Contacts of the helix formed by residues 126 - 136 (chain E) in PDB entry 3GUT
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 126 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87E PRO* 3.7 10.5 - - + -
121E VAL* 3.6 25.8 - - + -
122E LYS 3.3 5.6 + - - +
123E LYS* 3.9 27.6 - - + +
124E ARG 3.1 3.8 + - - +
125E ASP* 1.3 76.1 - - - +
127E GLU* 1.3 76.2 + - + +
128E GLN 3.3 0.2 - - - -
129E ALA* 3.1 12.4 + - - +
130E ILE* 3.1 36.3 + - + +
152E TYR* 4.4 9.2 - - + -
154E LEU* 3.7 26.9 - - + -
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Residues in contact with GLU 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E ARG 5.3 4.5 - - - +
125E ASP 3.7 0.2 - - - -
126E LEU* 1.3 84.7 - - + +
128E GLN* 1.3 57.1 + - - +
130E ILE* 3.4 16.9 + - - +
131E SER* 3.1 29.5 + - - -
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Residues in contact with GLN 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E ASP* 3.3 36.5 + - - +
126E LEU 3.3 0.6 - - - -
127E GLU* 1.3 76.5 - - - +
129E ALA* 1.3 60.4 + - - +
131E SER* 3.1 18.2 + - - +
132E GLN* 3.7 10.6 + - - +
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Residues in contact with ALA 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E PRO* 3.6 29.6 - - + +
89E GLU* 6.1 0.4 - - - +
121E VAL* 3.7 12.8 - - + -
125E ASP 3.6 13.5 + - - +
126E LEU 3.1 10.6 + - - +
128E GLN* 1.3 78.4 - - - +
130E ILE* 1.3 61.5 + - - +
131E SER 3.2 0.2 - - - -
132E GLN* 3.0 22.8 + - - +
133E ARG* 3.4 21.4 + - - +
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Residues in contact with ILE 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E PRO* 5.7 3.1 - - + +
87E PRO* 3.9 10.3 - - + -
126E LEU* 3.1 30.9 + - + +
127E GLU* 3.8 15.7 - - - +
129E ALA* 1.3 77.6 - - - +
131E SER* 1.3 60.0 + - - +
133E ARG* 3.1 21.4 + - + +
134E ILE* 3.2 15.5 + - + +
148E GLN* 4.3 17.3 - - + +
152E TYR* 3.1 45.1 - - + +
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Residues in contact with SER 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E GLU 3.1 15.3 + - - -
128E GLN* 3.1 21.7 + - - +
130E ILE* 1.3 76.9 - - - +
132E GLN* 1.3 56.9 + - - +
134E ILE* 3.5 10.2 + - - +
135E GLN* 3.1 29.0 + - - +
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Residues in contact with GLN 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E GLU* 3.6 19.5 + - - +
97E ASP* 3.5 32.3 + - - +
128E GLN 4.0 9.7 - - - +
129E ALA* 3.0 12.0 + - - +
131E SER* 1.3 79.1 + - - +
133E ARG* 1.3 79.1 + - - +
134E ILE 3.3 0.2 - - - -
135E GLN* 3.4 23.9 - - + +
136E THR* 2.8 31.1 + - + +
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Residues in contact with ARG 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E PRO* 3.9 29.2 - - + +
86E HIS 3.1 26.2 + - - +
87E PRO* 3.0 22.4 + - + -
88E HIS 3.7 3.3 + - - -
89E GLU* 3.2 29.8 + - - +
97E ASP 2.8 27.9 + - - -
98E GLY* 4.2 2.4 - - - -
129E ALA* 3.5 22.7 + - - +
130E ILE* 3.1 14.8 + - + +
132E GLN* 1.3 100.4 + - - +
134E ILE* 1.3 64.3 + - + +
136E THR* 4.0 4.0 - - - +
137E ASN 3.3 2.9 + - - -
138E ASN* 2.8 50.8 + - - +
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Residues in contact with ILE 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E PRO* 4.9 6.3 - - + -
130E ILE* 3.2 23.6 - - + +
131E SER* 3.6 10.3 - - - +
133E ARG* 1.3 84.2 - - + +
135E GLN* 1.3 61.8 + - - +
137E ASN* 3.2 23.0 + - - -
138E ASN 5.6 0.4 - - - +
139E ASN* 5.8 4.3 - - + -
145E ILE* 4.4 20.0 - - + -
148E GLN* 3.0 37.5 - - - +
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Residues in contact with GLN 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ASP* 4.5 4.5 + - - +
131E SER 3.1 21.3 + - - +
132E GLN* 3.4 29.6 - - - +
134E ILE* 1.3 76.8 - - - +
136E THR* 1.3 67.7 + - - +
137E ASN* 3.4 4.6 + - - -
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Residues in contact with THR 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E ARG* 4.6 1.4 + - - -
96E ARG* 3.8 8.8 + - - -
97E ASP* 2.8 46.6 + - + +
99E TYR* 3.8 11.8 + - + -
132E GLN* 2.8 24.2 - - - +
133E ARG* 3.7 8.1 - - - +
135E GLN* 1.3 84.9 + - - +
137E ASN* 1.3 72.9 + - - +
138E ASN* 3.8 15.5 - - + -
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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