Contacts of the strand formed by residues 68 - 75 (chain E) in PDB entry 4DOH
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 THR 68 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66E LYS* 3.7 21.3 + - - +
67E VAL* 1.3 77.2 + - - +
69E TYR* 1.3 66.5 + - - +
89E ASN* 3.0 27.5 + - - +
90E ILE 2.7 47.3 + - - +
91E ASN* 4.3 3.9 + - - +
114E ALA* 3.1 4.5 - - - -
115E ILE* 2.5 58.4 + - - +
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Residues in contact with TYR 69 (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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40E PRO* 4.3 6.5 - - + -
56E TRP* 3.2 35.7 - + + -
58E PRO* 3.2 28.2 - - - +
59E PRO* 3.5 14.5 - - + +
67E VAL* 3.7 20.3 - - + +
68E THR* 1.3 80.2 - - - +
70E THR* 1.3 63.1 + - - +
71E VAL* 5.3 0.2 - - - -
87E CYS 4.0 0.2 - - - +
89E ASN* 3.2 6.2 + - - -
90E ILE* 3.1 33.2 + - + +
91E ASN 3.9 5.6 - - - -
92E ARG 2.8 30.1 - - - -
93E THR* 3.3 17.1 - - + +
112E VAL* 3.9 4.9 - - + -
113E ARG 3.1 6.5 - - - +
114E ALA* 3.4 33.2 - - + -
115E ILE* 4.6 1.1 - - - +
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Residues in contact with THR 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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69E TYR* 1.3 74.1 - - - +
71E VAL* 1.3 62.7 + - - +
72E GLN* 6.4 0.2 - - - -
87E CYS 3.5 4.5 - - - -
88E ARG* 3.7 20.6 - - - -
89E ASN* 2.8 38.4 - - + +
112E VAL* 3.2 3.3 - - - -
113E ARG* 2.9 59.8 + - - +
115E ILE* 4.4 7.1 - - + +
123E TRP* 3.3 11.4 - - - -
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Residues in contact with VAL 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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54E LEU* 4.1 17.3 - - + -
56E TRP* 3.6 30.3 - - + -
70E THR* 1.3 78.2 - - - +
72E GLN* 1.3 72.2 + - - +
84E LYS* 4.0 18.3 + - + +
87E CYS* 3.4 29.1 + - + +
90E ILE* 4.9 2.5 - - + -
95E CYS* 3.9 17.0 - - + -
97E LEU* 4.7 11.2 - - + -
111E ARG 3.1 12.6 - - - +
112E VAL* 4.0 6.7 - - + -
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Residues in contact with GLN 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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70E THR* 4.3 0.8 + - - -
71E VAL* 1.3 79.6 - - - +
73E TYR* 1.3 60.6 + - - +
81E TRP* 3.6 21.8 + - + +
82E LEU 3.4 10.7 - - - +
83E ASN* 3.1 28.0 + - - +
84E LYS 5.0 0.2 - - - +
110E ALA* 3.2 5.0 - - - +
111E ARG* 2.7 77.0 + - + +
123E TRP* 3.3 24.4 - - + -
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Residues in contact with TYR 73 (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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72E GLN* 1.3 74.5 - - - +
74E PHE* 1.3 68.6 + - - +
75E ILE* 4.5 12.1 - - + -
81E TRP* 3.4 5.2 - - - -
82E LEU* 2.9 75.1 + - + +
83E ASN 3.9 14.5 + - - -
84E LYS* 4.5 6.1 - - + -
97E LEU* 4.3 20.2 - - + -
100E GLU* 3.3 49.7 - - + +
101E THR* 5.4 2.5 - - + -
108E TYR* 4.9 6.1 - + + -
109E TYR 3.6 11.2 - - - +
110E ALA* 4.5 4.3 - - + -
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Residues in contact with PHE 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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60C ILE* 3.3 43.7 - - + -
61C ASP* 4.2 4.9 - - + -
73E TYR* 1.3 75.6 - - - +
75E ILE* 1.3 102.0 + - - +
76E TYR* 3.8 2.0 - - - -
78E GLN 3.1 24.5 - - - -
79E LYS 3.7 18.4 - - - -
80E LYS 3.7 11.7 - - - -
81E TRP* 3.2 54.1 - + + -
82E LEU* 5.8 0.2 - - - -
108E TYR* 3.4 12.5 - - - +
109E TYR* 3.0 32.6 + + + +
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Residues in contact with ILE 75 (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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73E TYR* 4.5 16.4 - - + -
74E PHE* 1.3 96.8 - - - +
76E TYR* 1.3 75.2 + - - +
78E GLN* 2.9 54.9 + - + +
80E LYS 5.0 2.2 + - - -
82E LEU* 5.0 9.4 - - + +
100E GLU 5.2 2.5 - - - +
106E HIS* 4.2 22.9 - - + +
107E GLN 3.7 7.4 - - - +
108E TYR* 3.7 23.3 - - + -
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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