Contacts of the helix formed by residues 132 - 139 (chain J) in PDB entry 2I2R
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 CYS 132 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104J HIS* 3.5 2.2 - - - -
105J TYR* 3.4 40.2 - - + +
128J ILE* 3.5 14.6 - - + -
129J GLY 3.3 2.2 + - - -
131J CYS* 1.3 79.0 - - - +
133J TYR* 1.3 51.2 + - - +
134J GLU 2.9 5.8 - - - -
135J GLU* 2.8 10.7 + - + +
136J TYR* 2.7 33.8 + - - +
606J ZN 1.9 41.7 - - - -
110K CYS* 3.7 11.9 - - - -
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Residues in contact with TYR 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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126J GLU* 5.0 13.7 - - + +
128J ILE* 3.3 20.8 - - + +
129J GLY 3.1 17.8 + - - +
130J ASP* 4.9 4.3 - - - +
132J CYS* 1.3 74.7 - - - +
134J GLU* 1.3 59.5 + - - +
136J TYR* 3.9 14.1 - - + +
137J LYS* 3.4 20.1 + - - +
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Residues in contact with GLU 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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130J ASP 3.6 16.0 + - - +
131J CYS 4.0 11.9 - - - +
133J TYR* 1.3 77.4 - - - +
135J GLU* 1.3 61.9 + - + +
137J LYS* 3.4 9.9 + - - +
138J ASP* 3.3 24.1 + - - +
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Residues in contact with GLU 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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105J TYR* 4.1 13.8 - - + +
107J ARG* 4.3 21.6 - - + +
131J CYS 5.3 2.5 - - - +
132J CYS* 2.8 14.4 + - - +
134J GLU* 1.3 74.9 - - + +
136J TYR* 1.3 64.4 + - - +
137J LYS 3.1 2.4 + - - -
138J ASP* 4.3 13.7 - - - +
139J ARG* 3.4 46.7 + - - +
139K ARG* 6.0 2.9 - - - +
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Residues in contact with TYR 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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105J TYR* 4.1 11.6 - + + -
111J ILE* 3.7 25.5 - - + +
114J TYR* 4.1 15.0 - + - -
115J ASP* 3.2 37.4 + - - -
118J LEU* 5.5 0.6 - - + +
125J PRO* 4.2 27.3 - - + +
126J GLU* 5.1 9.4 - - + -
128J ILE* 3.5 27.8 - - + -
132J CYS 2.7 19.5 + - - +
133J TYR* 3.9 12.6 - - + -
135J GLU* 1.3 69.4 - - - +
137J LYS* 1.3 66.8 + - - +
140J LYS* 3.1 32.9 + - + +
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Residues in contact with LYS 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 TYR 3.4 12.7 + - - +
134J GLU* 3.4 13.1 + - - +
135J GLU 3.1 0.4 - - - -
136J TYR* 1.3 80.1 - - - +
138J ASP* 1.3 58.8 + - - +
139J ARG 2.8 12.9 + - - -
140J LYS* 2.9 19.0 + - - +
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Residues in contact with ASP 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 GLU* 3.3 15.4 + - - +
135J GLU* 3.5 17.8 + - - +
137J LYS* 1.3 79.5 - - - +
139J ARG* 1.3 59.9 + - - +
140J LYS 3.8 0.2 - - - -
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Residues in contact with ARG 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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107I ARG* 4.5 15.3 - - - +
135I GLU* 6.0 3.0 - - - +
105J TYR* 3.1 26.3 + - + +
107J ARG 4.1 15.0 + - - -
108J TYR* 3.8 16.2 + - - +
109J GLU 3.2 15.9 + - - -
110J CYS* 3.7 15.0 - - - +
111J ILE* 2.8 24.3 - - + +
135J GLU* 3.4 30.9 + - - +
137J LYS 2.8 5.5 + - - -
138J ASP* 1.3 77.4 - - - +
140J LYS* 1.3 58.0 + - - +
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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