Contacts of the helix formed by residues 139 - 150 (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 ASP 139 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A GLN* 5.6 5.4 - - - +
235A ALA* 3.3 27.5 - - + +
236A GLU* 4.3 2.5 - - - +
138D ILE* 1.3 78.7 - - - +
140D PHE* 1.3 63.8 + - - +
141D ARG* 3.8 17.3 + - - +
142D THR* 2.5 32.3 + - - -
143D ARG* 3.1 20.2 + - - +
164D VAL* 5.6 1.4 - - - +
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Residues in contact with PHE 140 (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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235A ALA 2.9 19.0 + - - +
236A GLU* 3.8 15.8 - - - +
237A ASP* 3.9 14.8 - - - +
238A GLU* 4.0 27.8 - - + +
239A GLU* 5.9 5.6 - - + -
139D ASP* 1.3 71.1 - - - +
141D ARG* 1.3 68.8 + - + +
143D ARG* 3.1 34.3 + - - +
144D GLU* 2.8 66.8 + - + +
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Residues in contact with ARG 141 (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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90A ARG* 6.3 2.5 - - - +
139D ASP* 3.4 14.0 + - - +
140D PHE* 1.3 87.1 - - + +
142D THR* 1.3 57.4 + - - +
144D GLU* 3.6 4.8 + - - +
145D SER* 3.1 29.8 + - - -
160D GLU* 6.0 0.4 - - - -
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Residues in contact with THR 142 (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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138D ILE* 4.0 23.1 - - + -
139D ASP* 2.5 26.6 + - - -
141D ARG* 1.3 74.8 - - - +
143D ARG* 1.3 60.9 + - - +
145D SER* 3.5 5.9 + - - -
146D THR* 2.9 33.7 + - - +
160D GLU* 4.4 15.5 + - + +
161D ALA* 4.0 26.5 - - + +
164D VAL* 4.6 14.1 - - + +
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Residues in contact with ARG 143 (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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236A GLU* 3.0 29.9 + - - +
237A ASP* 5.7 1.6 - - - +
124D TYR* 4.5 8.1 + - - +
128D VAL* 3.4 34.8 - - + +
129D HIS* 4.9 0.4 - - - +
130D SER* 3.8 29.4 + - - +
135D GLN* 4.9 10.8 - - - +
138D ILE* 4.0 19.4 + - + +
139D ASP 3.1 17.5 + - - +
140D PHE* 3.1 35.0 + - - +
142D THR* 1.3 76.8 - - - +
144D GLU* 1.3 66.4 + - - +
146D THR* 3.6 4.4 + - - -
147D ALA* 3.0 27.9 + - - +
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Residues in contact with GLU 144 (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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140D PHE* 2.8 59.6 + - + +
141D ARG* 3.8 6.3 - - - +
143D ARG* 1.3 82.8 + - + +
145D SER* 1.3 60.5 + - - +
147D ALA* 3.2 12.7 + - - +
148D LYS* 3.1 34.2 + - + +
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Residues in contact with SER 145 (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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141D ARG 3.1 14.8 + - - -
142D THR 3.5 6.1 + - - -
144D GLU* 1.3 76.4 - - - +
146D THR* 1.3 66.0 + - - +
148D LYS* 3.7 8.1 + - - +
149D LYS* 3.2 38.0 + - - +
160D GLU* 2.6 35.1 + - - -
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Residues in contact with THR 146 (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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124D TYR* 4.3 4.5 - - + -
128D VAL* 4.3 18.6 - - + +
138D ILE* 5.2 0.2 - - - +
142D THR* 2.9 23.7 + - - +
143D ARG* 3.8 5.1 - - - -
144D GLU 3.2 0.2 - - - -
145D SER* 1.3 76.7 + - - +
147D ALA* 1.3 65.6 + - - +
149D LYS* 3.0 20.1 + - - +
150D ILE* 3.3 12.7 + - + +
157D CYS* 4.9 7.4 + - - +
158D PHE* 3.6 37.4 - - + -
160D GLU* 5.1 2.9 - - - +
161D ALA* 4.1 18.4 + - + +
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Residues in contact with ALA 147 (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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124D TYR* 3.5 30.7 - - + +
143D ARG 3.0 18.8 + - - +
144D GLU* 3.2 17.2 + - - +
146D THR* 1.3 77.5 - - - +
148D LYS* 1.3 62.0 + - + +
149D LYS 3.3 0.7 + - - -
150D ILE* 3.3 16.2 + - - +
151D LYS* 4.3 2.6 + - - +
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Residues in contact with LYS 148 (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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144D GLU* 3.1 19.2 + - + +
145D SER* 4.0 8.5 - - - +
146D THR 3.3 0.4 - - - -
147D ALA* 1.3 76.8 - - + +
149D LYS* 1.3 62.6 + - + +
150D ILE 3.6 0.5 + - - -
151D LYS* 3.9 15.1 + - - +
152D ALA 4.8 0.9 + - - -
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Residues in contact with LYS 149 (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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145D SER* 3.2 26.0 - - - +
146D THR* 3.0 9.6 + - - +
148D LYS* 1.3 76.0 - - + +
150D ILE* 1.3 63.4 + - - +
151D LYS 3.2 3.2 + - - -
152D ALA 3.5 5.6 - - - +
153D PRO* 3.2 25.8 - - - +
156D THR 5.8 0.2 - - - +
157D CYS* 3.7 36.5 - - + +
160D GLU* 3.7 24.6 + - + +
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Residues in contact with ILE 150 (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* 4.8 4.3 - - - +
120D ALA* 3.7 10.2 - - + +
121D GLU* 4.1 34.3 - - + +
124D TYR* 3.8 26.5 - - + -
146D THR 3.3 13.0 - - - +
147D ALA* 3.3 11.1 + - - +
149D LYS* 1.3 76.3 - - - +
151D LYS* 1.3 65.7 + - - +
153D PRO* 3.4 16.6 - - - +
157D CYS* 3.9 10.1 - - - -
158D PHE* 3.4 38.6 - - + -
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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