Contacts of the helix formed by residues 132 - 143 (chain i) in PDB entry 5JPQ
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 132 (chain i).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130i ALA 4.1 1.0 + - - -
131i ILE* 1.3 70.9 - - - +
133i PRO* 1.3 63.0 - - - +
134i ASN* 3.3 3.6 - - - -
135i ILE* 3.2 19.9 + - - +
136i LEU* 3.1 17.5 + - - +
170i HIS* 3.9 12.4 - - - +
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Residues in contact with PRO 133 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131i ILE* 3.5 7.4 - - + +
132i THR* 1.3 69.2 - - - +
134i ASN* 1.3 65.3 - - - +
136i LEU* 3.0 10.1 + - + +
137i ALA* 2.9 22.3 + - - +
494i LEU* 6.5 0.7 - - + -
553i PRO* 4.1 22.4 - - + +
557i GLN* 5.8 7.2 - - + -
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Residues in contact with ASN 134 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132i THR* 3.3 2.6 - - - -
133i PRO* 1.3 75.5 - - - +
135i ILE* 1.3 64.9 + - - +
137i ALA* 3.1 8.2 + - - +
138i ARG* 2.8 24.6 + - - +
417i TYR* 4.9 13.2 - - + +
552i SER* 6.3 2.0 - - - -
553i PRO* 4.6 14.9 - - + +
554i ASN* 5.7 5.1 - - + +
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Residues in contact with ILE 135 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59i ALA* 5.6 9.2 - - + -
132i THR* 3.2 20.8 + - - +
133i PRO 3.1 0.6 - - - -
134i ASN* 1.3 79.8 - - - +
136i LEU* 1.3 63.1 + - - +
138i ARG* 3.8 5.6 - - - +
139i THR* 2.8 26.0 + - - -
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Residues in contact with LEU 136 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125i LEU* 5.4 13.5 - - + -
132i THR 3.1 9.1 + - - +
133i PRO* 3.0 13.4 + - + +
135i ILE* 1.3 80.4 - - - +
137i ALA* 1.3 62.8 + - - +
139i THR* 3.1 6.0 + - - -
140i ILE* 3.0 21.7 + - - +
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Residues in contact with ALA 137 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133i PRO 2.9 12.6 + - - +
134i ASN* 3.6 6.7 - - - +
136i LEU* 1.3 75.8 - - - +
138i ARG* 1.3 63.2 + - - +
140i ILE* 3.2 14.9 + - - +
141i GLU* 3.3 12.1 + - - +
417i TYR* 4.3 21.1 - - + +
490i LEU* 4.9 17.3 - - + -
494i LEU* 5.6 9.2 - - + -
553i PRO* 6.4 0.9 - - + -
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Residues in contact with ARG 138 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134i ASN 2.8 16.3 + - - +
135i ILE* 3.8 5.6 - - - +
137i ALA* 1.3 75.6 - - - +
139i THR* 1.3 64.8 + - - +
141i GLU* 3.1 17.9 + - - +
142i THR* 3.4 10.2 + - - -
417i TYR* 5.5 3.3 - - + +
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Residues in contact with THR 139 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59i ALA* 5.3 13.0 - - - -
123i CYS* 5.5 10.8 - - - -
125i LEU* 5.9 5.8 - - - -
135i ILE 2.8 17.6 + - - -
136i LEU* 3.1 6.5 + - - -
138i ARG* 1.3 78.2 - - - +
140i ILE* 1.3 64.0 + - - +
142i THR* 3.1 17.3 + - - -
143i VAL* 3.6 8.7 + - - +
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Residues in contact with ILE 140 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136i LEU 3.0 12.7 + - - +
137i ALA* 3.2 10.0 + - - +
139i THR* 1.3 75.8 - - - +
141i GLU* 1.3 54.1 + - - +
143i VAL* 2.7 33.7 + - - +
486i VAL* 5.6 14.1 - - + +
487i GLU* 6.1 2.0 - - - -
490i LEU* 5.3 10.5 - - + -
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Residues in contact with GLU 141 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137i ALA 3.3 7.8 + - - +
138i ARG* 3.1 12.1 + - - +
140i ILE* 1.3 78.5 - - - +
142i THR* 1.3 58.8 + - - +
143i VAL 3.5 2.8 + - - +
287i ARG* 5.2 13.7 - - + -
288i GLY* 6.5 0.7 - - - -
479i ARG* 5.4 7.1 - - - +
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Residues in contact with THR 142 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115i ILE* 5.3 8.1 - - - -
116i LEU* 5.2 6.5 - - - -
118i ASN 4.0 17.0 - - - -
119i THR* 3.2 28.6 - - - -
120i TYR* 3.3 5.1 + - - -
138i ARG 3.4 6.5 + - - -
139i THR* 3.1 12.0 + - - -
140i ILE 3.0 1.0 - - - -
141i GLU* 1.3 80.4 - - - +
143i VAL* 1.4 61.3 + - - +
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Residues in contact with VAL 143 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119i THR* 5.2 0.2 - - - -
120i TYR* 3.5 11.4 - - + +
122i MET* 5.1 9.9 - - - +
123i CYS* 5.8 5.4 - - + -
139i THR 3.6 5.9 + - - +
140i ILE* 2.7 25.8 + - - +
141i GLU 3.3 3.0 - - - +
142i THR* 1.4 72.3 - - - +
144i GLU* 1.4 67.6 + - - +
147i GLY* 5.2 7.4 - - - -
148i LEU 5.7 3.1 - - - +
149i VAL* 6.0 4.7 - - + -
479i ARG* 5.3 7.4 - - - +
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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