Contacts of the helix formed by residues 119 - 131 (chain E) in PDB entry 1S9D
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 119 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117E GLU* 3.4 26.3 - - - +
118E ARG* 1.3 85.0 + - - +
120E GLU* 1.3 65.9 + - - +
121E LEU* 4.4 3.1 - - + +
122E ASN* 3.1 31.0 + - - +
123E LEU* 3.1 9.2 + - - +
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Residues in contact with GLU 120 (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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118E ARG 3.5 2.3 + - - +
119E GLU* 1.3 69.5 - - - +
121E LEU* 1.3 66.7 + - - +
123E LEU* 3.2 28.0 + - - +
124E ALA* 3.0 23.7 + - - +
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Residues in contact with LEU 121 (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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91E ASN* 4.5 20.2 - - - +
93E PRO* 4.1 26.2 - - + -
96E ILE* 4.5 8.3 - - + -
114E TYR* 4.6 11.7 - - - +
119E GLU* 3.2 2.6 - - + +
120E GLU* 1.3 78.9 - - - +
122E ASN* 1.3 67.9 + - - +
124E ALA* 3.1 5.3 + - - +
125E VAL* 2.9 38.2 + - + +
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Residues in contact with ASN 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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114E TYR* 2.9 51.0 - - - +
115E LEU* 4.3 4.8 - - - +
117E GLU* 3.5 33.2 - - - +
119E GLU* 3.1 26.1 + - - +
121E LEU* 1.3 86.8 - - - +
123E LEU* 1.3 57.1 + - - +
125E VAL* 3.4 10.4 + - - +
126E LEU* 2.8 27.5 + - - +
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Residues in contact with LEU 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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115E LEU 5.4 0.2 - - - +
117E GLU 3.6 16.4 - - - +
118E ARG* 3.6 15.9 - - - +
119E GLU 3.1 11.0 + - - +
120E GLU* 3.2 33.4 + - - +
122E ASN* 1.3 73.5 - - - +
124E ALA* 1.3 58.2 + - - +
126E LEU* 3.2 8.9 + - + +
127E HIS* 2.8 44.9 + - + +
162E ARG* 3.1 38.4 - - + +
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Residues in contact with ALA 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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93E PRO* 3.7 25.5 - - + +
120E GLU 3.0 13.0 + - - +
121E LEU* 3.3 9.9 - - - +
123E LEU* 1.3 74.7 - - - +
125E VAL* 1.3 64.3 + - - +
127E HIS* 3.5 6.5 + - - +
128E ALA* 3.0 23.0 + - - +
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Residues in contact with VAL 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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93E PRO* 3.7 27.1 - - + -
96E ILE* 3.9 28.9 - - + -
97E ALA* 3.8 16.2 - - - +
100E LEU* 4.0 1.6 - - + -
114E TYR* 4.0 14.8 - - + +
115E LEU* 3.8 20.0 - - + -
121E LEU* 2.9 29.2 + - + +
122E ASN* 3.6 9.0 - - - +
124E ALA* 1.3 73.3 - - - +
126E LEU* 1.3 54.5 + - - +
128E ALA 3.1 1.7 + - - -
129E PHE* 2.7 36.9 + - - +
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Residues in contact with LEU 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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115E LEU* 3.9 42.0 - - + +
122E ASN 2.8 18.0 + - - +
123E LEU* 3.5 9.2 - - + +
124E ALA 3.2 0.4 - - - -
125E VAL* 1.3 75.4 - - - +
127E HIS* 1.3 61.5 + - + +
129E PHE* 3.2 3.2 + - + +
130E VAL* 2.8 46.3 + - + +
147E PHE* 4.6 8.5 - - + -
162E ARG* 4.3 24.2 - - + +
163E MET* 4.2 27.1 - - + -
166E ALA* 4.2 19.5 - - + -
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Residues in contact with HIS 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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123E LEU* 2.8 39.7 + - + +
124E ALA* 3.9 6.3 - - - +
125E VAL 3.3 0.2 - - - -
126E LEU* 1.3 82.9 - - + +
128E ALA* 1.3 54.9 + - - +
130E VAL* 3.3 7.8 + - - +
131E ASP* 2.9 36.9 + - - +
162E ARG* 5.9 3.2 - - - +
166E ALA* 3.9 25.8 + - + +
169E GLN* 3.9 30.5 + - - -
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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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93E PRO* 4.0 11.9 - - + +
94E GLU* 4.0 20.6 - - + +
97E ALA* 3.8 14.4 - - + -
124E ALA 3.0 16.6 + - - +
125E VAL 3.8 3.4 - - - +
127E HIS* 1.3 74.6 - - - +
129E PHE* 1.3 61.0 + - - +
131E ASP* 3.2 24.5 + - + +
132E LEU* 3.4 15.6 + - - +
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Residues in contact with PHE 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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97E ALA* 3.6 25.3 - - + +
100E LEU* 3.9 14.6 - - + -
101E TYR* 3.8 28.9 - + + -
111E ILE* 4.3 4.0 - - + -
115E LEU* 3.6 33.7 - - + -
125E VAL 2.7 18.5 + - - +
126E LEU* 3.4 7.6 - - + +
128E ALA* 1.3 74.3 - - - +
130E VAL* 1.3 66.7 + - + +
132E LEU* 3.2 13.7 + - - +
133E HIS* 3.0 32.7 + + - -
147E PHE* 4.4 7.9 - + - -
150E SER* 3.7 29.6 - - - -
151E PHE* 3.9 14.4 - + - -
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Residues in contact with VAL 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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126E LEU* 2.8 22.3 + - + +
127E HIS* 3.3 8.9 + - - +
129E PHE* 1.3 76.7 - - - +
131E ASP* 1.3 62.1 + - - +
132E LEU 3.0 1.6 + - - -
133E HIS* 3.1 25.3 + - - +
135E PHE* 4.4 6.1 - - + -
147E PHE* 3.7 28.5 - - + -
166E ALA* 3.7 34.1 - - + +
167E PHE* 4.0 7.0 - - - -
170E ARG* 3.4 32.6 - - + +
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Residues in contact with ASP 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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127E HIS* 2.9 20.3 + - - +
128E ALA* 3.3 18.5 - - - +
129E PHE 3.1 0.6 - - - -
130E VAL* 1.3 77.1 - - - +
132E LEU* 1.3 57.4 + - + +
133E HIS 3.2 0.7 - - - -
170E ARG* 2.9 47.3 + - - +
173E LEU* 5.9 1.0 - - - +
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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