - - +
83C ALA* 1.3 77.5 - - - +
85C GLU* 1.3 63.7 + - + +
87C ASN* 3.0 16.0 + - - +
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Residues in contact with GLU 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 ARG* 3.0 44.0 + - + +
82C LYS* 3.3 12.6 + - - +
84C LYS* 1.3 80.5 - - + +
86C ARG* 1.3 62.7 + - + +
87C ASN* 3.3 1.1 + - - +
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Residues in contact with ARG 86 (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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24C LYS* 5.7 1.4 - - - +
54C ILE 5.4 1.8 + - - -
57C LEU* 3.1 50.9 + - - +
58C GLU* 4.4 8.5 + - - +
61C GLU* 2.8 29.7 + - - +
82C LYS* 3.0 24.7 + - - +
83C ALA 4.2 0.2 - - - +
85C GLU* 1.3 81.1 - - + +
87C ASN* 1.3 72.0 + - - +
88C LEU* 3.3 22.2 + - + +
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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