Contacts of the helix formed by residues 130 - 139 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A LEU 3.4 0.8 + - - -
129A ASN* 1.3 81.1 + - - +
131A TYR* 1.3 58.2 + - - +
132A ARG 3.4 2.5 - - - -
133A GLU* 3.4 34.5 + - + +
134A ASN* 2.8 37.4 + - - +
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Residues in contact with TYR 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LEU* 3.6 20.0 - - + +
125A VAL* 3.5 23.6 - - + -
126A THR* 3.8 33.4 - - + +
128A LEU* 3.2 25.3 + - + +
129A ASN 3.1 2.8 + - - -
130A ASP* 1.3 77.2 - - - +
132A ARG* 1.3 75.3 + - + +
134A ASN* 3.4 3.6 + - - +
135A VAL* 3.0 54.5 + - + +
145A LEU* 3.6 23.7 - - + +
146A ASP* 2.7 34.4 + - - -
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Residues in contact with ARG 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ASP 3.4 0.2 - - - -
131A TYR* 1.3 91.0 - - + +
133A GLU* 1.3 66.3 + - - +
135A VAL* 3.4 0.9 + - - +
136A PHE* 2.9 53.7 + - + -
145A LEU* 2.6 40.6 + - + +
146A ASP* 4.1 9.7 + - - +
148A TYR* 2.9 41.9 + - - +
149A ASP* 3.2 17.0 + - - -
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Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ASP* 3.4 36.2 + - + +
132A ARG* 1.3 78.1 - - - +
134A ASN* 1.3 58.0 + - - +
136A PHE* 3.6 4.4 + - - +
137A LYS* 3.1 56.6 + - + +
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Residues in contact with ASN 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU* 3.6 33.1 - - + +
128A LEU* 4.6 7.8 - - + +
129A ASN 3.5 14.6 + - - -
130A ASP* 2.8 30.6 + - - +
131A TYR* 3.7 4.3 - - - +
133A GLU* 1.3 71.8 - - - +
135A VAL* 1.3 59.0 + - - +
137A LYS* 3.3 23.6 - - - +
138A LEU* 3.0 29.3 + - - +
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Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU* 3.8 18.6 - - + -
106A ILE* 4.1 14.1 - - + -
118A LEU* 4.5 2.2 - - + -
120A LEU* 4.9 0.4 - - + -
125A VAL* 5.3 0.4 - - + -
131A TYR* 3.0 42.8 + - + +
134A ASN* 1.3 74.2 - - - +
136A PHE* 1.3 57.8 + - - +
138A LEU* 3.4 5.4 + - - +
139A LEU* 2.9 48.8 + - + +
142A LEU* 4.4 5.1 - - + +
145A LEU* 3.9 31.0 - - + -
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Residues in contact with PHE 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ARG* 2.9 61.0 + - + +
133A GLU* 4.1 4.5 - - - +
135A VAL* 1.3 72.6 - - - +
137A LYS* 1.3 62.7 + - - +
139A LEU 4.2 2.9 - - - -
140A PRO* 3.4 24.9 - - + +
142A LEU* 4.1 31.2 - - + -
143A THR 3.7 23.3 - - - -
145A LEU* 3.5 32.1 - - + -
149A ASP* 4.1 14.1 - - - -
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Residues in contact with LYS 137 (chain A).
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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133A GLU* 3.1 47.0 + - + +
134A ASN* 3.3 24.9 - - - +
136A PHE* 1.3 76.8 - - - +
138A LEU* 1.3 62.3 + - - +
140A PRO* 3.8 11.1 - - - +
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU* 3.5 41.3 - - + +
106A ILE* 3.9 22.2 - - + +
107A GLU* 3.9 35.4 - - + +
110A LYS* 3.8 21.9 - - - +
134A ASN 3.0 14.3 + - - +
135A VAL* 3.6 4.0 - - - +
137A LYS* 1.3 81.6 - - - +
139A LEU* 1.3 68.5 + - + +
140A PRO* 3.3 8.1 - - - +
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ILE* 3.6 20.0 - - + +
107A GLU 4.4 0.2 - - - +
109A LEU* 3.7 14.6 - - + -
110A LYS* 3.5 30.3 - - + +
115A LEU* 4.8 2.9 - - + -
118A LEU* 3.7 30.1 - - + -
135A VAL* 2.9 26.0 + - + +
136A PHE* 3.5 8.4 - - - +
138A LEU* 1.3 92.2 - - + +
140A PRO* 1.4 62.4 - - - +
141A GLN* 3.1 17.5 + - - +
142A LEU* 3.2 29.7 + - + +
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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