Contacts of the helix formed by residues 132 - 146 (chain E) in PDB entry 1CSE
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 132 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104E TYR* 4.0 28.8 - - - +
108E VAL* 5.1 0.2 - - - +
131E GLY* 1.3 77.1 - - - -
133E THR* 1.3 61.1 + - - +
134E ALA* 3.3 7.8 + - - +
135E MET* 3.0 22.0 + - - +
136E LYS* 2.9 25.1 + - - +
171E TYR* 3.1 10.7 + - - -
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Residues in contact with THR 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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132E SER* 1.3 76.4 + - - +
134E ALA* 1.3 65.7 + - + +
136E LYS* 3.8 9.0 - - - +
137E GLN* 3.0 23.9 + - - +
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Residues in contact with ALA 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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108E VAL* 3.9 21.6 - - + +
132E SER* 3.2 6.7 + - - +
133E THR* 1.3 82.9 - - + +
135E MET* 1.4 60.1 - - - +
137E GLN* 3.5 10.8 + - - +
138E ALA* 2.9 28.9 + - - +
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Residues in contact with MET 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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104E TYR* 4.0 31.4 - - + -
107E ILE* 4.2 23.1 - - + -
108E VAL* 3.7 14.8 - - + +
111E ILE* 4.0 17.3 - - + -
131E GLY* 4.0 10.5 - - - -
132E SER* 3.0 18.9 + - - +
134E ALA* 1.4 75.9 - - - +
136E LYS* 1.3 66.0 + - - +
138E ALA* 3.0 2.4 + - - -
139E VAL* 2.8 27.3 + - + +
167E TYR* 4.1 3.4 - - + -
168E PRO* 3.9 29.6 - - + -
171E TYR* 3.7 24.5 - - + -
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Residues in contact with LYS 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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132E SER 2.9 15.0 + - - +
133E THR* 3.8 11.0 - - - +
135E MET* 1.3 76.2 - - - +
137E GLN* 1.3 65.4 + - - +
139E VAL* 3.3 3.6 - - - +
140E ASP* 2.9 45.5 + - - +
171E TYR* 3.6 45.6 - - + +
172E ASP* 5.9 4.8 + - - +
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Residues in contact with GLN 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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112E GLU* 5.7 1.0 - - - +
133E THR 3.0 14.6 + - - +
134E ALA* 3.5 13.4 - - - +
136E LYS* 1.3 81.4 - - - +
138E ALA* 1.3 59.3 + - - +
140E ASP* 3.6 5.5 - - - +
141E ASN* 2.9 53.7 + - - +
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Residues in contact with ALA 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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108E VAL* 4.1 20.9 - - + +
111E ILE* 3.6 26.8 - - + +
112E GLU* 4.7 10.3 - - + +
115E THR* 4.9 0.3 + - - -
134E ALA 2.9 18.4 + - - +
135E MET* 3.0 3.8 + - - +
137E GLN* 1.3 78.7 - - - +
139E VAL* 1.3 65.3 + - - +
141E ASN* 3.3 7.9 + - - +
142E ALA* 2.9 24.9 + - - +
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Residues in contact with VAL 139 (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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111E ILE* 3.7 25.6 - - + -
124E MET* 4.0 14.8 - - + -
135E MET* 2.8 20.1 + - + +
136E LYS* 3.3 10.1 - - - +
138E ALA* 1.3 74.4 - - - +
140E ASP* 1.4 63.7 + - - +
142E ALA* 3.3 6.1 + - - +
143E TYR* 3.0 29.6 + - - +
149E VAL* 4.3 8.4 - - + +
168E PRO* 4.5 7.2 - - + -
171E TYR* 4.0 16.8 - - + -
173E SER* 3.2 18.3 + - - +
174E VAL* 3.8 26.5 - - + -
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Residues in contact with ASP 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 LYS* 2.9 41.1 + - - +
137E GLN* 3.6 7.3 - - + +
139E VAL* 1.4 74.1 - - - +
141E ASN* 1.3 70.8 - - - +
143E TYR* 3.3 2.9 + - - +
144E ALA* 2.9 24.2 + - - +
171E TYR* 5.3 1.4 - - - +
172E ASP 5.6 0.2 + - - -
173E SER* 2.8 28.2 + - - -
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Residues in contact with ASN 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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115E THR* 4.4 6.8 - - + +
137E GLN* 2.9 43.9 + - - +
138E ALA* 3.7 7.2 - - - +
140E ASP* 1.3 84.9 - - - +
142E ALA* 1.4 59.5 + - - +
144E ALA* 3.3 7.7 + - - +
145E ARG* 2.8 28.6 + - - +
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Residues in contact with ALA 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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111E ILE* 4.1 10.8 - - + -
115E THR* 3.4 29.8 + - - +
122E ILE* 4.1 17.7 - - + -
138E ALA 2.9 17.3 + - - +
139E VAL 3.7 4.3 - - - +
141E ASN* 1.4 75.1 - - - +
143E TYR* 1.3 66.1 + - - +
145E ARG* 2.9 11.4 + - - -
146E GLY 3.2 0.5 + - - -
147E VAL* 3.1 24.7 + - + +
149E VAL* 4.1 5.8 - - + -
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Residues in contact with TYR 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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139E VAL 3.0 17.0 + - - +
140E ASP 3.8 2.7 - - - +
142E ALA* 1.3 77.6 - - - +
144E ALA* 1.4 57.0 + - - +
146E GLY* 3.0 20.8 + - - -
147E VAL 3.4 20.4 + - - +
148E VAL* 5.0 4.3 - - + -
149E VAL* 4.4 3.8 - - + +
172E ASP 5.1 0.2 - - - -
173E SER* 3.5 33.0 - - - +
243E ALA* 4.0 21.5 - - + +
244E SER* 3.6 28.2 + - - -
247E ARG* 3.3 41.8 + - + -
248E ASN* 5.1 1.0 + - - -
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Residues in contact with ALA 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 ASP 2.9 17.5 + - - +
141E ASN* 3.6 8.3 - - - +
143E TYR* 1.4 76.5 - - - +
145E ARG* 1.4 60.0 + - - +
146E GLY* 3.2 1.4 + - - -
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Residues in contact with ARG 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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114E ALA 3.7 1.4 + - - -
115E THR* 3.0 49.4 + - + -
118E GLY* 3.7 8.5 - - - -
119E MET 3.0 38.4 + - - +
120E ASP* 5.2 3.8 + - - +
141E ASN 2.8 14.8 + - - +
142E ALA 2.9 10.0 + - - +
144E ALA* 1.4 75.0 - - - +
146E GLY* 1.3 65.3 + - - +
147E VAL* 3.4 22.0 - - + +
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Residues in contact with GLY 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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120E ASP* 3.9 8.1 - - - +
143E TYR 3.0 11.7 + - - -
144E ALA 3.2 1.6 - - - -
145E ARG* 1.3 85.2 + - - +
147E VAL* 1.3 65.3 + - - +
148E VAL* 3.8 2.4 + - - +
243E ALA* 3.7 20.1 + - - +
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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