Contacts of the helix formed by residues 69 - 78 (chain A) in PDB entry 1WZ3
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 SER 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ASP 3.8 2.2 + - - -
68A GLU* 1.3 82.4 - - - +
70A VAL* 1.3 63.0 + - - +
71A ILE* 3.1 21.6 - - - +
72A ASP* 3.2 19.3 + - - -
73A LEU* 3.4 17.2 + - - +
34B GLY 3.6 11.2 - - - -
35B SER* 4.6 8.3 - - - -
36B ASP 3.4 8.7 - - - -
37B LYS* 4.3 6.7 - - - +
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A SER* 1.3 71.2 - - - +
71A ILE* 1.3 61.3 + - - +
73A LEU* 3.3 7.5 + - - +
74A TYR* 2.9 26.7 + - - +
83A LEU* 4.5 8.5 - - + -
12B ILE* 4.1 27.4 - - + -
14B VAL* 4.3 16.2 - - + -
32B VAL* 4.1 19.7 - - + -
33B SER 4.1 4.7 - - - +
34B GLY* 3.2 5.1 + - - +
36B ASP 2.8 27.1 + - - +
37B LYS 4.1 11.2 - - - +
38B PHE* 4.3 9.4 - - + -
41B VAL* 4.4 11.0 - - + -
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Residues in contact with ILE 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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69A SER* 3.1 15.9 - - - +
70A VAL* 1.3 77.6 - - - +
72A ASP* 1.3 65.1 + - - +
74A TYR* 3.2 12.7 + - + +
75A ASN* 2.9 50.8 + - - +
10B GLN* 5.8 5.8 - - + -
12B ILE* 3.6 25.6 - - + -
34B GLY* 2.9 28.0 + - - +
35B SER* 4.8 1.8 - - - +
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Residues in contact with ASP 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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68A GLU* 3.5 22.3 - - + +
69A SER* 3.2 22.6 + - - +
71A ILE* 1.3 90.8 - - - +
73A LEU* 1.3 62.4 + - - +
75A ASN* 3.2 11.4 + - - +
76A ASN* 3.0 34.4 + - - +
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Residues in contact with LEU 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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62A PHE* 5.0 1.8 - - + -
64A PRO* 3.8 26.5 - - + -
68A GLU* 3.6 28.9 - - + +
69A SER 3.4 12.3 + - - +
70A VAL* 3.3 7.9 + - - +
72A ASP* 1.3 75.8 - - - +
74A TYR* 1.3 58.2 + - - +
77A PHE* 2.8 60.2 + - + +
78A GLY 3.7 0.2 + - - -
83A LEU* 3.8 14.3 - - + +
38B PHE* 3.5 46.4 - - + -
58B VAL* 5.7 1.6 - - + -
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Residues in contact with TYR 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 VAL 2.9 17.5 + - - +
71A ILE* 3.4 9.2 - - + +
73A LEU* 1.3 78.2 - - - +
75A ASN* 1.3 74.8 + - - +
78A GLY* 2.7 36.7 + - - +
81A GLY* 3.7 21.4 + - - -
82A LYS* 3.7 35.9 - - - -
83A LEU* 4.1 8.0 - - + +
12B ILE* 3.7 45.8 - - + -
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Residues in contact with ASN 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 ILE* 2.9 40.1 + - - +
72A ASP* 3.2 12.9 + - - +
74A TYR* 1.3 93.2 - - - +
76A ASN* 1.3 64.2 + - - +
78A GLY 4.8 0.4 - - - +
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Residues in contact with ASN 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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68A GLU* 4.1 11.3 + - - -
72A ASP* 3.0 25.3 + - - +
75A ASN* 1.3 83.0 - - - +
77A PHE* 1.3 91.1 + - + +
78A GLY 5.4 0.4 - - - -
93B TRP* 4.2 11.6 - - - -
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Residues in contact with PHE 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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62A PHE* 3.4 34.5 - + - -
68A GLU* 5.6 0.4 - - - -
73A LEU* 2.8 43.3 + - + +
76A ASN* 1.3 98.5 - - + +
78A GLY* 1.3 65.8 + - - +
79A PHE* 3.9 0.9 + - - +
83A LEU* 4.0 7.9 - - + +
84A VAL 5.4 1.7 + - - -
58B VAL* 3.6 24.1 - - + +
59B ASN 3.5 19.7 - - - +
60B SER* 4.3 12.8 - - - -
93B TRP* 3.2 29.1 + + - +
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Residues in contact with GLY 78 (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 LEU 3.7 1.0 + - - -
74A TYR* 2.7 38.6 + - - +
75A ASN 5.7 0.3 - - - +
77A PHE* 1.3 77.7 + - - +
79A PHE* 1.3 60.7 + - - +
82A LYS 3.2 14.6 - - - -
83A LEU* 4.0 6.0 - - - +
93B TRP* 3.8 10.0 - - - +
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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