Contacts of the helix formed by residues 144 - 156 (chain E) in PDB entry 5DST
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 144 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81E ALA* 3.1 23.2 - - - +
142E CYS 4.0 0.4 + - - -
143E SER* 1.3 69.9 + - - +
145E ILE* 1.3 65.6 + - - +
146E SER* 3.0 2.7 - - - -
147E ASP* 3.1 26.1 + - - +
148E TYR* 4.1 7.8 - - - -
166E LYS* 3.8 23.1 - - - +
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Residues in contact with ILE 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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80E TYR 3.6 12.3 - - - +
81E ALA* 3.8 19.7 - - - +
83E PHE* 4.7 8.5 - - - -
86E HIS* 3.6 28.7 - - + +
121E GLY* 4.0 10.1 - - - +
122E THR* 4.2 13.7 - - + +
141E GLU* 3.5 31.6 - - + -
143E SER* 3.0 9.6 + - - -
144E SER* 1.3 79.8 + - - +
146E SER* 1.3 58.7 + - - +
148E TYR* 2.8 38.8 + - + +
149E SER 3.1 8.7 + - - -
250F ILE* 4.6 18.4 - - + -
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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
----------------------------------------------------------
141E GLU* 4.1 18.4 - - - -
143E SER 2.7 22.7 + - - -
144E SER 3.8 0.3 - - - -
145E ILE* 1.3 79.6 - - - +
147E ASP* 1.3 63.3 + - - -
149E SER* 2.8 27.8 + - - -
150E GLU* 3.0 13.5 + - - +
164E ILE* 4.2 11.4 - - - -
166E LYS* 2.9 35.1 - - - +
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Residues in contact with ASP 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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144E SER* 3.1 19.3 + - - +
145E ILE 3.1 0.2 + - - -
146E SER* 1.3 78.9 + - - +
148E TYR* 1.3 68.7 + - + +
150E GLU* 3.5 12.9 + - - +
151E LYS* 3.4 32.1 + - - +
166E LYS* 3.4 29.5 + - - +
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Residues in contact with TYR 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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81E ALA 5.4 5.4 - - - -
122E THR* 6.3 0.2 - - - -
144E SER 4.1 11.7 - - - -
145E ILE* 2.8 24.7 + - + +
147E ASP* 1.3 79.9 - - + +
149E SER* 1.3 58.4 + - - +
151E LYS* 3.2 20.4 + - - +
152E ILE* 2.8 35.7 + - + +
249F CYS* 3.9 27.4 - - + -
250F ILE* 4.1 26.7 - - + -
253F VAL* 3.3 38.3 - - + +
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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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120E SER* 4.1 1.0 + - - -
121E GLY 3.3 18.9 + - - -
122E THR* 3.0 29.5 + - - +
123E GLY* 3.9 6.5 - - - -
145E ILE 3.1 4.9 + - - -
146E SER* 2.8 25.3 + - - -
148E TYR* 1.3 74.9 - - - +
150E GLU* 1.3 57.1 + - - +
152E ILE* 3.5 1.8 - - - +
153E ILE* 2.8 40.3 + - - +
164E ILE* 3.6 19.1 - - - +
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Residues in contact with GLU 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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146E SER* 3.0 15.6 + - - +
147E ASP* 3.7 14.9 - - - +
149E SER* 1.3 74.2 + - - +
151E LYS* 1.3 66.7 + - + +
153E ILE* 3.8 6.7 - - - +
154E LYS* 3.0 24.6 + - - +
159E ASP* 5.6 0.9 - - - +
164E ILE* 3.8 36.5 + - + +
166E LYS* 6.0 4.5 - - - +
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Residues in contact with LYS 151 (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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147E ASP* 3.4 19.0 + - - +
148E TYR* 3.2 26.6 + - + +
150E GLU* 1.3 78.0 - - + +
152E ILE* 1.3 57.7 + - - +
154E LYS* 3.3 7.0 + - - +
155E ALA* 2.9 30.4 + - - +
249F CYS* 4.0 25.8 - - + -
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Residues in contact with ILE 152 (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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122E THR* 3.5 21.1 - - + +
127E MET* 3.8 22.2 - - + -
148E TYR 2.8 27.1 + - - +
149E SER 3.5 4.5 - - - +
151E LYS* 1.3 76.5 - - - +
153E ILE* 1.3 60.5 + - + +
155E ALA* 3.1 13.9 + - - +
156E ASN* 2.5 39.2 + - - +
246F ASP 3.7 7.6 - - - +
247F MET* 4.0 24.9 - - + -
249F CYS* 3.6 15.5 - - - -
250F ILE* 3.8 28.5 - - + -
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Residues in contact with ILE 153 (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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123E GLY* 4.7 8.1 - - - +
126E SER* 5.4 0.2 - - - -
127E MET* 4.0 27.8 - - + -
149E SER* 2.8 27.6 + - - +
150E GLU* 3.8 5.2 - - - +
152E ILE* 1.3 73.6 - - + +
154E LYS* 1.3 63.5 + - - +
156E ASN* 3.0 12.6 + - - +
157E HIS 3.2 8.5 + - - -
158E LEU* 3.3 18.3 + - + +
159E ASP* 3.5 28.9 - - + +
162E ILE* 3.6 31.4 - - + +
164E ILE* 3.7 25.4 - - + -
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Residues in contact with LYS 154 (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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150E GLU 3.0 18.1 + - - +
151E LYS* 3.6 6.5 - - - +
153E ILE* 1.3 77.2 - - - +
155E ALA* 1.3 62.4 + - - +
157E HIS* 3.0 20.4 + - - -
159E ASP* 3.6 34.5 - - + +
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Residues in contact with ALA 155 (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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151E LYS 2.9 14.3 + - - +
152E ILE* 3.1 13.0 + - - +
154E LYS* 1.3 76.6 - - - +
156E ASN* 1.3 61.4 + - - +
157E HIS* 3.3 16.8 + - - -
246F ASP* 4.1 23.3 - - - +
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Residues in contact with ASN 156 (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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127E MET* 3.8 10.7 - - - -
131E LYS* 5.4 4.2 + - - -
152E ILE* 2.5 34.8 + - - +
153E ILE 3.0 7.6 + - - +
155E ALA* 1.3 76.7 - - - +
157E HIS* 1.3 76.6 + - - +
158E LEU* 3.4 14.0 + - + +
244F GLY 4.8 1.0 - - - +
245F PHE* 3.5 22.8 - - + +
246F ASP* 2.8 45.8 + - - +
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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