Contacts of the helix formed by residues 148 - 159 (chain A) in PDB entry 1GOT
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 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A SER* 3.6 21.2 + - - -
80A ILE* 5.0 0.2 - - + -
136A PHE* 4.2 5.2 - - + -
144A LEU* 3.7 33.7 - - + -
145A ASN* 3.3 17.4 + - - +
146A ASP 3.3 2.0 - - - -
147A SER* 1.3 76.6 - - - +
149A GLY* 1.3 63.7 + - - +
151A TYR* 4.1 1.1 - - - +
152A LEU* 3.0 35.6 + - + +
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Residues in contact with GLY 149 (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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127A TRP* 3.9 22.7 - - - -
136A PHE* 3.8 16.0 - - - -
146A ASP 4.8 2.2 + - - -
147A SER 3.4 0.2 - - - -
148A ALA* 1.3 78.3 - - - +
150A TYR* 1.3 57.5 + - - +
153A SER* 2.8 38.5 + - - -
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Residues in contact with TYR 150 (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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146A ASP 5.3 0.6 + - - -
147A SER* 3.2 12.8 + - - +
149A GLY* 1.3 78.0 - - - +
151A TYR* 1.3 90.5 + + - +
153A SER* 4.1 2.7 - - - -
154A ASP* 3.6 18.8 + - + +
157A ARG* 3.9 10.9 + - - -
158A LEU* 5.9 0.2 - - + -
166A THR* 4.4 0.9 + - - -
168A GLN* 3.2 37.7 - - + +
169A ASP* 2.8 28.5 + - - -
172A ARG* 3.4 51.6 - - + +
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Residues in contact with TYR 151 (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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69A ILE* 3.6 28.0 - - + +
72A ASN* 4.0 26.0 - - + -
73A THR* 3.2 30.3 - - + +
76A SER* 5.4 1.3 - - - -
147A SER* 3.0 25.6 + - - +
148A ALA* 4.3 1.3 - - - +
150A TYR* 1.3 100.8 - + - +
152A LEU* 1.3 66.8 + - + +
154A ASP* 3.0 14.4 + - - -
155A LEU* 3.0 14.4 + - - +
158A LEU* 3.8 13.3 - - + +
169A ASP* 2.6 32.1 + - + -
172A ARG* 3.0 18.3 - - + -
173A SER* 2.9 21.7 + - - -
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Residues in contact with LEU 152 (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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73A THR* 3.7 29.2 - - + +
76A SER* 4.2 12.8 - - - -
77A ILE* 4.1 11.0 - - + +
80A ILE* 4.0 18.8 - - + -
123A ILE* 3.4 33.0 - - + -
124A GLN* 5.9 0.9 - - - +
127A TRP* 3.6 50.3 - - + +
128A LYS* 5.0 2.1 + - - -
148A ALA 3.0 25.1 + - - +
149A GLY 4.3 0.2 - - - +
151A TYR* 1.3 77.0 - - + +
153A SER* 1.3 61.3 + - - +
154A ASP 3.3 0.7 + - - -
155A LEU* 3.6 15.9 + - + +
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Residues in contact with SER 153 (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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127A TRP* 3.2 29.0 + - - +
149A GLY* 2.8 22.7 + - - -
150A TYR* 4.1 4.0 - - - -
152A LEU* 1.3 76.2 - - - +
154A ASP* 1.3 60.8 + - - +
155A LEU 3.6 0.4 - - - -
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Residues in contact with ASP 154 (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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150A TYR* 3.6 14.6 + - + +
151A TYR* 3.0 6.9 + - - +
153A SER* 1.3 80.5 - - - +
155A LEU* 1.3 64.4 + - - +
156A GLU* 3.3 4.1 - - - +
157A ARG* 2.8 60.1 + - - +
158A LEU* 3.4 13.4 + - + +
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A TYR* 5.7 1.3 - - + -
73A THR* 4.0 21.5 - - + -
115A MSE 4.5 9.6 - - + -
120A SER* 3.9 14.1 - - - +
123A ILE* 3.5 41.1 - - + -
124A GLN* 3.7 24.7 - - + +
151A TYR 3.0 7.4 + - - +
152A LEU* 3.6 15.0 + - + +
153A SER 3.6 1.8 - - - -
154A ASP* 1.3 77.6 - - - +
156A GLU* 1.3 62.3 + - - +
158A LEU* 3.2 14.1 + - + -
159A VAL* 3.1 38.7 + - + +
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Residues in contact with GLU 156 (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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124A GLN* 2.9 36.4 + - - +
154A ASP* 3.3 1.5 - - - +
155A LEU* 1.3 76.3 - - - +
157A ARG* 1.3 62.9 + - - +
159A VAL* 3.1 14.5 + - - +
160A THR* 2.8 36.0 + - - +
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Residues in contact with ARG 157 (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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150A TYR* 3.9 10.9 + - - -
154A ASP* 2.8 49.4 + - - +
156A GLU* 1.3 76.8 - - - +
158A LEU* 1.3 72.7 + - - +
159A VAL 3.2 1.0 + - - -
160A THR* 3.2 20.6 + - - -
163A TYR* 3.5 23.9 - - + +
164A VAL 5.2 0.2 + - - -
166A THR* 4.2 14.8 + - - +
169A ASP* 2.9 41.6 + - - -
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Residues in contact with LEU 158 (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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69A ILE* 4.0 12.6 - - + -
70A TYR* 2.7 37.0 + - + -
73A THR* 4.0 9.9 - - - +
150A TYR* 5.9 0.2 - - + -
151A TYR* 3.8 39.9 - - + +
154A ASP* 3.4 15.5 - - + +
155A LEU* 3.2 18.1 + - + +
157A ARG* 1.3 96.7 - - - +
159A VAL* 1.3 53.9 + - - +
163A TYR* 3.0 48.2 - - + +
169A ASP* 4.2 4.9 - - - +
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Residues in contact with VAL 159 (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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70A TYR* 3.9 12.1 - - + +
115A MSE 3.5 36.6 - - + +
117A LYS* 6.4 0.2 - - - -
120A SER* 4.1 21.8 - - - +
124A GLN* 4.6 4.0 - - - +
155A LEU* 3.1 21.7 + - + +
156A GLU* 3.1 19.3 + - - +
158A LEU* 1.3 80.5 - - - +
160A THR* 1.3 64.8 + - - +
161A PRO* 3.4 8.3 - - - +
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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