Contacts of the helix formed by residues 132 - 143 (chain j) 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 j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130j ALA 4.1 0.8 + - - -
131j ILE* 1.3 72.1 - - - +
133j PRO* 1.3 64.1 - - - +
134j ASN* 3.3 3.8 - - - -
135j ILE* 3.2 18.3 + - - +
136j LEU* 3.1 17.5 + - - +
170j HIS* 3.9 12.2 - - - +
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Residues in contact with PRO 133 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131j ILE* 3.5 7.3 - - + +
132j THR* 1.3 69.8 - - - +
134j ASN* 1.3 65.5 + - - +
136j LEU* 3.0 10.4 + - + +
137j ALA* 2.9 23.0 + - - +
494j LEU* 6.5 0.7 - - + -
553j PRO* 4.1 22.7 - - + +
557j GLN* 5.8 7.0 - - + -
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Residues in contact with ASN 134 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132j THR* 3.3 2.8 - - - -
133j PRO* 1.3 75.7 - - - +
135j ILE* 1.3 65.2 + - - +
137j ALA* 3.1 8.1 + - - +
138j ARG* 2.8 24.4 + - - +
417j TYR* 4.9 13.5 - - + +
552j SER* 6.3 2.5 - - - -
553j PRO* 4.6 14.5 - - + +
554j ASN* 5.7 5.3 - - + +
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Residues in contact with ILE 135 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59j ALA* 5.6 9.4 - - + -
132j THR* 3.2 20.8 + - - +
133j PRO 3.1 0.4 - - - -
134j ASN* 1.3 79.8 - - - +
136j LEU* 1.3 62.3 + - - +
138j ARG* 3.7 5.6 - - - +
139j THR* 2.8 26.1 + - - -
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Residues in contact with LEU 136 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125j LEU* 5.4 13.9 - - + -
132j THR 3.1 8.4 + - - +
133j PRO* 3.0 13.2 + - + +
135j ILE* 1.3 80.4 - - - +
137j ALA* 1.3 63.4 + - - +
139j THR* 3.1 6.0 + - - -
140j ILE* 3.0 21.7 + - - +
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Residues in contact with ALA 137 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133j PRO 2.9 11.5 + - - +
134j ASN* 3.6 6.7 - - - +
136j LEU* 1.3 76.2 - - - +
138j ARG* 1.3 64.1 + - - +
140j ILE* 3.2 14.8 + - - +
141j GLU* 3.3 12.0 + - - +
417j TYR* 4.3 21.1 - - + +
490j LEU* 4.9 17.0 - - + -
494j LEU* 5.6 9.0 - - + -
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Residues in contact with ARG 138 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134j ASN 2.8 16.6 + - - +
135j ILE* 3.8 5.8 - - - +
137j ALA* 1.3 75.2 - - - +
139j THR* 1.3 64.8 + - - +
141j GLU* 3.1 17.7 + - - +
142j THR* 3.4 10.2 + - - -
417j TYR* 5.5 1.7 - - - +
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Residues in contact with THR 139 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59j ALA* 5.3 13.2 - - - -
123j CYS* 5.5 10.5 - - - -
125j LEU* 5.9 5.4 - - - -
135j ILE 2.8 17.6 + - - -
136j LEU* 3.6 6.1 - - - -
138j ARG* 1.3 77.6 - - - +
140j ILE* 1.3 64.2 + - - +
142j THR* 3.1 17.3 + - - -
143j VAL* 3.6 8.8 + - - +
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Residues in contact with ILE 140 (chain j).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136j LEU 3.0 12.5 + - - +
137j ALA* 3.2 9.8 + - - +
139j THR* 1.3 77.3 - - - +
141j GLU* 1.3 55.5 + - - +
143j VAL* 2.7 33.5 + - - +
149j VAL* 5.8 10.5 - - + -
486j VAL* 5.6 13.0 - - + +
487j GLU* 6.1 2.5 - - - -
490j LEU* 5.3 11.0 - - + -
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Residues in contact with GLU 141 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137j ALA 3.3 7.3 + - - +
138j ARG* 3.1 12.8 + - - +
140j ILE* 1.3 77.8 - - - +
142j THR* 1.3 59.4 + - - +
143j VAL 3.5 3.1 + - - +
287j ARG* 5.2 14.6 - - + -
288j GLY* 6.5 0.7 - - - -
479j ARG* 5.4 7.3 - - - +
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Residues in contact with THR 142 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115j ILE* 5.3 7.9 - - - -
116j LEU* 5.3 7.2 - - - -
118j ASN 4.0 18.2 - - - -
119j THR* 3.2 28.4 - - - -
120j TYR* 3.3 5.3 + - - -
138j ARG 3.4 6.8 + - - -
139j THR* 3.1 12.2 + - - -
140j ILE 3.0 1.0 - - - -
141j GLU* 1.3 79.8 - - - +
143j VAL* 1.3 59.9 + - - +
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Residues in contact with VAL 143 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119j THR* 5.2 0.2 - - - -
120j TYR* 3.5 11.7 - - + +
122j MET* 5.1 9.4 - - - +
123j CYS* 5.8 5.8 - - + +
139j THR 3.6 6.1 + - - +
140j ILE* 2.7 25.7 + - - +
141j GLU 4.5 2.8 - - - +
142j THR* 1.3 73.0 - - - +
144j GLU* 1.4 69.8 + - - +
147j GLY* 5.2 7.0 - - - -
148j LEU 5.7 3.6 - - - +
149j VAL* 6.0 4.3 - - + -
479j ARG* 5.3 6.6 - - - +
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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