Contacts of the helix formed by residues 64 - 76 (chain E) in PDB entry 2WP9
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 ASN 64 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E ALA* 4.0 4.6 - - - +
63E ASP* 1.3 88.0 + - - +
65E TRP* 1.3 66.1 + - - +
66E GLU* 2.8 43.2 + - - +
67E TRP* 2.8 56.6 + - + +
68E HIS* 3.3 5.0 + - - +
126E PHE* 5.5 1.8 - - - -
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Residues in contact with TRP 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E ALA* 3.9 16.6 - - + +
64E ASN* 1.3 80.1 + - - +
66E GLU* 1.3 89.1 + - + +
68E HIS* 3.2 6.1 + - - +
69E MET* 2.8 40.1 + - + -
86E GLU* 3.9 40.4 - - + -
89E CYS* 3.5 27.3 - - + +
90E LYS* 3.8 48.9 - - + +
93E PRO* 5.5 3.6 - - + -
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Residues in contact with GLU 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E ASN* 2.8 19.6 + - - +
65E TRP* 1.3 115.5 + - + +
67E TRP* 1.3 57.9 + - - +
69E MET* 3.6 8.6 - - - +
70E TYR* 3.0 27.4 + - - +
126E PHE* 3.7 27.3 - - + -
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Residues in contact with TRP 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E GLU* 3.6 28.0 - - + -
63E ASP* 3.2 24.7 - - - -
64E ASN* 2.8 37.1 + - + +
66E GLU* 1.3 70.7 - - - +
68E HIS* 1.3 58.0 + - - +
70E TYR* 3.2 9.5 + - - +
71E ASP* 2.9 31.0 + - - +
123E SER 3.8 6.5 - - - +
124E LYS* 3.6 27.4 - - + -
125E ASN* 3.3 48.8 - - - +
126E PHE* 3.7 34.4 - + - +
133E ARG* 3.6 12.8 - - - +
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Residues in contact with HIS 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E THR* 3.5 48.1 + - + +
55E VAL* 4.1 2.7 - - - -
56E ALA* 4.3 12.3 + - + +
64E ASN 3.3 3.4 + - - +
65E TRP* 3.2 14.1 + - - +
67E TRP* 1.3 77.3 - - - +
69E MET* 1.3 65.0 + - - +
71E ASP* 3.3 4.0 + - + +
72E THR* 2.9 42.4 + - - -
88E MET* 5.2 8.9 - - + +
89E CYS* 3.5 29.2 + - + +
92E GLY* 6.6 0.2 - - - -
133E ARG* 3.9 27.9 - - - +
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Residues in contact with MET 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E TRP* 2.8 36.0 + - + +
66E GLU* 3.6 14.1 - - - +
68E HIS* 1.3 74.3 - - - +
70E TYR* 1.3 67.4 + - - +
72E THR* 3.1 2.1 + - - -
73E VAL* 2.8 33.8 + - + +
82E GLN* 3.7 44.6 - - + +
85E ILE* 3.8 16.2 - - + -
86E GLU* 4.0 17.0 - - + +
89E CYS* 3.7 13.4 - - - -
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Residues in contact with TYR 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E GLU 3.0 15.2 + - - +
67E TRP* 3.4 7.4 - - - +
69E MET* 1.3 74.5 - - - +
71E ASP* 1.3 71.7 + - - +
73E VAL* 3.8 4.3 - - + +
74E LYS* 2.8 67.5 + - + +
78E TYR* 5.3 5.6 + + - -
123E SER* 4.3 0.4 - - - -
126E PHE* 3.7 47.8 + + + -
127E GLY* 3.4 24.9 - - - -
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Residues in contact with ASP 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E TRP 2.9 13.9 + - - +
68E HIS* 3.7 7.6 - - + +
69E MET 3.2 0.2 - - - -
70E TYR* 1.3 83.5 - - - +
72E THR* 1.3 58.9 + - - +
74E LYS* 4.0 3.8 - - - +
75E GLY* 2.8 26.5 + - - -
121E GLY* 3.1 28.8 - - - +
123E SER* 2.7 52.0 + - - +
133E ARG* 2.9 19.0 + - - +
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Residues in contact with THR 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E HIS* 2.9 34.2 + - - -
69E MET 3.6 2.9 - - - -
71E ASP* 1.3 76.6 - - - +
73E VAL* 1.3 59.6 + - - +
75E GLY* 3.1 2.2 + - - -
76E SER* 2.9 30.6 + - - -
85E ILE* 3.7 33.7 - - + -
88E MET* 4.5 12.5 - - + +
89E CYS* 4.3 2.1 - - - -
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Residues in contact with VAL 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E MET* 2.8 40.0 + - + +
70E TYR* 3.8 4.5 - - - +
72E THR* 1.3 70.6 - - - +
74E LYS* 1.3 63.1 + - - +
76E SER* 2.8 23.9 + - - +
78E TYR* 3.4 30.6 + - + -
80E GLY 5.5 1.3 - - - +
82E GLN* 3.6 41.5 - - + +
85E ILE* 3.7 21.1 - - + -
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Residues in contact with LYS 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E TYR* 2.8 54.2 + - + +
71E ASP* 4.0 4.5 - - - +
73E VAL* 1.3 73.4 - - - +
75E GLY* 1.3 65.1 + - - +
77E ASP* 2.9 15.6 + - - +
78E TYR* 4.0 29.1 - - + +
127E GLY* 6.1 1.8 - - - -
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Residues in contact with GLY 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E ASP 2.8 22.8 + - - -
72E THR* 3.1 3.5 + - - -
74E LYS* 1.3 77.8 - - - +
76E SER* 1.3 56.4 + - - +
77E ASP* 3.0 5.2 + - - +
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Residues in contact with SER 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E THR* 2.9 14.5 + - - -
73E VAL* 2.8 18.1 + - - -
75E GLY* 1.3 76.4 - - - +
77E ASP* 1.3 67.5 + - - +
78E TYR* 3.2 3.3 + - - -
79E ILE* 3.5 16.3 + - - +
80E GLY* 3.1 32.8 + - - -
85E ILE* 5.1 2.5 - - - -
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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