Contacts of the helix formed by residues 117 - 131 (chain e) in PDB entry 5OOM
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 ALA 117 (chain e).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87e HIS* 5.1 10.9 - - + +
90e ARG 4.0 12.7 + - - +
91e ALA* 3.8 29.8 - - + -
95e ASN* 5.8 2.5 - - - +
116e LEU* 1.3 74.3 - - - +
118e GLN* 1.3 63.8 + - + +
120e LEU* 3.3 12.6 + - + +
121e GLU* 2.9 37.9 + - - +
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Residues in contact with GLN 118 (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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95e ASN* 5.2 12.5 + - - +
116e LEU* 3.3 22.7 - - + +
117e ALA* 1.3 78.2 - - + +
119e ASP* 1.3 58.4 + - - +
121e GLU* 3.9 10.1 - - - +
122e ASP* 2.9 41.1 + - - +
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Residues in contact with ASP 119 (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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116e LEU* 3.3 39.8 + - + +
117e ALA 3.3 0.4 - - - -
118e GLN* 1.3 78.8 - - - +
120e LEU* 1.3 60.5 + - + +
122e ASP* 3.9 7.5 - - - +
123e MET* 2.9 44.0 + - + +
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Residues in contact with LEU 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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87e HIS* 5.1 7.6 - - + +
90e ARG* 6.6 0.4 - - + -
116e LEU 3.1 23.1 + - - +
117e ALA* 3.3 14.6 + - + +
119e ASP* 1.3 78.3 - - + +
121e GLU* 1.3 57.3 + - - +
123e MET* 3.9 11.0 - - + +
124e TRP* 3.0 67.4 + - + -
70m GLU* 6.4 1.1 - - + -
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Residues in contact with GLU 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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87e HIS* 4.0 23.9 + - + +
88e GLU* 5.0 4.7 - - - +
117e ALA* 2.9 24.5 + - - +
118e GLN* 4.0 10.6 - - - +
120e LEU* 1.3 77.1 - - - +
122e ASP* 1.3 60.0 + - - +
124e TRP* 3.7 11.3 - - + +
125e GLU* 2.8 42.8 + - + +
71m PRO* 5.5 6.6 - - + +
73m ARG* 5.2 0.3 + - - -
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Residues in contact with ASP 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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118e GLN* 2.9 31.7 + - - +
119e ASP* 3.9 9.0 - - - +
120e LEU 3.3 0.2 - - - -
121e GLU* 1.3 75.5 - - - +
123e MET* 1.3 59.4 + - + +
125e GLU* 3.3 20.4 + - - +
126e GLN* 2.9 34.1 + - - +
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Residues in contact with MET 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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119e ASP* 2.9 26.9 + - + +
120e LEU* 4.0 12.1 - - + +
122e ASP* 1.3 73.4 - - + +
124e TRP* 1.3 64.0 + - + +
126e GLN* 3.4 22.6 - - - +
127e LYS* 2.9 67.9 + - + +
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Residues in contact with TRP 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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87e HIS* 3.5 24.9 - + - -
120e LEU* 3.0 55.7 + - + +
121e GLU* 3.8 10.1 - - + +
123e MET* 1.3 80.1 - - + +
125e GLU* 1.3 58.2 + - - +
127e LYS* 3.8 11.2 - - + +
128e PHE* 2.9 29.1 + - - +
70m GLU* 3.2 33.2 - - + -
71m PRO 3.2 19.1 - - - +
72m ARG* 3.4 38.7 - - + +
73m ARG* 3.3 23.2 - - + +
74m MET 5.7 2.7 - - - -
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Residues in contact with GLU 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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121e GLU* 2.8 26.5 + - + +
122e ASP* 3.3 23.9 - - - +
123e MET 3.3 0.2 - - - -
124e TRP* 1.3 76.1 - - - +
126e GLN* 1.3 59.1 + - - +
128e PHE* 3.2 5.4 + - - +
129e LEU* 2.9 34.5 + - + +
73m ARG* 3.4 42.6 + - - +
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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 ASP* 2.9 19.9 + - - +
123e MET* 3.4 31.1 - - - +
125e GLU* 1.3 77.3 - - - +
127e LYS* 1.3 63.6 + - + +
129e LEU* 2.9 18.6 + - + +
130e GLN* 2.9 40.3 + - - +
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Residues in contact with LYS 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 MET* 2.9 53.6 + - + +
124e TRP* 4.2 11.8 - - + +
126e GLN* 1.3 77.4 - - + +
128e PHE* 1.3 63.8 + - - +
130e GLN* 3.3 40.6 + - - +
131e PHE* 3.7 9.5 + - - +
74m MET* 4.7 9.8 - - + +
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Residues in contact with PHE 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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124e TRP 2.9 20.6 + - - +
125e GLU 3.2 6.7 + - - +
127e LYS* 1.3 77.9 - - - +
129e LEU* 1.3 70.5 + - + +
130e GLN 3.5 0.2 + - - -
131e PHE 3.7 14.4 - - - +
133e LEU* 5.6 11.9 - - + -
55m LEU* 3.9 26.5 - - + -
73m ARG* 3.4 52.2 - - + +
74m MET* 3.9 12.7 - - + +
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Residues in contact with LEU 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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125e GLU* 2.9 21.0 + - + +
126e GLN* 2.9 19.8 + - + +
128e PHE* 1.3 87.1 - - + +
130e GLN* 1.3 63.7 + - - +
131e PHE 4.9 1.5 - - - -
132e LYS* 5.1 5.4 + - - +
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Residues in contact with GLN 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 GLN* 2.9 22.4 + - - +
127e LYS* 3.4 40.4 - - - +
128e PHE 3.3 1.0 - - - -
129e LEU* 1.3 79.8 - - - +
131e PHE* 1.3 65.8 + - - +
132e LYS* 3.2 11.1 + - - +
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Residues in contact with PHE 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 LYS 3.7 9.1 + - - +
128e PHE 3.7 13.3 - - - +
129e LEU 4.9 0.7 - - - -
130e GLN* 1.3 77.0 - - + +
132e LYS* 1.3 84.9 + - - +
133e LEU* 3.8 10.4 + - + +
134e GLY 5.1 3.1 - - - -
57m VAL* 4.7 3.8 - - + -
61m GLY* 4.1 29.4 - - - -
63m THR* 4.6 14.1 - - + -
74m MET* 4.2 28.4 - - + +
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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