Contacts of the helix formed by residues 133 - 142 (chain O) in PDB entry 1JJ2
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 SER 133 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17930 C 3.4 40.6 + - - -
17940 G 3.5 7.6 - - - -
97O ARG* 5.4 0.4 - - - +
101O GLN* 3.6 14.4 + - - +
131O PHE* 3.3 2.2 - - - +
132O ASP* 1.3 81.2 - - - +
134O VAL* 1.3 65.6 + - - +
135O ALA* 3.7 3.4 + - - +
136O ASP* 3.3 20.6 + - - +
137O LEU* 3.0 21.0 + - - +
139O ARG* 4.5 2.3 + - - -
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Residues in contact with VAL 134 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17940 G 3.0 22.3 + - - +
17950 G 4.7 4.9 - - - +
100O ALA* 3.8 37.0 - - + +
101O GLN* 4.1 6.7 - - + +
104O LYS* 4.0 22.0 - - + -
133O SER* 1.3 70.9 - - - +
135O ALA* 1.3 55.9 + - - +
137O LEU* 2.7 27.7 + - - +
138O GLU* 2.7 39.7 + - - +
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Residues in contact with ALA 135 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17930 C 3.6 23.3 + - - +
17940 G 5.1 1.0 + - - -
133O SER* 3.9 1.1 - - - +
134O VAL* 1.3 81.3 - - - +
136O ASP* 1.3 55.6 + - - +
138O GLU* 3.1 12.7 + - - +
139O ARG* 2.8 56.8 + - - +
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Residues in contact with ASP 136 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130O GLU 4.5 3.6 - - - +
131O PHE* 4.1 8.7 - - - -
132O ASP* 3.6 28.8 + - + +
133O SER* 3.3 28.0 + - - +
134O VAL 3.1 0.4 - - - -
135O ALA* 1.3 78.3 - - - +
137O LEU* 1.3 61.8 + - - +
139O ARG* 3.5 25.7 + - - +
140O TYR* 3.2 21.5 + - - +
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Residues in contact with LEU 137 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101O GLN* 4.0 21.8 - - + +
104O LYS* 4.3 16.2 - - + -
105O LEU* 3.4 39.9 - - + -
122O LEU* 4.4 10.1 - - + -
131O PHE* 3.4 47.5 - - + +
133O SER 3.0 12.0 + - - +
134O VAL* 2.7 16.8 + - - +
136O ASP* 1.3 69.6 - - - +
138O GLU* 1.3 66.0 + - - +
140O TYR* 3.0 5.8 + - + +
141O ILE* 2.9 31.2 + - + +
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Residues in contact with GLU 138 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104O LYS* 3.4 35.1 + - + -
108O LEU* 5.8 0.7 - - + -
134O VAL* 2.7 36.3 + - + +
135O ALA* 3.5 11.9 + - - +
137O LEU* 1.3 74.2 - - - +
139O ARG* 1.3 62.9 + - + +
141O ILE* 3.1 27.3 + - + +
142O ASP* 3.3 18.0 + - - +
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Residues in contact with ARG 139 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17930 C 5.1 1.8 + - - -
133O SER* 4.5 3.0 + - - -
135O ALA* 2.8 36.8 + - - +
136O ASP* 3.5 39.1 + - - +
138O GLU* 1.3 77.2 - - + +
140O TYR* 1.3 63.3 + - - +
142O ASP* 3.1 19.3 + - - +
143O ALA 3.4 11.6 - - - +
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Residues in contact with TYR 140 (chain O).
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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121O ASP* 5.0 0.6 + - - -
122O LEU* 3.5 34.5 - - + -
125O LYS* 2.7 34.5 + - + -
131O PHE* 3.8 24.5 - + + -
136O ASP 3.2 10.9 + - - +
137O LEU 3.0 8.6 + - - +
139O ARG* 1.3 78.9 - - - +
141O ILE* 1.3 64.6 + - - +
143O ALA* 3.1 20.8 + - - -
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Residues in contact with ILE 141 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105O LEU* 4.5 3.1 - - + -
108O LEU* 3.5 31.6 - - + -
113O THR* 5.7 5.4 - - + -
114O LEU* 4.6 12.3 - - + -
122O LEU* 4.1 29.2 - - + -
137O LEU* 2.9 34.3 + - + +
138O GLU* 3.1 16.3 + - + +
140O TYR* 1.3 74.9 - - - +
142O ASP* 1.3 66.5 + - - +
143O ALA 2.8 12.1 + - - -
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Residues in contact with ASP 142 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138O GLU* 3.3 17.7 - - - +
139O ARG* 3.1 10.5 + - - +
141O ILE* 1.3 83.3 - - - +
143O ALA* 1.3 74.3 + - - +
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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