Contacts of the helix formed by residues 130 - 139 (chain D) in PDB entry 2JE0
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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128D LEU 3.4 1.0 + - - -
129D ASN* 1.3 81.3 - - - +
131D TYR* 1.3 58.2 + - - +
132D ARG 3.5 1.8 - - - -
133D GLU* 3.4 35.9 - - + +
134D ASN* 2.9 38.9 + - - +
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Residues in contact with TYR 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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120D LEU* 3.7 21.8 - - + +
125D VAL* 3.5 29.8 - - + -
126D THR* 3.8 32.4 + - + +
128D LEU* 3.2 25.3 + - + +
129D ASN 3.1 3.6 + - - -
130D ASP* 1.3 75.3 - - - +
132D ARG* 1.3 81.2 + - + +
134D ASN* 3.7 3.9 - - - +
135D VAL* 3.0 47.4 + - + +
145D LEU* 3.7 10.8 - - + +
146D ASP* 2.6 32.9 + - - -
1150D GOL 3.8 17.5 - - - +
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Residues in contact with ARG 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 3.5 0.4 - - - -
131D TYR* 1.3 88.3 - - + +
133D GLU* 1.3 59.2 + - - +
135D VAL* 3.3 0.9 + - - -
136D PHE* 2.9 61.1 + - + -
145D LEU* 2.7 39.9 + - + +
146D ASP* 4.3 9.1 + - - +
148D TYR* 2.9 39.7 + - - +
149D ASP* 3.0 18.0 + - - -
1150D GOL 4.0 15.7 - - - +
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Residues in contact with GLU 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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130D ASP* 3.4 37.9 - - + +
132D ARG* 1.3 78.0 - - - +
134D ASN* 1.3 56.3 + - - +
136D PHE* 3.6 4.8 + - - +
137D LYS* 3.1 53.0 + - + +
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Residues in contact with ASN 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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103D LEU* 3.7 33.1 - - + +
128D LEU* 4.6 10.1 - - - +
129D ASN 3.6 14.1 + - - -
130D ASP* 2.9 30.7 + - - +
131D TYR* 3.7 4.3 - - - +
133D GLU* 1.3 72.9 - - - +
135D VAL* 1.3 58.1 + - - +
137D LYS* 3.3 26.0 + - - +
138D LEU* 3.0 28.8 + - - +
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Residues in contact with VAL 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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103D LEU* 4.0 10.5 - - + -
106D ILE* 3.8 24.0 - - + -
118D LEU* 4.6 0.7 - - + -
120D LEU* 5.0 0.7 - - + -
125D VAL* 5.2 0.2 - - + -
131D TYR* 3.0 40.7 + - + +
132D ARG 3.3 0.2 + - - -
134D ASN* 1.3 74.7 - - - +
136D PHE* 1.3 57.4 + - - +
138D LEU* 3.3 5.8 + - - +
139D LEU* 2.9 47.8 + - + +
142D LEU* 4.2 4.9 - - + -
145D LEU* 3.6 34.8 - - + -
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Residues in contact with PHE 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 ARG* 2.9 64.5 + - + +
133D GLU* 4.0 4.5 - - - +
135D VAL* 1.3 74.6 - - - +
137D LYS* 1.3 62.5 + - - +
139D LEU 4.2 2.5 - - - -
140D PRO* 3.4 25.4 - - + +
142D LEU* 3.9 33.2 - - + -
143D THR 3.7 26.9 - - - -
145D LEU* 3.7 21.3 - - + -
149D ASP* 4.1 13.9 - - - -
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Residues in contact with LYS 137 (chain D).
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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133D GLU* 3.1 45.8 + - + +
134D ASN* 3.3 29.1 + - - +
136D PHE* 1.3 76.5 - - - +
138D LEU* 1.3 62.6 + - - +
139D LEU 3.7 0.2 + - - -
140D PRO* 3.7 11.5 - - - +
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Residues in contact with LEU 138 (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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103D LEU* 3.4 42.2 - - + +
106D ILE* 3.8 24.2 - - + -
107D GLU* 4.0 33.0 - - + +
110D LYS* 3.9 15.1 - - + +
134D ASN 3.0 12.9 + - - +
135D VAL* 3.6 4.5 - - - +
136D PHE 3.3 0.2 - - - -
137D LYS* 1.3 80.9 - - - +
139D LEU* 1.3 69.0 + - + +
140D PRO* 3.3 8.7 - - - +
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Residues in contact with LEU 139 (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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106D ILE* 3.6 20.2 - - + +
107D GLU 4.5 0.4 - - - +
109D LEU* 3.8 13.7 - - + -
110D LYS* 3.6 30.3 - - + +
115D LEU* 4.7 3.8 - - + -
118D LEU* 3.7 30.3 - - + -
135D VAL* 2.9 24.2 + - + +
136D PHE* 3.5 8.4 - - - +
138D LEU* 1.3 93.9 - - + +
140D PRO* 1.4 63.1 - - - +
141D GLN* 3.1 17.6 + - - +
142D LEU* 3.2 31.4 + - + +
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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