Contacts of the helix formed by residues 72 - 86 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B TYR* 3.4 47.2 - + + +
5B TYR* 3.6 24.5 - - + +
6B THR* 3.4 21.7 - - + +
70B ASP* 2.9 9.1 + - - +
71B LEU* 1.3 102.6 - - + +
73B GLU* 1.3 65.0 + - - +
74B GLU* 3.7 6.3 - - - +
75B MET* 3.1 15.9 + - + +
76B LEU* 3.2 16.5 + - - +
1002B SAH 2.8 20.7 + - - +
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Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU 3.9 2.6 + - - -
72B HIS* 1.3 72.3 - - - +
74B GLU* 1.3 63.1 + - - +
76B LEU* 3.2 8.2 + - - +
77B ARG* 2.9 32.5 + - + +
80B ARG* 2.5 38.4 + - - -
94B GLN* 3.7 27.5 - - + +
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Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B TYR 3.5 12.6 - - - +
6B THR* 3.7 36.3 - - - +
9B ALA* 3.6 14.4 - - + +
10B GLU* 4.7 2.1 - - - +
72B HIS* 3.7 11.3 - - - +
73B GLU* 1.3 88.5 + - + +
75B MET* 1.3 60.2 + - - +
77B ARG* 3.7 12.7 - - - +
78B VAL* 3.5 18.2 - - - +
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Residues in contact with MET 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU 4.3 1.3 - - - +
5B TYR* 3.4 51.8 - - + +
9B ALA* 3.9 16.6 - - - -
12B TYR* 3.8 20.0 - - + -
51B GLY* 3.6 28.7 - - - +
52B THR* 3.8 21.8 - - + +
70B ASP* 4.0 9.0 - - - +
72B HIS* 3.1 9.3 + - + +
74B GLU* 1.3 76.3 - - - +
76B LEU* 1.3 65.2 + - - +
78B VAL* 3.1 17.0 + - - +
79B ALA 3.1 9.4 + - - -
1002B SAH 3.5 21.8 - - - +
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B CYS* 3.7 18.8 - - - -
51B GLY 4.4 1.1 - - - +
70B ASP* 3.6 26.5 - - + +
72B HIS 3.6 10.8 - - - +
73B GLU* 3.2 16.3 + - - +
75B MET* 1.3 77.5 - - - +
77B ARG* 1.3 57.1 + - - +
79B ALA* 3.2 4.2 + - - +
80B ARG* 2.8 55.7 + - - +
92B PHE* 4.1 15.9 - - + -
93B LEU 3.4 26.5 - - - +
94B GLN* 3.6 24.7 - - + +
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Residues in contact with ARG 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLU* 4.2 7.6 + - - +
73B GLU* 2.9 19.5 + - + +
74B GLU* 3.7 11.0 - - - +
75B MET 3.2 0.2 - - - -
76B LEU* 1.3 75.9 - - - +
78B VAL* 1.3 61.2 + - - +
80B ARG* 4.0 11.5 - - - +
81B ARG* 3.1 36.3 + - - +
1005B SO4 2.9 41.6 + - - +
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Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ALA 4.0 16.8 - - - +
10B GLU* 3.7 28.7 - - - +
13B ASP* 4.0 15.3 - - - +
52B THR* 3.8 22.9 - - + -
74B GLU 3.5 17.0 - - - +
75B MET* 3.1 6.9 + - - +
77B ARG* 1.3 74.4 - - - +
79B ALA* 1.3 65.2 + - - +
81B ARG* 3.2 17.3 + - - +
82B LYS* 3.0 30.2 + - + +
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLY 3.8 8.3 - - - +
52B THR 3.3 31.8 + - - +
57B LEU* 4.2 3.0 - - - +
75B MET 3.1 5.6 + - - +
76B LEU* 3.6 8.5 - - - +
78B VAL* 1.3 79.4 - - - +
80B ARG* 1.3 56.1 + - - +
82B LYS* 3.3 3.1 + - - +
83B ALA* 2.9 28.8 + - - +
92B PHE* 3.5 32.8 - - + -
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Residues in contact with ARG 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B GLU* 2.5 33.7 + - - -
76B LEU* 2.8 46.3 + - - +
77B ARG* 4.0 7.2 - - - +
79B ALA* 1.3 72.1 - - - +
81B ARG* 1.3 57.9 + - - +
83B ALA* 3.4 4.3 + - - +
84B LYS* 3.0 31.0 + - - +
92B PHE* 3.2 50.6 + - + +
93B LEU* 4.7 1.6 - - - +
94B GLN 4.9 1.6 - - - +
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Residues in contact with ARG 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLU* 2.9 43.8 + - - -
77B ARG* 3.1 31.9 + - - +
78B VAL* 3.2 21.4 + - - +
80B ARG* 1.3 78.1 - - - +
82B LYS* 1.3 59.4 + - - +
84B LYS* 3.4 7.3 + - - +
85B GLU* 2.9 52.3 + - + +
1005B SO4 2.9 42.4 + - - +
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Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ASP* 2.7 31.7 + - - +
20B ILE* 5.2 1.6 - - - +
52B THR* 3.0 36.9 + - - -
53B GLY 4.5 0.2 - - - -
54B ILE* 3.9 14.8 - - - +
57B LEU* 3.5 19.2 - - + +
78B VAL* 3.0 24.9 + - + +
79B ALA* 3.8 1.6 - - - +
81B ARG* 1.3 77.3 - - + +
83B ALA* 1.3 65.8 + - - +
85B GLU* 3.3 16.0 + - - +
86B ARG* 3.0 35.9 + - - +
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 3.7 10.0 - - + +
79B ALA 2.9 16.7 + - - +
80B ARG* 3.7 5.8 - - - +
82B LYS* 1.3 76.4 - - - +
84B LYS* 1.3 57.4 + - - +
86B ARG* 3.2 1.4 + - - -
87B ASN 2.9 9.2 + - - -
88B LEU* 2.9 45.4 + - + +
90B ILE* 4.4 13.2 - - + +
92B PHE* 4.2 17.7 - - + -
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Residues in contact with LYS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ARG 3.0 17.5 + - - +
81B ARG* 3.6 7.4 - - - +
83B ALA* 1.3 77.3 - - - +
85B GLU* 1.3 63.3 + - + +
87B ASN* 3.1 21.2 + - - +
88B LEU 5.1 0.9 - - - -
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Residues in contact with GLU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ARG* 2.9 40.2 + - + +
82B LYS* 3.3 23.3 + - - +
84B LYS* 1.3 77.2 - - + +
86B ARG* 1.3 62.0 + - + +
87B ASN* 3.3 8.5 + - - +
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Residues in contact with ARG 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LYS* 5.5 1.2 - - - +
54B ILE* 5.6 1.8 + - - +
57B LEU* 3.4 43.1 + - - +
58B GLU* 4.5 8.7 + - - +
61B GLU* 2.9 30.5 + - - +
82B LYS* 3.0 29.3 + - - +
83B ALA 4.1 0.2 - - - +
85B GLU* 1.3 82.1 - - + +
87B ASN* 1.3 73.0 + - - +
88B LEU* 3.2 23.9 + - + +
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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