Contacts of the helix formed by residues 118 - 129 (chain A) in PDB entry 5G49
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 THR 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A ARG* 4.2 7.0 - - - +
116A THR* 3.8 15.5 - - + +
117A ILE* 1.3 77.1 - - - +
119A ALA* 1.3 64.4 + - - +
120A GLU* 3.2 15.7 + - - +
121A ASP* 2.8 47.1 + - - +
122A VAL* 3.1 18.5 + - - +
90B SER* 4.1 8.3 - - - -
93B ALA* 4.5 1.8 - - - -
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A THR* 1.3 73.4 - - - +
120A GLU* 1.3 63.8 + - - +
122A VAL* 3.1 7.8 + - - +
123A LEU* 3.1 25.8 + - - +
142A LEU* 3.8 24.0 - - + -
146A ARG* 3.9 8.7 - - - +
90B SER* 4.6 3.6 + - - -
92B GLU* 3.8 26.3 + - + -
93B ALA* 4.5 13.5 - - - +
96B VAL* 4.0 12.0 - - + +
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ARG* 4.8 2.5 - - - +
118A THR* 3.1 12.6 + - - +
119A ALA* 1.3 79.1 + - - +
121A ASP* 1.3 58.4 + - - +
123A LEU* 3.2 10.3 + - + +
124A TRP* 2.9 30.9 + - - +
142A LEU* 4.1 6.7 - - - +
143A HIS* 5.4 2.3 + - - -
146A ARG* 3.0 40.7 + - - -
92B GLU* 4.8 0.2 - - - +
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Residues in contact with ASP 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ALA* 3.6 20.3 - - + +
108A ARG* 3.1 20.9 + - - +
109A CYS* 3.5 11.6 - - - -
114A ARG* 2.7 45.4 + - - -
116A THR 3.5 0.2 - - - +
117A ILE* 4.2 2.7 - - + -
118A THR* 2.8 39.7 + - - +
120A GLU* 1.3 75.5 - - - +
122A VAL* 1.3 58.1 + - - +
124A TRP* 3.6 3.2 + - + +
125A ALA* 2.9 30.5 + - - +
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Residues in contact with VAL 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ILE* 4.1 16.8 - - + -
102A THR* 6.3 0.7 - - - -
105A ALA* 4.6 6.7 - - + -
117A ILE* 4.2 10.8 - - + -
118A THR 3.1 14.4 + - - +
119A ALA* 3.1 8.5 + - - +
121A ASP* 1.3 77.0 - - - +
123A LEU* 1.3 58.4 + - - +
125A ALA* 3.2 3.8 + - - +
126A MET* 2.9 36.0 + - - +
80B MET* 5.3 0.7 - - + -
93B ALA* 4.0 22.2 - - + -
96B VAL* 3.8 25.6 - - + -
97B PHE* 4.2 22.7 - - + -
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Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ALA 3.1 13.1 + - - +
120A GLU* 4.0 10.5 - - + +
122A VAL* 1.3 71.3 - - - +
124A TRP* 1.3 67.1 + - - +
126A MET* 3.3 7.8 + - - +
127A SER* 2.9 25.3 + - - -
135A ILE* 4.0 14.9 - - + +
138A LEU* 3.7 34.5 - - + -
139A THR* 3.9 27.1 - - + +
142A LEU* 3.7 30.1 - - + -
96B VAL* 4.1 17.3 - - + -
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Residues in contact with TRP 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A GLU* 3.7 45.8 - - + -
105A ALA* 4.5 1.8 - - - -
108A ARG* 3.3 65.0 - - + +
111A ARG* 4.1 10.8 - - - -
120A GLU 2.9 17.6 + - - +
121A ASP* 3.7 5.2 - - - +
123A LEU* 1.3 75.5 - - - +
125A ALA* 1.3 77.9 + - + +
127A SER* 3.3 7.7 + - - -
128A LYS* 2.8 57.3 + - + +
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Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ILE* 3.7 14.1 - - + +
104A GLU* 3.7 12.8 - - + -
105A ALA* 3.7 26.5 - - + +
121A ASP 2.9 18.4 + - - +
122A VAL 3.2 3.1 + - - +
124A TRP* 1.3 84.1 - - + +
126A MET* 1.3 68.0 + - - +
128A LYS* 3.2 1.6 + - - +
129A LEU* 2.9 31.2 + - - +
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Residues in contact with MET 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A TYR* 3.1 27.1 - - - +
101A ILE* 3.7 27.1 - - + -
122A VAL* 2.9 35.3 + - - +
123A LEU* 3.7 7.4 - - - +
125A ALA* 1.3 75.0 - - - +
127A SER* 1.3 61.9 + - - +
129A LEU* 3.4 0.7 + - - -
130A GLY 3.2 4.9 + - - -
131A PHE* 2.9 41.6 + - + -
134A TYR* 3.8 18.6 - - + -
135A ILE* 3.8 11.2 - - + -
138A LEU* 3.5 34.3 - - + -
96B VAL* 4.8 1.3 - - - -
97B PHE* 5.5 0.4 - - - -
100B ALA* 4.0 6.7 - - + -
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Residues in contact with SER 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU 2.9 17.7 + - - -
124A TRP* 3.6 7.2 - - - -
126A MET* 1.3 75.4 - - - +
128A LYS* 1.3 64.7 + - - +
130A GLY* 3.1 12.9 + - - +
131A PHE 4.6 1.8 - - - +
132A ASP* 4.2 11.0 + - - +
135A ILE* 3.7 22.3 - - - +
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Residues in contact with LYS 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A GLU* 3.4 26.7 - - - +
124A TRP* 2.8 53.1 + - + +
125A ALA* 3.2 5.4 + - - +
127A SER* 1.3 73.5 - - - +
129A LEU* 1.3 60.2 + - + +
130A GLY* 3.5 0.9 + - - -
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Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A PHE* 3.8 49.1 - - + +
101A ILE* 4.1 15.0 - - + -
104A GLU* 3.7 43.3 - - + +
125A ALA 2.9 20.7 + - - +
126A MET 3.9 3.1 - - - +
127A SER 3.1 0.2 - - - -
128A LYS* 1.3 79.5 - - + +
130A GLY* 1.3 58.4 + - - +
131A PHE* 3.6 17.0 + - + -
138B ILE* 4.8 7.4 - - - +
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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