Contacts of the helix formed by residues 141 - 150 (chain E) in PDB entry 2I5B
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 ASN 141 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139E THR 3.8 0.4 + - - -
140E PRO* 1.3 72.8 - - - +
142E LEU* 1.3 57.1 + - - +
143E PHE* 3.1 7.5 + - - +
144E GLU* 3.0 41.5 + - - +
145E ALA* 2.7 33.3 + - - +
177E ILE* 4.8 0.4 - - - -
178E THR* 3.2 22.9 + - - +
182E LYS* 4.3 8.2 - - + +
701E ADP 3.1 44.8 + - - +
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Residues in contact with LEU 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E ASN* 1.3 77.0 - - - +
143E PHE* 1.3 65.0 + - - +
145E ALA* 3.7 4.5 - - - +
146E SER* 3.2 20.3 + - - -
153E GLU* 5.8 1.7 - - + -
154E LEU* 3.9 31.9 + - + +
160E MET* 3.8 30.5 - - + -
177E ILE* 4.2 3.8 - - + -
178E THR 3.3 16.8 + - - +
179E GLY* 4.0 9.9 - - - +
182E LYS* 3.8 44.1 - - + +
183E LEU* 4.0 18.6 - - + +
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Residues in contact with PHE 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E MET* 4.2 10.3 - - + -
113E LYS* 3.7 41.3 - - + -
115E ALA 3.9 9.0 - - - -
116E ASN* 3.7 32.3 - - + -
117E GLU 3.8 18.8 - - - -
118E VAL* 3.9 17.9 - - + -
141E ASN* 3.2 8.3 + - - +
142E LEU* 1.3 76.4 - - - +
144E GLU* 1.3 70.3 + - + +
146E SER* 3.0 22.7 + - - -
147E GLN* 3.1 22.2 + - + +
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Residues in contact with GLU 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E ASP* 3.7 14.5 - - - +
108E PRO* 3.2 29.6 - - + +
109E VAL* 3.7 16.5 - - - +
110E MET* 3.9 22.7 + - + +
113E LYS* 5.7 4.7 - - - -
139E THR 3.9 0.5 - - - +
140E PRO* 3.4 14.1 - - + +
141E ASN* 3.0 45.4 + - - +
143E PHE* 1.3 81.4 - - + +
145E ALA* 1.3 57.3 + - - +
147E GLN* 3.4 2.6 + - - +
148E LEU* 3.0 33.6 + - - +
701E ADP 4.6 4.4 + - - -
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Residues in contact with ALA 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E PRO* 3.5 11.6 - - + +
141E ASN 2.7 20.5 + - - +
142E LEU 3.7 0.2 - - - +
144E GLU* 1.3 73.8 - - - +
146E SER* 1.3 51.5 + - - +
148E LEU* 3.3 4.4 + - - +
149E SER* 2.6 39.2 + - - -
154E LEU* 3.7 19.7 - - + -
163E ALA* 4.5 1.1 - - + -
167E ILE* 4.0 2.3 - - - +
177E ILE* 3.6 32.8 - - + -
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Residues in contact with SER 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E ASN* 4.8 5.9 + - - +
142E LEU 3.2 10.5 + - - -
143E PHE* 3.0 18.7 + - - -
145E ALA* 1.3 79.2 - - - +
147E GLN* 1.3 64.8 + - - +
149E SER* 3.3 6.7 - - - -
150E GLY* 3.0 23.7 + - - -
151E MET* 3.1 28.6 + - - +
152E ASP 3.5 19.1 - - - -
153E GLU* 4.5 4.9 - - - -
154E LEU* 4.2 7.8 - - - +
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Residues in contact with GLN 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E MET* 3.7 22.2 - - + -
116E ASN 3.2 25.1 + - - +
117E GLU* 3.5 12.3 - - - +
118E VAL* 3.2 45.7 + - + +
124E ALA* 4.4 5.5 - - + +
128E ARG* 3.6 20.6 + - - +
143E PHE* 3.1 16.4 + - + +
144E GLU 3.5 8.7 - - - +
146E SER* 1.3 88.8 + - - +
148E LEU* 1.3 64.2 + - - +
149E SER 3.6 0.3 + - - -
150E GLY* 3.7 6.4 + - - -
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Residues in contact with LEU 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E PRO* 3.8 28.7 - - + -
110E MET* 4.2 12.3 - - + -
124E ALA 4.4 0.9 - - - +
127E LEU* 4.2 15.5 - - + +
128E ARG* 3.5 57.6 + - + +
132E ALA* 5.2 0.4 - - + -
138E ILE* 3.9 19.3 - - + -
140E PRO* 4.1 11.9 - - + -
144E GLU 3.0 21.0 + - - +
145E ALA 3.3 3.6 + - - +
147E GLN* 1.3 76.0 - - - +
149E SER* 1.3 60.6 + - - +
150E GLY 3.3 0.2 - - - -
167E ILE* 4.0 16.8 - - + -
170E LEU* 4.0 11.4 - - + +
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Residues in contact with SER 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E ALA 2.6 22.8 + - - -
146E SER* 3.3 4.7 - - - -
148E LEU* 1.3 77.0 - - - +
150E GLY* 1.3 60.5 + - - +
151E MET* 3.1 38.9 + - - +
163E ALA* 4.1 4.6 - - - +
166E LYS* 3.7 27.1 - - - +
167E ILE* 3.8 17.3 - - - +
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Residues in contact with GLY 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E ARG* 5.8 2.5 - - - -
146E SER 3.0 9.1 + - - -
147E GLN 3.7 6.0 + - - -
148E LEU 3.3 2.8 - - - -
149E SER* 1.3 78.0 - - - +
151E MET* 1.3 60.7 + - - +
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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