Contacts of the helix formed by residues 125 - 134 (chain f) 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 f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123f GLU* 4.0 6.0 + - - -
124f ILE* 1.3 76.8 - - - +
126f LEU* 1.3 62.1 + - - +
127f LEU* 3.5 8.1 - - - -
128f GLU* 3.9 15.7 - - - +
129f LEU* 3.1 24.9 + - - +
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Residues in contact with LEU 126 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84f VAL* 5.4 12.1 - - + -
87f LEU* 6.2 4.3 - - + -
125f THR* 1.3 73.7 - - - +
127f LEU* 1.3 61.5 + - - +
129f LEU* 3.1 8.3 + - - +
130f ILE* 2.9 28.6 + - - +
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Residues in contact with LEU 127 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80f HIS* 5.7 9.0 - - + +
84f VAL* 5.5 11.5 - - + +
125f THR* 3.5 5.2 - - - -
126f LEU* 1.3 77.4 - - - +
128f GLU* 1.3 57.9 + - - +
130f ILE* 3.4 7.0 + - - +
131f LYS* 2.9 29.5 + - - +
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Residues in contact with GLU 128 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124f ILE* 5.9 0.2 - - + -
125f THR* 3.7 23.0 + - - +
126f LEU 3.2 0.4 - - - -
127f LEU* 1.3 78.0 - - - +
129f LEU* 1.3 59.3 + - - +
131f LYS* 3.8 6.0 - - - +
132f ALA* 2.9 29.5 + - - +
132g ALA* 4.3 29.3 - - + +
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Residues in contact with LEU 129 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125f THR 3.1 15.1 + - - +
126f LEU* 3.1 13.7 + - - +
128f GLU* 1.3 75.0 - - - +
130f ILE* 1.3 60.1 + - - +
132f ALA* 3.4 6.5 + - - +
133f LEU* 2.9 27.6 + - - +
132g ALA* 6.1 0.7 - - - -
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Residues in contact with ILE 130 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80f HIS* 4.8 20.0 - - + +
83f ILE* 5.9 4.9 - - + -
126f LEU 2.9 15.4 + - - +
127f LEU* 3.8 6.7 - - - +
128f GLU 3.3 0.2 - - - -
129f LEU* 1.3 75.6 - - - +
131f LYS* 1.3 59.6 + - - +
133f LEU* 3.1 7.6 + - - +
134f GLY 3.0 22.7 + - - -
135f VAL* 3.7 17.4 + - + +
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Residues in contact with LYS 131 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80f HIS* 5.9 0.8 - - - +
127f LEU 2.9 18.1 + - - +
128f GLU* 3.9 6.7 - - - +
130f ILE* 1.3 75.9 - - - +
132f ALA* 1.3 60.4 + - - +
134f GLY* 3.4 12.9 + - - +
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Residues in contact with ALA 132 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128f GLU 2.9 19.8 + - - +
129f LEU* 3.7 7.6 - - - +
131f LYS* 1.3 75.9 - - - +
133f LEU* 1.3 57.7 + - - +
134f GLY 3.5 0.3 + - - -
502f CA 2.6 28.8 - - - -
123g GLU 3.4 3.0 - - - +
124g ILE* 4.6 9.1 - - + -
128g GLU* 4.2 30.8 - - + +
132g ALA* 5.2 3.4 - - + -
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Residues in contact with LEU 133 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129f LEU 2.9 16.8 + - - +
130f ILE* 3.1 9.6 + - - +
132f ALA* 1.3 76.8 - - - +
134f GLY* 1.3 62.5 + - - +
135f VAL* 4.7 4.7 - - + +
502f CA 4.5 0.9 - - - -
108g ILE* 6.1 5.2 - - + -
121g TYR* 3.9 10.4 - - + +
122g ASP* 3.5 23.9 + - - +
123g GLU 4.0 14.7 + - - +
124g ILE* 5.3 5.1 - - + +
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Residues in contact with GLY 134 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130f ILE 3.0 6.2 + - - -
131f LYS* 3.4 9.8 + - - -
132f ALA 3.3 3.6 - - - -
133f LEU* 1.3 79.4 - - - +
135f VAL* 1.3 66.2 + - - +
136f ARG* 3.3 5.2 + - - +
120g GLU 3.2 12.7 - - - +
121g TYR* 3.9 3.0 - - - -
122g ASP* 4.7 1.9 + - - +
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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