Contacts of the helix formed by residues 101 - 112 (chain E) in PDB entry 2BWJ
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 GLU 101 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68D ASP* 5.8 0.2 - - - +
72E SER* 5.7 0.9 + - - -
99E PRO* 3.5 7.4 - - - +
100E ARG* 1.3 80.9 - - - +
102E VAL* 1.3 65.4 + - - +
103E LYS* 3.2 23.4 - - + +
104E GLN* 3.3 43.8 + - + +
105E GLY 3.3 8.5 + - - -
162E PRO* 5.8 2.9 - - - -
163E VAL* 3.6 11.0 - - - +
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Residues in contact with VAL 102 (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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134A GLN* 4.2 17.3 - - + +
99E PRO* 5.9 0.4 - - - -
101E GLU* 1.3 74.2 - - - +
103E LYS* 1.3 59.1 + - - +
105E GLY* 2.9 6.2 + - - -
106E GLU* 2.8 37.8 + - - +
162E PRO* 3.7 38.1 - - + +
163E VAL* 4.1 2.2 - - - +
166E TYR* 3.5 42.9 - - + -
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Residues in contact with LYS 103 (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 SER* 5.8 2.2 - - - +
101E GLU* 3.2 28.7 - - + +
102E VAL* 1.3 78.4 - - - +
104E GLN* 1.3 58.6 + - + +
106E GLU* 3.6 16.8 + - - +
107E GLU* 3.1 33.9 + - + +
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Residues in contact with GLN 104 (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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66D ARG 5.5 4.4 + - - -
68D ASP* 5.3 5.3 + - - -
72E SER* 3.8 33.9 - - - +
76E LEU* 5.3 0.2 - - - +
98E TYR* 3.2 33.9 + - - +
99E PRO* 3.8 5.6 - - + -
100E ARG* 3.0 35.0 + - - +
101E GLU* 3.3 35.1 + - + +
102E VAL 3.1 0.6 - - - -
103E LYS* 1.3 76.9 - - + +
105E GLY* 1.3 60.9 + - - +
107E GLU* 3.5 7.0 + - - +
108E PHE* 2.9 28.2 + - - +
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Residues in contact with GLY 105 (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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99E PRO* 3.7 11.1 - - - +
101E GLU 3.3 4.6 + - - -
102E VAL* 2.9 8.2 + - - -
104E GLN* 1.3 75.8 - - - +
106E GLU* 1.3 61.0 + - - +
108E PHE* 3.5 6.4 - - - +
109E GLY* 2.9 24.4 + - - -
166E TYR* 4.7 5.5 - - - -
167E TYR* 3.2 28.5 + - - -
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Residues in contact with GLU 106 (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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102E VAL* 2.8 26.1 + - - +
103E LYS* 3.6 23.7 - - - +
104E GLN 3.3 0.2 - - - -
105E GLY* 1.3 76.6 - - - +
107E GLU* 1.3 58.4 + - + +
109E GLY* 3.2 3.2 + - - -
110E ARG* 3.0 30.4 + - - +
166E TYR* 3.4 31.6 + - + +
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Residues in contact with GLU 107 (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 SER* 5.6 5.6 - - - +
76E LEU* 3.7 15.1 - - + +
103E LYS* 3.1 21.3 + - + +
104E GLN* 3.7 7.0 - - - +
105E GLY 3.4 0.2 - - - -
106E GLU* 1.3 73.1 - - + +
108E PHE* 1.3 65.5 + - - +
110E ARG* 3.1 43.2 + - - +
111E ARG* 3.0 37.1 + - - +
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Residues in contact with PHE 108 (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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13E ILE* 4.2 11.4 - - + -
15E PHE* 3.5 29.2 - + + -
76E LEU* 3.6 25.7 - - + +
79E LEU* 3.5 27.4 - - + -
83E MET* 4.2 1.8 - - - -
95E ILE* 3.9 23.1 - - + -
98E TYR* 4.0 9.9 - + + -
104E GLN 2.9 18.9 + - - +
105E GLY* 3.5 10.3 - - - +
107E GLU* 1.3 78.3 - - - +
109E GLY* 1.3 55.8 + - - +
112E ILE* 2.8 59.5 + - + +
113E GLY 3.0 37.3 + - - +
115E PRO* 4.9 2.0 - - + -
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Residues in contact with GLY 109 (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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105E GLY 2.9 14.5 + - - -
106E GLU* 3.2 5.1 + - - -
108E PHE* 1.3 78.2 - - - +
110E ARG* 1.3 60.7 + - - +
112E ILE 4.2 0.3 - - - -
113E GLY* 3.4 28.5 + - - -
114E ASP* 3.7 18.8 - - - +
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Residues in contact with ARG 110 (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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106E GLU 3.0 17.7 + - - +
107E GLU* 3.1 40.1 + - - +
108E PHE 3.4 0.2 - - - -
109E GLY* 1.3 77.5 - - - +
111E ARG* 1.3 85.2 + - - +
112E ILE 5.3 0.2 - - - -
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Residues in contact with ARG 111 (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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8E LEU 4.1 11.5 + - - -
76E LEU* 3.7 24.0 - - + +
77E GLU* 3.2 28.1 + - - +
80E LYS* 5.1 13.6 - - + +
107E GLU* 3.0 21.3 + - - +
110E ARG* 1.3 109.8 - - - +
112E ILE* 1.3 66.3 + - + +
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Residues in contact with ILE 112 (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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8E LEU 3.7 18.3 + - - +
9E ARG* 3.8 17.9 + - + +
13E ILE* 4.5 3.8 - - + -
76E LEU* 3.6 22.7 - - + -
79E LEU* 4.4 0.7 - - + -
80E LYS* 3.9 42.6 - - + +
83E MET* 3.6 31.4 - - + -
108E PHE* 2.8 46.5 + - + +
109E GLY 4.2 0.9 - - - -
111E ARG* 1.3 81.2 - - + +
113E GLY* 1.3 58.8 + - - +
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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