Contacts of the helix formed by residues 81 - 91 (chain E) in PDB entry 3J41
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 81 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74E ARG* 3.1 34.1 - - - +
76E MET* 3.6 17.1 - - - +
78E ASP* 3.2 25.9 + - - +
80E ASP* 1.3 70.4 - - - +
82E GLU* 1.3 56.6 + - - +
83E GLU 3.3 1.3 - - - -
84E GLU* 3.6 25.7 - - - +
85E ILE* 2.8 26.2 + - - +
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Residues in contact with GLU 82 (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 ALA* 4.0 10.6 - - - +
74E ARG* 2.7 50.3 + - + +
80E ASP 2.8 10.7 + - - +
81E SER* 1.3 69.2 - - - +
83E GLU* 1.3 61.3 + - + +
85E ILE* 3.2 7.8 + - - +
86E ARG* 3.1 29.1 + - - +
138E TYR* 2.6 37.4 + - + +
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Residues in contact with GLU 83 (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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80E ASP 3.9 7.2 + - - +
81E SER* 3.3 0.6 - - - -
82E GLU* 1.3 78.8 - - + +
84E GLU* 1.3 57.2 + - + +
86E ARG* 2.7 52.1 + - - +
87E GLU* 2.8 31.2 + - - +
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Residues in contact with GLU 84 (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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74E ARG 5.4 0.4 - - - +
76E MET* 5.9 2.7 - - + -
81E SER* 3.2 31.3 + - - +
83E GLU* 1.3 74.9 - - + +
85E ILE* 1.3 58.6 + - - +
87E GLU* 4.3 10.6 - - - +
88E ALA* 2.8 35.4 + - - +
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Residues in contact with ILE 85 (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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241A ARG* 5.1 4.9 - - - +
72E MET 5.9 1.1 - - - +
73E ALA 3.9 14.1 - - - +
74E ARG 3.8 11.9 - - - +
75E LYS* 3.9 31.2 - - + -
81E SER 2.8 18.8 + - - +
82E GLU 3.2 8.5 + - - +
84E GLU* 1.3 71.1 - - - +
86E ARG* 1.3 55.5 + - - +
88E ALA* 3.3 7.0 + - + +
89E PHE* 2.8 48.1 + - + -
138E TYR* 3.5 31.4 - - + -
141E PHE* 3.9 28.5 - - + -
142E VAL* 5.9 1.6 - - + -
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Residues in contact with ARG 86 (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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82E GLU 3.1 13.6 + - - +
83E GLU* 2.7 46.1 + - - +
85E ILE* 1.3 75.0 - - - +
87E GLU* 1.3 56.6 + - + +
89E PHE* 3.3 13.5 - - + +
90E ARG* 3.1 39.7 + - - +
98E GLY* 6.1 3.6 - - - -
138E TYR* 3.9 29.8 - - + -
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Residues in contact with GLU 87 (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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83E GLU* 2.8 20.4 + - + +
84E GLU* 4.3 14.4 - - - +
86E ARG* 1.3 69.1 - - - +
88E ALA* 1.3 57.9 + - - +
90E ARG* 2.7 58.6 + - - +
91E VAL* 2.8 35.0 + - + +
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Residues in contact with ALA 88 (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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241A ARG* 2.7 39.9 + - + +
75E LYS* 5.9 5.2 - - - -
84E GLU* 2.8 25.9 + - - +
85E ILE* 3.6 11.2 - - + +
87E GLU* 1.3 71.7 - - - +
89E PHE* 1.3 58.6 + - - +
91E VAL* 3.9 9.7 + - - +
92E PHE* 3.8 14.2 + - - -
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Residues in contact with PHE 89 (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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241A ARG* 3.4 11.4 - - - +
85E ILE* 2.8 44.3 + - + -
86E ARG* 3.3 15.9 - - + +
88E ALA* 1.3 72.8 - - - +
90E ARG* 1.3 52.8 + - + +
92E PHE* 3.0 7.4 + - - +
93E ASP* 2.8 38.0 + - - +
98E GLY* 3.5 26.7 - - - -
99E TYR 4.9 0.2 - - - -
100E ILE* 3.4 28.3 - - + +
136E VAL 3.4 21.1 - - - -
137E ASN 3.4 20.9 - - - -
138E TYR* 3.9 11.7 - + + -
141E PHE* 3.6 27.4 - + + -
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Residues in contact with ARG 90 (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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86E ARG* 3.1 24.8 + - - +
87E GLU* 2.7 51.6 + - - +
89E PHE* 1.3 74.3 - - + +
91E VAL* 1.3 62.7 + - - +
93E ASP* 3.2 21.4 - - - +
94E LYS* 5.1 0.9 - - - -
95E ASP 4.2 6.5 + - - -
96E GLY* 3.7 37.6 + - - +
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Residues in contact with VAL 91 (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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87E GLU* 2.8 25.8 + - + +
88E ALA* 3.9 11.4 - - - +
89E PHE 3.4 0.2 - - - -
90E ARG* 1.3 71.2 - - - +
92E PHE* 1.3 70.4 + - + +
93E ASP 4.2 2.0 - - - +
94E LYS* 4.7 6.8 - - - -
108E VAL* 4.6 8.7 - - + +
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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