Contacts of the helix formed by residues 139 - 150 (chain A) in PDB entry 2A19
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 HIS 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A TYR* 4.4 10.0 - + - -
100A LYS* 3.8 25.5 + - + -
103A LYS* 3.9 15.5 - - + -
104A SER* 2.8 45.9 + - - -
107A VAL* 4.2 5.8 - - + -
133A LEU 4.9 0.4 - - - -
134A SER* 3.4 11.0 - - - -
137A PHE* 3.3 5.7 + - - +
138A GLY* 1.3 77.4 - - - +
140A ALA* 1.3 74.0 + - + +
141A TYR* 3.0 29.8 + - + +
142A GLU* 2.9 29.6 + - + +
143A ALA* 3.2 9.5 + - - +
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Residues in contact with ALA 140 (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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107A VAL* 4.2 18.6 - - + -
130A ALA* 3.5 42.0 - - + +
133A LEU* 4.5 2.0 - - + -
134A SER* 3.7 10.2 - - - +
139A HIS* 1.3 77.0 + - + +
141A TYR* 1.3 51.3 + - - +
143A ALA* 3.2 8.7 + - - +
144A PHE* 2.8 43.4 + - + -
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Residues in contact with TYR 141 (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 LYS* 3.4 50.7 - - + -
106A THR* 3.7 29.8 - - + +
107A VAL* 3.8 9.2 - - + +
139A HIS* 3.0 19.9 + - + +
140A ALA* 1.3 76.1 - - - +
142A GLU* 1.3 67.4 + - - +
144A PHE* 3.0 9.8 + + + +
145A LYS* 2.7 54.4 + - + +
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Residues in contact with GLU 142 (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 LYS* 2.6 36.7 + - - +
137A PHE* 3.8 19.7 - - + +
139A HIS* 2.9 22.6 + - + +
141A TYR* 1.3 83.6 - - - +
143A ALA* 1.3 57.0 + - - +
145A LYS* 3.1 34.6 + - - +
146A LEU* 2.9 31.9 + - - +
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Residues in contact with ALA 143 (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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133A LEU* 3.7 30.3 - - + -
137A PHE* 3.5 36.1 - - + +
139A HIS 3.2 5.4 + - - +
140A ALA 3.3 10.5 - - - +
142A GLU* 1.3 77.6 - - - +
144A PHE* 1.3 63.2 + - - +
146A LEU* 3.3 3.4 + - - -
147A SER* 3.0 24.9 + - - -
153A VAL* 3.8 7.4 - - + +
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Residues in contact with PHE 144 (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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107A VAL* 4.3 29.4 - - + -
110A ILE* 4.1 27.4 - - + -
111A LEU* 4.2 13.0 - - + -
129A ILE* 4.3 6.5 - - + -
130A ALA* 5.4 1.6 - - + -
133A LEU* 3.9 24.2 - - + -
140A ALA* 2.8 26.8 + - + +
141A TYR* 3.3 11.4 - + + +
143A ALA* 1.3 72.6 - - - +
145A LYS* 1.3 62.6 + - - +
147A SER* 2.8 25.7 + - - -
148A ILE* 3.7 1.4 + - - +
154A TRP* 4.1 12.6 - + - -
168A LEU* 3.7 25.4 - - + -
172A ILE* 3.5 33.1 - - + +
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Residues in contact with LYS 145 (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 LYS* 5.7 0.6 - - - +
141A TYR* 2.7 33.8 + - + +
142A GLU* 3.1 36.9 + - - +
144A PHE* 1.3 75.5 - - - +
146A LEU* 1.3 64.9 + - + +
148A ILE* 3.6 28.7 + - + +
149A ILE* 4.4 4.3 + - - +
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Residues in contact with LEU 146 (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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137A PHE* 6.0 8.5 - - + -
142A GLU 2.9 15.5 + - - +
143A ALA* 4.4 2.0 - - - +
145A LYS* 1.3 78.6 - - + +
147A SER* 1.3 54.7 + - - +
148A ILE 3.2 2.2 - - - -
149A ILE* 3.4 25.5 + - + +
150A ASP* 2.8 43.1 + - + +
153A VAL* 4.2 12.1 - - + -
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Residues in contact with SER 147 (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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143A ALA 3.0 13.3 + - - -
144A PHE* 2.8 19.7 + - - -
146A LEU* 1.3 74.5 - - - +
148A ILE* 1.3 64.0 + - - +
150A ASP 3.2 21.2 - - - +
151A GLU* 4.8 6.2 - - - +
153A VAL* 3.5 15.9 - - - +
154A TRP* 3.9 23.9 + - - -
172A ILE* 3.6 18.5 - - - +
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Residues in contact with ILE 148 (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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144A PHE 3.9 4.7 - - - +
145A LYS* 3.6 25.1 - - + +
146A LEU 3.2 0.2 - - - -
147A SER* 1.3 80.1 + - - +
149A ILE* 1.3 73.8 + - + +
150A ASP 5.3 0.2 - - - -
172A ILE* 3.8 32.3 - - + +
173A SER* 4.8 16.8 - - - -
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Residues in contact with ILE 149 (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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145A LYS 5.0 3.1 - - - +
146A LEU* 3.4 25.5 + - + -
148A ILE* 1.3 90.8 - - + +
150A ASP* 1.3 59.1 + - + +
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Residues in contact with ASP 150 (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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146A LEU* 2.8 26.4 + - + +
147A SER* 3.2 18.4 - - - +
148A ILE 3.4 1.2 + - - -
149A ILE* 1.3 84.1 - - + +
151A GLU* 1.3 60.5 + - - +
152A THR* 2.7 42.6 + - - +
153A VAL* 3.2 19.3 + - + +
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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