Contacts of the helix formed by residues 121 - 133 (chain E) in PDB entry 6R8Y
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 MET 121 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108E THR* 4.7 0.2 - - - +
117E ARG* 4.0 15.3 - - - +
119E THR* 3.9 16.4 - - + +
120E ILE* 1.3 80.7 - - - +
122E PRO* 1.3 81.7 - - + +
123E LYS* 3.2 18.4 - - + +
124E ASP* 2.9 29.9 + - - +
125E ILE* 3.5 2.9 + - - +
48F SER* 5.1 8.5 - - - +
50F LEU* 5.9 5.6 - - + -
51F ILE* 3.7 10.1 - - - +
70J T 5.2 0.9 - - - +
71J G 3.1 34.3 - - - +
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Residues in contact with PRO 122 (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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121E MET* 1.3 92.0 - - + +
123E LYS* 1.3 63.8 + - - +
125E ILE 3.0 3.0 + - - +
126E GLN* 2.9 34.6 + - - +
48F SER* 5.2 2.2 - - - +
50F LEU* 4.2 39.5 - - + +
51F ILE* 4.4 7.9 - - + -
54F GLU* 3.4 30.2 - - + +
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Residues in contact with LYS 123 (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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114A HIS* 3.7 23.7 + - + +
116A LYS* 5.6 9.5 - - - +
117E ARG* 4.2 17.0 - - - +
121E MET* 4.6 18.6 - - + -
122E PRO* 1.3 79.2 - - - +
124E ASP* 1.3 66.2 - - - +
126E GLN* 3.4 17.9 + - - +
127E LEU* 2.9 29.1 + - - +
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Residues in contact with ASP 124 (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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114A HIS* 3.0 28.8 + - - +
108E THR* 3.4 23.8 - - + +
111E CYS* 4.6 4.3 - - + +
112E ALA* 3.3 35.9 + - - +
117E ARG* 3.7 9.9 + - - -
121E MET* 2.9 25.3 + - - +
123E LYS* 1.3 83.9 - - - +
125E ILE* 1.3 62.9 + - - +
127E LEU* 3.1 4.9 + - - +
128E ALA* 3.0 24.3 + - - +
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Residues in contact with ILE 125 (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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104E LEU* 4.3 14.8 - - + -
105E PHE* 4.5 11.9 - - + -
108E THR* 3.5 29.2 - - + +
121E MET 3.5 2.2 + - - +
122E PRO 3.0 1.6 + - - +
124E ASP* 1.3 77.4 - - - +
126E GLN* 1.3 62.9 + - - +
128E ALA* 3.4 1.6 + - - +
129E ARG* 2.9 40.6 + - - +
51F ILE* 3.5 27.4 - - + -
54F GLU* 3.2 36.6 - - - +
55F THR* 4.3 15.9 - - + +
58F VAL* 4.6 4.7 - - + -
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Residues in contact with GLN 126 (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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122E PRO* 2.9 27.5 + - - +
123E LYS* 3.6 17.2 - - - +
125E ILE* 1.3 75.4 - - - +
127E LEU* 1.3 57.5 + - - +
129E ARG* 3.4 4.8 + - - +
130E ARG* 2.8 32.6 + - - +
54F GLU* 3.4 21.7 + - - +
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Residues in contact with LEU 127 (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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110A LEU* 3.9 33.4 - - + +
111A CYS* 4.4 7.9 - - - +
114A HIS* 3.4 44.0 - - + +
127A LEU* 6.1 0.2 - - + -
111E CYS* 4.1 17.5 - - + -
123E LYS 2.9 16.6 + - - +
124E ASP 3.1 4.0 + - - +
126E GLN* 1.3 75.4 - - - +
128E ALA* 1.3 67.9 + - - +
130E ARG* 3.1 5.0 + - + +
131E ILE* 2.9 47.4 + - + +
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Residues in contact with ALA 128 (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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131A ILE* 4.8 4.1 - - + +
104E LEU* 4.2 14.1 - - + -
107E ASP* 4.1 27.4 - - + +
108E THR* 4.3 8.7 - - - +
111E CYS* 4.6 6.7 - - - -
124E ASP 3.0 15.6 + - - +
125E ILE 3.9 3.1 - - - +
127E LEU* 1.3 75.7 - - - +
129E ARG* 1.3 64.8 + - - +
131E ILE* 3.0 10.7 + - - +
132E ARG* 3.0 28.3 + - - +
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Residues in contact with ARG 129 (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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100E TYR* 3.7 14.6 + - - +
104E LEU* 3.7 20.6 - - + -
125E ILE* 2.9 26.3 + - - +
126E GLN* 3.9 5.4 - - - +
128E ALA* 1.3 75.5 - - - +
130E ARG* 1.3 62.4 + - - +
132E ARG* 3.5 6.2 + - - +
133E GLY 3.3 3.3 + - - -
134E GLU* 2.5 74.7 + - + +
135E ARG* 3.7 12.1 + - - +
136E ALA* 3.8 19.6 - - - +
54F GLU* 5.5 0.4 - - - -
58F VAL* 3.5 42.6 + - - +
61F VAL* 4.4 11.1 - - - +
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Residues in contact with ARG 130 (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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106A GLU* 3.5 27.5 + - - -
107A ASP* 4.8 2.8 + - - -
110A LEU* 3.3 31.9 - - - +
126E GLN 2.8 19.7 + - - +
127E LEU* 3.1 6.7 + - - +
129E ARG* 1.3 78.3 - - - +
131E ILE* 1.3 62.9 - - - +
133E GLY* 3.6 9.0 + - - -
135E ARG* 5.3 23.0 - - + +
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Residues in contact with ILE 131 (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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107A ASP* 3.7 43.2 - - + +
110A LEU* 5.2 1.1 - - + -
111A CYS* 3.6 30.5 - - - -
128A ALA* 4.8 5.2 - - - +
131A ILE* 4.4 29.6 - - + -
132A ARG* 4.6 18.1 + - + +
111E CYS* 5.4 0.2 - - - -
127E LEU* 2.9 35.9 + - + +
128E ALA* 3.0 7.2 + - - +
130E ARG* 1.3 82.9 - - - +
132E ARG* 1.3 63.9 + - - +
133E GLY* 3.1 1.7 + - - -
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Residues in contact with ARG 132 (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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131A ILE* 4.4 19.4 - - + +
132A ARG* 5.8 4.7 - - - +
100C ARG* 4.9 12.9 + - - +
100E TYR* 4.9 10.6 - - - -
103E GLY* 3.3 30.6 + - - -
104E LEU* 4.0 14.3 - - - +
107E ASP* 2.5 30.9 + - - +
128E ALA 3.0 18.1 + - - +
129E ARG* 4.1 7.0 - - - +
130E ARG 3.5 0.2 - - - -
131E ILE* 1.3 77.1 - - - +
133E GLY* 1.3 58.9 + - - +
134E GLU* 4.3 16.1 - - + +
96F ARG* 3.2 32.5 - - - +
100G ARG* 5.1 9.4 + - - -
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Residues in contact with GLY 133 (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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129E ARG 3.3 3.9 + - - -
130E ARG* 3.6 7.5 + - - -
131E ILE 3.1 6.8 + - - -
132E ARG* 1.3 77.9 - - - +
134E GLU* 1.3 56.9 + - - +
135E ARG* 2.9 26.9 + - - +
96G LYS* 5.1 6.1 - - - -
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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