Contacts of the helix formed by residues 115 - 128 (chain D) in PDB entry 2GTP
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 LEU 115 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111D THR* 4.4 12.1 - - + -
112D GLU* 2.9 11.6 + - + +
114D ASP* 1.3 77.3 - - + +
116D LEU* 1.3 61.7 + - - +
117D PRO* 3.4 3.4 - - - -
118D CYS* 3.4 10.3 + - + +
119D LYS* 3.2 23.4 + - + +
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Residues in contact with LEU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D TYR* 3.6 48.0 - - + +
111D THR* 3.7 24.2 - - + +
112D GLU 3.4 8.3 - - - +
113D SER* 3.5 24.9 - - - +
114D ASP 3.4 0.2 - - - -
115D LEU* 1.3 75.8 - - - +
117D PRO* 1.3 63.9 - - + +
119D LYS* 4.3 1.8 - - - -
120D ALA* 2.7 36.9 + - - +
153D PRO* 4.1 15.7 - - - +
155D PRO* 4.3 31.0 - - + -
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Residues in contact with PRO 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D SER 4.1 3.8 - - - +
114D ASP 3.5 13.5 - - - +
115D LEU 3.4 4.3 - - - -
116D LEU* 1.3 94.1 - - + +
118D CYS* 1.3 59.2 + - - +
120D ALA* 3.9 1.7 - - - +
121D GLU* 3.1 29.5 + - - +
150D ILE 4.8 3.6 - - - +
151D LYS 5.7 1.6 - - - +
153D PRO* 3.7 25.9 - - + +
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Residues in contact with CYS 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D LEU* 3.4 11.3 + - + +
116D LEU 3.2 0.6 - - - -
117D PRO* 1.3 77.9 - - - +
119D LYS* 1.3 61.6 + - - +
121D GLU* 3.4 5.5 + - - +
122D GLU* 2.9 32.1 + - - +
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Residues in contact with LYS 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ASP* 4.2 13.9 - - - +
108D TYR* 3.8 22.4 - - + -
111D THR* 3.8 28.7 - - + +
115D LEU* 3.2 15.5 + - + +
116D LEU* 3.9 3.1 - - - +
118D CYS* 1.3 78.3 - - - +
120D ALA* 1.3 63.1 + - - +
122D GLU* 3.4 18.3 + - - +
123D ILE* 3.1 36.7 + - + +
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Residues in contact with ALA 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D TYR* 3.6 17.5 - - + +
116D LEU 2.7 22.3 + - - +
117D PRO 3.9 1.6 - - - +
119D LYS* 1.3 74.2 - - - +
121D GLU* 1.3 57.1 + - - +
124D TYR* 2.9 29.8 + - - +
150D ILE* 3.7 17.9 - - + +
153D PRO* 3.8 25.1 - - + -
158D PHE* 3.4 13.4 - - + -
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Residues in contact with GLU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D PRO 3.1 17.0 + - - +
118D CYS* 3.4 7.2 + - - +
120D ALA* 1.3 77.7 - - - +
122D GLU* 1.3 58.1 + - - +
124D TYR* 3.4 5.7 + - + +
125D LYS* 3.0 31.2 + - + +
150D ILE* 4.1 20.9 - - + +
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Residues in contact with GLU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D CYS 2.9 19.3 + - - +
119D LYS* 3.5 20.3 - - - +
120D ALA 3.3 0.2 - - - -
121D GLU* 1.3 76.7 - - - +
123D ILE* 1.3 62.7 + - - +
125D LYS* 3.4 5.1 + - - +
126D ALA* 2.9 34.2 + - + +
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Residues in contact with ILE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D PHE* 3.7 28.7 - - + -
104D ALA* 3.6 36.1 - - + +
105D CYS* 4.7 1.1 - - - +
108D TYR* 3.7 25.1 - - + -
119D LYS* 3.1 24.9 + - + +
122D GLU* 1.3 78.8 - - + +
124D TYR* 1.3 67.2 + - - +
126D ALA* 4.5 0.9 - - - -
127D PHE* 2.9 37.0 + - + +
128D VAL 3.7 0.5 + - - -
158D PHE* 3.9 21.5 - - + -
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Residues in contact with TYR 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D ALA 2.9 17.7 + - - +
121D GLU* 3.5 8.7 - - + +
123D ILE* 1.3 77.9 - - - +
125D LYS* 1.3 59.8 + - + +
128D VAL* 2.9 45.9 + - + -
129D HIS* 2.9 66.7 + + + -
143D ARG* 4.5 7.9 + - - +
146D THR* 4.3 2.5 - - + -
147D ALA* 3.5 36.7 - - + +
150D ILE* 3.8 29.8 - - + -
158D PHE* 4.1 1.2 - - - -
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Residues in contact with LYS 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D GLU* 3.0 19.3 + - + +
122D GLU* 3.8 5.2 - - - +
124D TYR* 1.3 78.5 - - + +
126D ALA* 1.3 63.2 + - - +
129D HIS* 4.5 9.8 - - - +
132D ALA* 3.3 20.6 + - - +
133D ALA 4.7 0.2 + - - -
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Residues in contact with ALA 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D GLU* 2.9 22.0 + - + +
123D ILE* 4.5 0.4 - - - -
124D TYR 3.3 0.2 - - - -
125D LYS* 1.3 80.4 - - - +
127D PHE* 1.3 77.7 + - + +
132D ALA* 3.3 11.5 - - - +
133D ALA* 4.0 2.4 + - - +
134D LYS* 3.4 23.6 + - + +
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Residues in contact with PHE 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D GLU* 3.8 8.7 - - + -
100D GLU* 3.9 27.4 - - + -
101D PHE* 3.5 49.1 - + + -
104D ALA* 4.0 19.5 - - + -
123D ILE* 2.9 23.1 + - + +
126D ALA* 1.3 92.2 - - + +
128D VAL* 1.3 59.6 + - - +
132D ALA* 3.8 4.5 - - - -
134D LYS* 3.3 35.2 - - + +
135D GLN* 3.2 5.9 - - - -
136D ILE* 2.9 31.4 + - + +
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Residues in contact with VAL 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D PHE* 4.2 15.5 - - + -
123D ILE 4.1 3.1 - - - +
124D TYR* 2.9 53.5 + - + +
127D PHE* 1.3 74.2 - - - +
129D HIS* 1.3 67.2 + - - +
135D GLN* 4.3 5.4 - - - +
136D ILE* 4.4 11.1 - - + +
138D ILE* 4.3 13.1 - - + +
143D ARG* 3.4 29.8 - - + -
146D THR* 4.3 13.2 - - + -
158D PHE* 4.1 17.5 - - + -
161D ALA* 5.4 1.1 - - + -
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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