Contacts of the helix formed by residues 130 - 136 (chain D) in PDB entry 1JZ3
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 ASP 130 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52D ARG* 4.8 2.8 - - - +
129D VAL* 1.3 77.9 - - - +
131D GLU* 1.3 70.2 + - - +
132D SER* 2.7 39.2 + - - -
133D TRP* 2.8 33.6 + - + +
134D LEU* 3.4 5.9 + - - +
8703D DMS 3.5 24.8 + - + +
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Residues in contact with GLU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D VAL 3.4 2.9 + - - -
130D ASP* 1.3 76.1 + - - +
132D SER* 1.3 60.2 + - - +
134D LEU* 2.9 41.5 + - - +
135D GLN* 3.0 32.4 + - - +
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Residues in contact with SER 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ASP* 2.7 27.8 + - - -
131D GLU* 1.3 76.1 - - - +
133D TRP* 1.4 57.0 + - - -
135D GLN* 3.1 34.9 + - - +
136D GLU* 3.1 17.0 + - - +
216D HIS* 4.4 4.1 - - - -
8703D DMS 3.0 23.2 - - - +
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Residues in contact with TRP 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D GLN 3.8 20.0 - - - -
50D GLN* 3.5 13.4 + - - -
52D ARG* 3.8 28.0 - - + -
129D VAL* 4.0 22.4 - - + -
130D ASP* 2.8 20.9 + - + +
132D SER* 1.4 75.9 - - - +
134D LEU* 1.3 66.3 + - - +
135D GLN 3.2 0.4 - - - -
136D GLU 3.6 9.1 - - - +
137D GLY 4.7 0.3 - - - +
139D THR* 3.8 35.3 + - + +
177D LEU* 4.7 1.6 - - + +
214D LEU* 4.0 28.5 - - + -
216D HIS* 3.4 43.8 + + + -
8703D DMS 2.9 36.1 - - + +
8705D DMS 3.4 14.9 - - - +
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Residues in contact with LEU 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D VAL* 3.7 29.6 - - + +
130D ASP 3.4 1.1 + - - +
131D GLU* 2.9 35.0 + - - +
133D TRP* 1.3 78.9 - - - +
135D GLN* 1.3 66.0 + - - +
177D LEU* 3.9 19.1 - - + +
178D ARG* 3.8 22.7 - - - +
179D ALA* 3.7 28.0 - - + +
180D GLY 5.0 0.9 - - - +
8705D DMS 3.2 19.3 + - + +
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Residues in contact with GLN 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D GLU* 3.0 38.2 + - - +
132D SER* 3.1 26.1 + - - +
134D LEU* 1.3 81.2 - - - +
136D GLU* 1.3 81.6 + - + +
8705D DMS 3.3 5.3 + - - +
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Residues in contact with GLU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D SER 3.1 5.5 + - - +
133D TRP 3.6 2.9 - - - +
135D GLN* 1.3 101.7 - - + +
137D GLY* 1.3 66.6 + - - +
216D HIS* 2.7 23.3 + - - -
219D THR* 5.7 2.4 - - - +
8705D DMS 3.1 9.3 + - - -
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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