Contacts of the helix formed by residues 130 - 141 (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 SER 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A GLY* 3.5 17.2 - - - -
128A LYS 3.6 3.0 + - - -
129A ASP* 1.3 71.6 + - - +
131A GLY* 1.3 62.4 + - - +
133A GLN* 3.7 8.2 - - - +
134A ALA* 2.8 29.5 + - - +
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Residues in contact with GLY 131 (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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84A MSE 3.7 10.3 - - - +
89A ILE* 3.8 6.0 - - - +
90A GLN 3.5 23.3 - - - -
92A GLY 3.8 1.7 - - - +
129A ASP* 2.9 10.7 + - - -
130A SER* 1.3 77.5 + - - +
132A ILE* 1.3 60.3 + - - +
134A ALA* 3.0 5.6 + - - +
135A CYS* 2.8 29.6 + - - +
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Residues in contact with ILE 132 (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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77A ILE* 4.8 4.9 - - + -
80A ILE* 3.9 20.2 - - + +
81A VAL* 4.4 11.9 - - + -
84A MSE 3.9 19.4 - - + -
91A TYR* 3.7 30.7 - - + -
126A LEU* 3.2 45.8 - - + +
127A TRP* 4.2 21.5 - - + +
129A ASP* 3.3 10.2 + - + +
131A GLY* 1.3 74.0 - - - +
133A GLN* 1.3 52.9 + - - +
135A CYS* 3.1 4.2 + - - +
136A PHE* 2.7 33.1 + - - +
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Residues in contact with GLN 133 (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* 2.8 62.2 + - - +
128A LYS 4.9 2.9 - - - +
129A ASP 2.9 21.0 + - - +
130A SER* 3.7 8.5 - - - +
131A GLY 3.3 0.2 - - - -
132A ILE* 1.3 77.4 - - - +
134A ALA* 1.3 60.3 + - - +
136A PHE* 3.5 19.3 + - - +
137A ASP* 3.1 34.9 + - - +
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Residues in contact with ALA 134 (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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89A ILE* 4.6 12.8 - - + -
130A SER 2.8 18.4 + - - +
131A GLY* 3.0 7.6 + - - +
133A GLN* 1.3 75.9 - - - +
135A CYS* 1.3 62.4 + - - +
137A ASP* 3.4 17.1 + - - +
138A ARG* 3.4 20.4 + - - +
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Residues in contact with CYS 135 (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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80A ILE* 3.5 16.4 - - + -
83A ALA* 3.4 43.1 - - - -
84A MSE 3.6 14.8 - - - -
87A LEU* 4.3 1.6 - - - -
89A ILE* 3.8 17.6 - - + +
131A GLY 2.8 12.6 + - - +
132A ILE 3.4 7.6 - - - +
134A ALA* 1.3 75.0 - - - +
136A PHE* 1.3 64.9 + - - +
138A ARG* 2.9 12.6 + - - +
142A TYR* 2.8 25.8 + - - -
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Residues in contact with PHE 136 (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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80A ILE* 3.8 26.6 - - + +
127A TRP* 3.9 18.6 - + + -
132A ILE 2.7 20.5 + - - +
133A GLN* 3.6 19.3 - - - +
134A ALA 3.4 0.2 - - - -
135A CYS* 1.3 72.5 - - - +
137A ASP* 1.3 77.7 + - - +
138A ARG 3.1 1.0 + - - -
139A ALA* 3.1 22.3 + - + +
142A TYR* 3.4 8.3 - - - -
144A LEU* 3.9 15.0 - - + -
148A ALA* 4.2 1.8 - - + -
149A GLY* 3.8 35.0 - - - -
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Residues in contact with ASP 137 (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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133A GLN* 3.1 20.9 + - - +
134A ALA* 3.6 11.5 - - - +
135A CYS 3.2 0.4 - - - -
136A PHE* 1.3 93.5 - - - +
138A ARG* 1.3 59.5 + - + +
139A ALA* 3.3 3.3 + - - +
276A LYS* 4.4 22.6 + - + +
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Residues in contact with ARG 138 (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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87A LEU* 3.8 29.0 + - + +
89A ILE* 3.3 32.7 - - - +
134A ALA* 3.7 14.4 - - - +
135A CYS 2.9 14.0 + - - +
137A ASP* 1.3 80.7 - - + +
139A ALA* 1.3 62.8 + - - +
140A SER* 3.2 4.9 - - - -
141A GLU* 3.0 52.5 + - - +
142A TYR* 3.1 11.3 - - - -
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Residues in contact with ALA 139 (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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136A PHE* 3.1 15.7 + - + +
137A ASP 3.3 3.4 + - - +
138A ARG* 1.3 77.2 - - - +
140A SER* 1.3 55.0 + - - +
142A TYR* 2.7 47.4 + - - +
144A LEU* 3.7 30.7 + - + -
228A LEU* 4.8 2.7 - - + +
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Residues in contact with SER 140 (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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138A ARG* 4.8 2.7 - - - -
139A ALA* 1.3 77.4 - - - +
141A GLU* 1.3 62.9 + - - +
142A TYR 3.3 3.9 + - - +
143A GLN* 5.8 0.5 + - - -
227A ASP* 3.1 35.2 + - - +
228A LEU* 3.5 23.3 - - - +
229A VAL* 5.1 6.2 + - - +
273A LYS* 3.8 4.9 + - - -
276A LYS* 3.0 28.5 + - - +
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Residues in contact with GLU 141 (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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87A LEU* 3.7 21.7 - - + +
138A ARG* 3.0 62.2 + - - +
139A ALA 3.0 1.6 + - - -
140A SER* 1.3 80.5 - - - +
142A TYR* 1.3 59.8 + - - +
229A VAL* 6.5 0.9 - - - -
234A GLU* 5.1 4.2 - - - +
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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