Contacts of the helix formed by residues 125 - 134 (chain E) in PDB entry 6QXT
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 THR 125 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123E GLU 4.3 0.4 + - - -
124E ILE* 1.3 76.5 - - - +
126E LEU* 1.3 61.5 + - - +
127E LEU* 3.2 9.6 - - - -
128E GLU* 3.2 16.5 + - - +
129E LEU* 2.9 26.7 + - - +
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Residues in contact with LEU 126 (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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84E VAL* 5.9 8.3 - - + -
87E LEU* 6.2 4.3 - - + -
97E ILE* 6.4 1.8 - - + -
125E THR* 1.3 73.2 - - - +
127E LEU* 1.3 57.8 + - - +
129E LEU* 3.1 9.8 + - - +
130E ILE* 2.9 28.1 + - - +
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Residues in contact with LEU 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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80E HIS* 6.2 4.9 - - + -
84E VAL* 5.9 4.1 - - - +
125E THR* 3.2 6.8 - - - -
126E LEU* 1.3 79.0 - - - +
128E GLU* 1.3 57.1 + - - +
130E ILE* 3.3 6.4 + - - +
131E LYS* 2.9 31.1 + - - +
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Residues in contact with GLU 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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124E ILE* 5.9 0.2 - - + -
125E THR* 3.2 23.2 + - - +
127E LEU* 1.3 79.3 - - - +
129E LEU* 1.3 57.6 + - - +
131E LYS* 4.2 5.5 - - - +
132E ALA* 2.9 30.0 + - - +
132H ALA* 4.1 28.5 - - + +
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Residues in contact with LEU 129 (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 THR 2.9 12.7 + - - +
126E LEU* 3.1 13.0 + - - +
128E GLU* 1.3 75.5 - - - +
130E ILE* 1.3 60.0 + - - +
132E ALA* 3.7 5.6 - - - +
133E LEU* 2.9 29.5 + - - +
104H ILE* 6.5 1.1 - - + -
124H ILE* 5.4 2.1 - - - +
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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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80E HIS* 5.0 18.6 - - + +
83E ILE* 5.9 6.1 - - + -
126E LEU 2.9 14.7 + - - +
127E LEU* 3.3 7.2 + - - +
129E LEU* 1.3 74.5 - - - +
131E LYS* 1.3 60.4 + - - +
133E LEU* 3.1 7.3 + - - +
134E GLY 3.0 22.7 + - - -
135E VAL* 3.5 20.6 + - + -
108H ILE* 6.3 2.7 - - + -
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Residues in contact with LYS 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 LEU 2.9 17.1 + - - +
128E GLU* 4.2 5.8 - - - +
130E ILE* 1.3 77.2 - - - +
132E ALA* 1.3 62.2 + - - +
134E GLY* 3.3 12.9 + - - +
135E VAL 5.4 0.4 - - - +
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Residues in contact with ALA 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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128E GLU 2.9 22.5 + - - +
129E LEU* 3.7 7.0 - - - +
130E ILE 3.2 0.2 - - - -
131E LYS* 1.3 79.1 - - - +
133E LEU* 1.3 56.3 + - - +
134E GLY 3.5 0.3 + - - -
502E CA 2.8 22.7 - - - -
123H GLU 3.5 3.0 - - - +
124H ILE* 4.5 9.7 - - + -
128H GLU* 4.3 31.6 - - + +
129H LEU* 6.0 0.7 - - - -
132H ALA* 5.1 3.8 - - + -
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Residues in contact with LEU 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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129E LEU 2.9 17.4 + - - +
130E ILE* 3.1 7.8 + - - +
132E ALA* 1.3 75.8 - - - +
134E GLY* 1.3 63.8 + - - +
135E VAL* 4.7 4.7 - - + +
502E CA 4.1 2.9 - - - -
108H ILE* 5.9 7.4 - - + -
121H TYR* 3.8 8.9 - - + +
122H ASP* 3.6 21.5 + - - +
123H GLU 3.7 17.0 + - - +
124H ILE* 4.8 8.5 - - + +
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Residues in contact with GLY 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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130E ILE 3.0 5.6 + - - -
131E LYS* 3.3 10.7 + - - -
132E ALA 3.2 4.4 - - - -
133E LEU* 1.3 80.3 - - - +
135E VAL* 1.3 66.3 + - - +
136E ARG* 3.3 7.7 + - - +
120H GLU 3.6 8.0 - - - +
121H TYR* 4.0 3.9 - - - -
122H ASP 5.0 0.2 + - - -
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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