Contacts of the helix formed by residues 132 - 146 (chain E) in PDB entry 1R4N
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 PRO 132 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130E GLN 4.3 2.7 - - - +
131E LEU* 1.3 93.7 - - + +
133E GLU* 1.3 70.6 + - - +
134E SER* 4.2 10.8 - - - +
135E THR* 3.1 17.7 + - - +
136E SER* 2.9 16.1 + - - -
433E ASP* 4.5 3.1 - - - +
436E HIS* 4.5 19.5 - - + +
442E TYR* 4.1 20.2 - - - +
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Residues in contact with GLU 133 (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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131E LEU 4.0 0.8 + - - -
132E PRO* 1.3 69.3 - - - +
134E SER* 1.3 69.6 + - - +
136E SER* 2.7 21.2 + - - -
137E LEU* 3.0 24.1 + - + +
402E TYR* 3.5 22.0 + - + +
430E ARG* 2.7 34.0 + - - +
433E ASP* 3.6 44.0 + - + +
434E ARG* 4.9 2.5 + - - +
436E HIS* 6.0 0.4 + - - -
437E LYS* 5.8 7.1 - - + +
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Residues in contact with SER 134 (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 GLU* 3.9 7.6 + - - -
132E PRO* 4.2 9.9 - - - +
133E GLU* 1.3 78.4 - - - +
135E THR* 1.3 73.9 + - - -
137E LEU* 4.2 5.6 - - - +
138E ARG* 3.2 22.9 + - - +
437E LYS* 5.9 9.0 - - - -
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Residues in contact with THR 135 (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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109E PRO* 4.3 15.7 - - + -
110E GLU* 2.5 41.2 + - + +
113E LEU* 4.6 9.0 - - + -
131E LEU* 4.2 20.6 - - + -
132E PRO* 3.1 22.1 + - - +
133E GLU 2.8 2.8 + - - -
134E SER* 1.3 82.8 + - - +
136E SER* 1.3 64.8 + - - +
138E ARG* 3.3 3.1 + - - +
139E LEU* 2.8 23.6 + - + +
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Residues in contact with SER 136 (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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131E LEU* 3.4 35.5 + - - +
132E PRO 2.9 8.6 + - - -
133E GLU* 2.7 17.5 + - - -
135E THR* 1.3 72.4 - - - +
137E LEU* 1.3 60.0 + - - -
139E LEU* 3.7 0.7 - - - +
140E ALA* 2.8 32.4 + - - +
152E ILE* 4.0 24.3 - - - +
398E LEU* 4.1 8.5 - - - -
402E TYR* 6.5 1.6 - - - -
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Residues in contact with LEU 137 (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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133E GLU* 3.0 24.4 + - - +
134E SER* 4.2 4.0 - - - +
136E SER* 1.3 80.7 - - - +
138E ARG* 1.3 64.9 + - - +
139E LEU 3.2 0.2 + - - -
140E ALA* 3.4 2.1 + - - +
141E ASP* 3.3 22.0 + - - +
398E LEU* 3.8 26.9 - - + +
399E ALA* 4.9 4.3 - - - +
402E TYR* 3.5 52.0 - - + -
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Residues in contact with ARG 138 (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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341A LYS* 5.1 7.1 - - - +
110E GLU* 2.9 28.6 + - - -
113E LEU* 2.7 48.4 + - + +
114E ASP* 2.8 33.9 + - - +
134E SER 3.2 18.1 + - - +
135E THR* 3.7 4.0 - - - +
136E SER 3.3 0.2 - - - -
137E LEU* 1.3 78.5 - - - +
139E LEU* 1.3 58.8 + - - +
141E ASP* 3.6 5.1 - - - +
142E VAL* 3.2 27.9 + - + +
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Residues in contact with LEU 139 (chain E).
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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36E ILE* 4.5 10.5 - - + -
109E PRO* 6.0 2.9 - - + -
113E LEU* 3.6 34.9 - - + +
120E PHE* 4.0 17.0 - - + -
126E VAL* 4.7 0.9 - - + -
128E ALA* 4.1 18.2 - - + -
131E LEU* 4.2 9.6 - - + -
135E THR* 2.8 20.6 + - + +
136E SER* 3.7 2.7 - - - +
138E ARG* 1.3 73.5 - - - +
140E ALA* 1.3 53.1 - - - +
141E ASP 2.7 16.0 + - - -
142E VAL* 3.1 1.7 + - + +
143E LEU* 2.9 47.4 + - + +
150E LEU* 3.8 25.1 - - + -
152E ILE* 5.8 0.2 - - + -
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Residues in contact with ALA 140 (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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136E SER 2.8 13.0 + - - +
137E LEU 3.9 2.2 - - - +
139E LEU* 1.3 72.2 - - - +
141E ASP* 1.3 56.6 + - - +
143E LEU* 4.8 0.6 - - - +
144E TRP* 3.2 23.7 + - - +
150E LEU* 3.3 26.6 - - + +
165E ILE* 3.7 11.1 - - + +
397E SER* 5.8 0.3 - - - -
398E LEU* 3.3 48.8 + - + +
399E ALA 6.1 0.2 - - - -
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Residues in contact with ASP 141 (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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137E LEU 3.3 15.9 + - - +
138E ARG* 3.6 7.2 - - - +
139E LEU 2.7 1.4 + - - -
140E ALA* 1.3 76.1 - - - +
142E VAL* 1.3 72.1 + - - +
143E LEU 3.0 0.7 - - - -
144E TRP* 2.7 18.6 + - - +
145E ASN* 2.9 31.4 + - - -
399E ALA* 5.2 12.0 - - + +
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Residues in contact with VAL 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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113E LEU* 3.8 27.4 - - + +
117E PRO* 3.8 36.8 - - + +
120E PHE* 5.4 2.7 - - + -
138E ARG* 3.2 22.0 + - + +
139E LEU 3.1 3.5 + - - +
141E ASP* 1.3 84.8 + - - +
143E LEU* 1.3 64.5 + - + +
145E ASN* 3.5 6.4 + - - +
146E SER* 3.0 36.5 + - - +
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Residues in contact with LEU 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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120E PHE* 3.4 35.7 - - + -
126E VAL* 3.9 11.7 - - + -
139E LEU* 2.9 38.0 + - + +
140E ALA 4.7 1.6 - - - +
142E VAL* 1.3 77.7 - - + +
144E TRP* 1.3 66.1 + - - +
146E SER* 3.2 3.7 + - - -
147E GLN 3.0 5.0 + - - -
148E ILE* 2.9 58.5 + - + +
150E LEU* 3.2 42.4 - - + -
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Residues in contact with TRP 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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140E ALA 3.2 21.5 + - - +
141E ASP* 2.7 15.2 + - - +
143E LEU* 1.3 74.6 - - - +
145E ASN* 1.3 77.0 + - - +
147E GLN* 3.0 22.8 + - - +
148E ILE 4.5 4.0 + - - -
165E ILE* 3.6 24.2 - - + -
167E LYS* 3.9 55.3 - - + +
395E CYS 3.6 15.5 - - - -
397E SER* 3.2 50.9 - - - -
400E GLU* 5.1 6.3 - - - -
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Residues in contact with ASN 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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141E ASP* 2.9 37.8 + - - -
142E VAL* 3.9 7.0 - - - +
144E TRP* 1.3 87.5 - - - +
146E SER* 1.3 59.8 + - - +
147E GLN* 3.1 17.1 + - - +
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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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117E PRO 5.3 2.1 + - - -
118E SER* 5.6 2.1 - - - -
120E PHE* 5.9 1.1 - - - -
121E CYS* 3.9 29.9 - - - -
142E VAL* 3.0 26.8 + - - +
143E LEU* 3.2 7.1 + - - -
145E ASN* 1.3 76.3 - - - +
147E GLN* 1.3 70.9 + - - +
148E ILE* 3.5 16.1 + - - +
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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